Family Pairwise Search

Protein Family Classification

Timothy L. Bailey and William N. Grundy, Classifying proteins by family using the product of correlated p-values, to appear in Proceedings of the Third International Conference on Computational Molecular Biology (RECOMB99).

>ICYA_MANSE

GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNS
FVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCD
YHPDKKAHSIHAWILSKSKVLEGNTKEVVDNVLKTFSHLIDASKFISNDFSEAACQYSTT
YSLTGPDRH

Query-to-family matches

Note: Only matches with E-values less than or equal to 10 are shown.

SCOP Superfamily	size	eff size	E-value
Lipocalins	11	4.63	1.34e-12
PDZ domain	1	1.00	2.69e+00
Catalytic domain of malonyl-CoA ACP transacylase	1	1.00	3.90e+00
Protocatechuate-3,4-dioxygenase, alpha and beta chains	2	1.90	5.47e+00
A sigma70 subunit fragment from RNA polymerase	1	1.00	7.47e+00
RecA protein, C-terminal domain	1	1.00	7.53e+00
Acylphosphatase	1	1.00	8.57e+00

Summaries of pairwise alignments

What follows are summaries of the pairwise alignments between the query and members of the given family. These summaries are intended to provide an explanation for the scores that FPS computes as well as insight into the similarities between the query and members of each family. No attempt has been made to produce true multiple alignments by employing information about similarities among family members. Pairwise alignments are listed in order of increasing p-value for each family. For clarity and speed, some pairwise alignments with high p-values may be omitted for some families.

alignment of ICYA_MANSE vs. Lipocalins 
 family size:              11
 effective family size:  4.63
 p-value of match:   2.32e-15
 E-value of match:   1.34e-12
 
 ICYA_MANSE      -         2 DIFYPGYCPDVKPVNDFDLSAFAGAWHEI---A--------KLPLENENQG--KCTIAEY
 d1bbpa_      3.84e-29     1 NVYHDGACPEVKPVDNFDWSNYHGKWWEV---A--------KYPNSVEKYG--KCGWAEY
 d1hbp__      1.19e-05    14                NFDKARFAGTWYAM---A--------KKDPEGLFLQ--DNIVAEF
 d1epba_      1.59e-04     1              VKDFDISKFLGFWYEI---AfaskmgtpGLAHKEEKMG---AMVVEL
 d1beba_      9.97e-04     7                  DIQKVAGTWYSL---A----------------MA--ASDISLL
 d1obpa_      7.34e-03     8                  NLSELSGPWRTVyigS--------TNPEKIQENGpfRTYFREL
 d1lfo__      1.01e-02     7                                                             
 
 ICYA_MANSE               49 KYDGK---------KASV--YNSFVSNGVKEYMEGD--LEI----------APD-AKYTK
 d1bbpa_                  48 TPEGK---------SVKV--SNYHVIHGKEYFIEGT--AYP----------VGD-SKI--
 d1hbp__                  46 SVDENghmsatakgRVRL--LNNW---DVCADMVGT--FTD----------TEDpAKF--
 d1epba_                  42 K--------------------ENLLALTTTYYSEDHcvLEK----------VTA-TEGDG
 d1beba_                  29 DAQSA---------PLRV--Y----VEELKPTPEGD--LEIllqkwengecAQK-KIIAE
 d1obpa_                  43 VFDDE---------KGTVdfYFSVKRDGKWKNVH---------------------VKATK
 d1lfo__                   7                                                             
 
 ICYA_MANSE               85 Q--GKYVMTFKFG----QRVVNLVPWVLATDYKNYAINYNCDYH---------------P
 d1bbpa_                  82 ---GKIYHKLTYGgvtkENVFN----VLSTDNKNYIIGYYCKYD---------------E
 d1hbp__                  87 K--MKYWGVASFL----QK-GNDDHWIIDTDYETFAVQYSC
 d1epba_                  71 P--AKFQVTRLSG----KKEV----VVEATDYLTYAI
 d1beba_                  71 K--TKIPAVFKID----ALNENKV-LVLDTDYKKYLL--FCMEN---------------S
 d1obpa_                  73 QddGTYVADYE-G----QNVFKIVS--LSRTHL-VAHNINVDKHgqtteltglfvklnvE
 d1lfo__                   7                                   YQVQSQENFE---------------P
 
 ICYA_MANSE              124 DKKAHSIHAWILSKSKVLEGNTKEVVDNVLKTFSHLIDASKFISNDFSEAACQ
 d1bbpa_                 120 DKKGHQDFVWVLSRSKVLTGEAKTAVENYL-IGSPVVDSQKLVYSDFSEAACK
 d1beba_                 107 AEPEQSLVCQCLVR-------TPEVDDEALEKFDKALKA
 d1obpa_                 125 DEDLEKF--WKLTEDK---GIDKKNVVNFLENEDH
 d1lfo__                  18 FMKAMGLPEDLIQKGKDIKG-VSEIVHEGKKVKLTITYGSKVIHNEFT
 
