GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Shewanella oneidensis MR-1

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 199967 SO0781 glycine cleavage system P protein (NCBI ptt file)

Query= reanno::Koxy:BWI76_RS23870
         (957 letters)



>FitnessBrowser__MR1:199967
          Length = 962

 Score = 1350 bits (3494), Expect = 0.0
 Identities = 661/960 (68%), Positives = 796/960 (82%), Gaps = 6/960 (0%)

Query: 3   QTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEAT 62
           QTL QLE  D F+ RHIGPD+ QQQEML  VGA+SL+ L  QIVP+ I+L+    +G++ 
Sbjct: 4   QTLTQLEQHDLFLRRHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSC 63

Query: 63  TEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVSQG 122
            E   +A ++ +A +N+ FKSYIGMGY   Q+P VI RN+LENPGWYTAYTPYQPE++QG
Sbjct: 64  GEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQVPNVILRNVLENPGWYTAYTPYQPEIAQG 123

Query: 123 RLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVHPQ 182
           RLE++LNFQQV++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FFVA DV PQ
Sbjct: 124 RLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFVADDVFPQ 183

Query: 183 TLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARKVI 242
           TLDVV+TRAE FGF+V+V  A +A++H+ +FG L Q     G++ D++ L A+L+A+ VI
Sbjct: 184 TLDVVKTRAECFGFEVVVGPASEAVNHE-LFGALFQYSNRFGQITDFTDLFAELRAKNVI 242

Query: 243 VSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGRII 302
           V+VAAD M+LVLL +PG  GAD+VFGSAQRFGVPMG+GGPHAAFF A+DE KRSMPGRII
Sbjct: 243 VTVAADIMSLVLLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRII 302

Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIAS 362
           GVSKD  GN ALRMAMQTREQHIRREKANSNICT+Q+LLAN+AS YAVFHGP GLK IAS
Sbjct: 303 GVSKDTRGNRALRMAMQTREQHIRREKANSNICTAQILLANMASFYAVFHGPQGLKTIAS 362

Query: 363 RIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAVGI 422
           RI+R  DILA GLQ KG+ L +  +FDT+ ++  D AAV ARA A  +NLR D    VG+
Sbjct: 363 RINRFADILAAGLQAKGVSLVNNTWFDTISIKGLDVAAVNARALAAEMNLRFDADGIVGV 422

Query: 423 TLDEATTREDVLNLFRAILGDDHGLDIDTLDKD-VALDSRSIPASMLRDDAILTHPVFNR 481
           +LDE T R D+  LF  ILG  HGLD+  LD   VA  S+SIPAS++R+DAIL+HP FNR
Sbjct: 423 SLDETTIRTDIDALFEVILGAGHGLDVAALDAQIVAQGSQSIPASLVREDAILSHPTFNR 482

Query: 482 YHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVDQ 541
           Y SETEMMRY+  LE KDLALN +MI LGSCTMKLNAA EMIP++WPEFA +HPFCP+DQ
Sbjct: 483 YQSETEMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQ 542

Query: 542 AEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIP 601
           A+GY Q+I +LS WLV +TGYDAVC+QPNSGAQGEYAGLLAIR YHESR E HR+ICLIP
Sbjct: 543 AKGYTQLIEELSSWLVNVTGYDAVCIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIP 602

Query: 602 SSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVYE 661
            SAHGTNPASAQ+AGMQVVV ACDK GN+DL DL+AKA + A NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMQVVVTACDKQGNVDLEDLKAKAAEVAENLSCIMITYPSTHGVYE 662

Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
           ET+RE+C +VHQ GGQVYLDGANMNAQVG+TSPGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ETVREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLNLHKTFAIPHGGGGPGM 722

Query: 722 GPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQA 781
           GPIGVK+HLA FV GH VV+        GAVSAAP+GSA ILPISWMYI+++G++GLK++
Sbjct: 723 GPIGVKAHLAPFVAGHVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSKGLKKS 782

Query: 782 SQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFG 841
           +Q A+LNANY+  +L + +PVL+ GR+ RVAHECI+D+RP+KE +G++E+DIAKRL D+G
Sbjct: 783 TQTALLNANYVMKKLSEHYPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYG 842

Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAP 901
           FHAPTMSFPVAGTLM+EPTESESKVELDRFIDAM++IR EI +V+AGEWP ++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAP 902

Query: 902 HTQGELVSAW--NHPYARELAVFPAGL--NNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
           HT  +++ +   + PY+RE+AVFP+     NK+WPTV R+DDVYGDRNLFC+CVP+S+Y+
Sbjct: 903 HTMADIMDSAFDSRPYSREVAVFPSAAVRTNKFWPTVNRIDDVYGDRNLFCACVPLSDYE 962


Lambda     K      H
   0.320    0.135    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2233
Number of extensions: 75
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 957
Length of database: 962
Length adjustment: 44
Effective length of query: 913
Effective length of database: 918
Effective search space:   838134
Effective search space used:   838134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate 199967 SO0781 (glycine cleavage system P protein (NCBI ptt file))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.26701.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26701.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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