GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Acidovorax sp. GW101-3H11

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Ac3H11_167 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)

Query= reanno::WCS417:GFF4367
         (946 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_167
          Length = 970

 Score = 1201 bits (3107), Expect = 0.0
 Identities = 602/958 (62%), Positives = 731/958 (76%), Gaps = 17/958 (1%)

Query: 5   LTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEA 64
           L  A EF+ RHIG    DE  ML+ +G  S   L  S++P SI  +  + L    +EA A
Sbjct: 14  LENAAEFLPRHIGIDAADEAHMLSVIGEASRRTLIDSIVPRSIARSRAMDLPAATTEAAA 73

Query: 65  LAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEAL 124
           LA++KAIAGKN++ K++IGQGYY  HTP  ILRN+LENPAWYTAYTPYQ EISQGR+EAL
Sbjct: 74  LAELKAIAGKNKVLKSFIGQGYYGTHTPGVILRNILENPAWYTAYTPYQAEISQGRMEAL 133

Query: 125 LNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQTLDVL 184
           +NFQT++ DLTG+PIANAS+LDEATAAAEAMT  KR  K+K SN F  +  +HPQT++V+
Sbjct: 134 VNFQTMVCDLTGMPIANASMLDEATAAAEAMTLAKRSVKSK-SNVFVVAGDAHPQTIEVI 192

Query: 185 RTRAEPLGIDVVVGDERELTD---VSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVA 241
           +TRA+PLG+DV + +  E  D      +F  L QYPA++G + D R   E+ HA      
Sbjct: 193 QTRAKPLGLDVRLANSAEEWDSLLAGDYFAVLAQYPATSGRIDDLRADVEKAHAKQAAFI 252

Query: 242 VAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGV 301
           VAADLLALTL+TPPGE GAD+ +G+ QRFG+P+G GGPHAA+ + +D FKR +PGRLVGV
Sbjct: 253 VAADLLALTLITPPGEQGADIVVGTTQRFGMPMGAGGPHAAFMACRDEFKRSLPGRLVGV 312

Query: 302 SVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRV 361
           SVD  GKPA RLA+QTREQHIRREKATSNICTAQVL A +ASMYAVYHGP+GL++IA+RV
Sbjct: 313 SVDVHGKPAYRLALQTREQHIRREKATSNICTAQVLPAVVASMYAVYHGPEGLSRIAQRV 372

Query: 362 HQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGVS 421
              TAILA+GL  LG  V +   FDTL L T   T ++  KA     NLR+     + +S
Sbjct: 373 ASYTAILARGLVQLGAPVREQATFDTLVLKTDGATKSIATKAIQSGANLRIYFESYLCIS 432

Query: 422 VDETTTQADIETLWAIFA-DGKALPDFAA---QVESTLPAALLRQSPVLSHPVFNRYHSE 477
           +DETTT+ADIE LW +FA DG+ALP F A    VE  +PAAL R S  L+HPVFN +HSE
Sbjct: 433 LDETTTRADIELLWKVFAKDGQALPTFDAFENGVEPLIPAALRRTSRYLTHPVFNTHHSE 492

Query: 478 TELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGY 537
           T ++RY+R+L+DKDLALDR+MIPLGSCTMKLNA SEMIP+TW EF  +HPFAPA+Q  GY
Sbjct: 493 TGMLRYIRQLSDKDLALDRSMIPLGSCTMKLNATSEMIPITWPEFANMHPFAPADQQQGY 552

Query: 538 LELTSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAH 597
             L   L A LC ATGY  ISLQPNAGSQGEYAGLLAI+ YH+SRG+  R+ICLIPSSAH
Sbjct: 553 KALDEQLRAWLCEATGYAGISLQPNAGSQGEYAGLLAIKGYHESRGEGHRNICLIPSSAH 612

Query: 598 GTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIR 657
           GTNPA+A M GM+VVVTACDA GNVD+ DL+AK  +H  ++A +MITYPSTHGVFE  ++
Sbjct: 613 GTNPASAQMVGMQVVVTACDANGNVDLADLQAKCEQHSGNIACVMITYPSTHGVFETSVK 672

Query: 658 EICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIG 717
           E+C ++H +GG+VY+DGANMNA+VG+ APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+ 
Sbjct: 673 ELCALVHSHGGRVYVDGANMNALVGVAAPGEFGGDVSHLNLHKTFCIPHGGGGPGVGPVC 732

Query: 718 VKSHLTPFLPG--------HAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRAS 769
           V   L PFLPG         +    K G V AAP G+A++LPI+WMYI MMG  GL+ A+
Sbjct: 733 VVEDLVPFLPGLPGQGDQPKSPATGKVGPVSAAPLGNAAVLPISWMYIRMMGADGLQAAT 792

Query: 770 QLAILNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGF 829
           + AIL+ANYIS RL++HYP LY   NG VAHECILDLR LKD+SG+  +DVAKRLID+GF
Sbjct: 793 ETAILSANYISARLKDHYPTLYASENGHVAHECILDLRGLKDTSGVMAEDVAKRLIDYGF 852

Query: 830 HAPTMSFPVAGTLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPH 889
           HAPT+SFPV  TLM+EPTESE+  E+DRF +AMIAIREEIR +E G L +D+NPLKNAPH
Sbjct: 853 HAPTLSFPVPNTLMVEPTESETLFEIDRFIDAMIAIREEIRQIEAGKLPQDNNPLKNAPH 912

Query: 890 TAAELVS-EWTHPYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
           TA  L+S EWT PYTRE A YPV +L + KYW PVGRVDNV+GDRNL C+C  +  YA
Sbjct: 913 TAENLLSGEWTRPYTREAAAYPVAALRQAKYWSPVGRVDNVWGDRNLSCSCIPVSDYA 970


Lambda     K      H
   0.319    0.135    0.398 

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: 2197
Number of extensions: 87
Number of successful extensions: 8
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: 946
Length of database: 970
Length adjustment: 44
Effective length of query: 902
Effective length of database: 926
Effective search space:   835252
Effective search space used:   835252
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 Ac3H11_167 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.19686.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19686.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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