 

alignment of ICYA_MANSE vs. PDZ domain 
 family size:               1
 effective family size:  1.00
 p-value of match:   4.64e-03
 E-value of match:   2.69e+00
 
 ICYA_MANSE      -        15 VNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYK
 d1pdr__      4.64e-03    56 VNSVDLRA---ASHEQAAAALKNAGQAVTIVAQYR
 
 

alignment of ICYA_MANSE vs. Catalytic domain of malonyl-CoA ACP transacylase 
 family size:               1
 effective family size:  1.00
 p-value of match:   6.73e-03
 E-value of match:   3.90e+00
 
 ICYA_MANSE      -         6 PGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNG
 d1mla_1      6.73e-03   128 PSHCALMKPAAD--------------KLAVE--------LAKITFNAPTVPVVNNV----
 
 ICYA_MANSE               66 VKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDK
 d1mla_1                 162 -------------DVKCETNGDAIRD-ALVRQLYNPVQWTKSVEY--------------M
 
 ICYA_MANSE              126 KAHSI-HAWILSKSKVLEGNTKEVVDNV
 d1mla_1                 194 AAQGVeHLYEVGPGKVLTGLTKRIVDTL
 
 

alignment of ICYA_MANSE vs. Protocatechuate-3,4-dioxygenase, alpha and beta chains 
 family size:               2
 effective family size:  1.90
 p-value of match:   9.45e-03
 E-value of match:   5.47e+00
 
 ICYA_MANSE      -         1 GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNS
 d2pcda_      1.51e-02    29              PTRDQEI------WNRLAKPDAPGEH---ILLLGQVYDGNGHLVRDS
 d2pcdm_      5.71e-02   179 GDPLIP-MCPIVKSIANPE-----AVQQLIAKLDMNNANPMDC--LAYRFD
 
 ICYA_MANSE               61 FV------SNGVKEYMEG-DLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLAT
 d2pcda_                  67 FLevwqadANG--EYQDAyNLENA----FNSFGRTATTFDAGE-------WTLHT
 
 

alignment of ICYA_MANSE vs. A sigma70 subunit fragment from RNA polymerase 
 family size:               1
 effective family size:  1.00
 p-value of match:   1.29e-02
 E-value of match:   7.47e+00
 
 ICYA_MANSE      -        29 EIAKLPLENENQGKCTIAEY---------KY------DGKKASVYNSFVSNGV-------
 d1sig__      1.29e-02     6 DIAKRIEDGINQVQCSVAEYpeaitylleQYnrveaeEARLSDLITGFVDDLAptathvg
 
 ICYA_MANSE               67 KEYMEGDLEIAPDAKYTK----QGKYVMT
 d1sig__                  66 SELSQEDLDIDPELAREKfaelRAQYVVT
 
 

alignment of ICYA_MANSE vs. RecA protein, C-terminal domain 
 family size:               1
 effective family size:  1.00
 p-value of match:   1.30e-02
 E-value of match:   7.53e+00
 
 ICYA_MANSE      -        58 YNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVNLVPWV
 d2reb_2      1.30e-02     3 YGELVDLGVKEKL---IEKA-GAWYSYKGE-----KIGQGKANATAWL
 
 

alignment of ICYA_MANSE vs. Acylphosphatase 
 family size:               1
 effective family size:  1.00
 p-value of match:   1.48e-02
 E-value of match:   8.57e+00
 
 ICYA_MANSE      -        97 RVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVDNVLKTF
 d1aps__      1.48e-02    31 RKIGVVGWVKNTSKGTVTGQVQ---GPEEKVNSMKSWL---SKV--GSPSSRIDRT--NF
 
 ICYA_MANSE              157 SHLIDASKFISNDFS
 d1aps__                  81 SNEKTISKLEYSNFS
 
 

Definitions

• size refers to the total number of sequences in the family.
• E size is the effective family size, which is an estimate of the degree of dissimilarity of the members of the family.
• The p-value of a query-to-family match is the probability that the similarity between the query and the family members occurs by chance.
• The E-value of a query-to-family match is the p-value multiplied by the number of families in the database. The E-value of a query-to-family match therefore reflects the probability of finding such a match by chance in the given family database.
• In the alignments, lower-case letters in the target sequences denote insertions.
• Clicking on an E-value takes you to the corresponding entry in the "matches" or "pairwise alignments" section.