GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Shewanella amazonensis SB2B

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 6938616 Sama_2719 glycine dehydrogenase (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6938616 Sama_2719 glycine dehydrogenase
           (RefSeq)
          Length = 962

 Score = 1355 bits (3506), Expect = 0.0
 Identities = 662/960 (68%), Positives = 791/960 (82%), Gaps = 6/960 (0%)

Query: 3   QTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEAT 62
           QTL +LE  + F+ RHIGPDA +QQ ML  VGA+SL  L  QIVP+ I+L     VG + 
Sbjct: 4   QTLTELEQHELFLTRHIGPDADEQQAMLNYVGAESLEDLTAQIVPESIRLGRELNVGASN 63

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

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

Query: 183 TLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARKVI 242
           TLDVV+TRAE FGFD++   A +A +H D+FG L Q     G++ D+++L A L+A+ VI
Sbjct: 184 TLDVVKTRAECFGFDIVTGPAAEAANHDDLFGALFQYTNRQGQLTDFTELFAQLRAKNVI 243

Query: 243 VSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGRII 302
           V+V AD M+LVLL +PG  GAD+VFGSAQRFGVPMG+GGPHAAFF +KDE KRSMPGRII
Sbjct: 244 VTVGADIMSLVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVSKDEHKRSMPGRII 303

Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIAS 362
           GVSKD  G TALRMAMQTREQHIRREKANSNICT+QVLLAN+AS YAVFHGP GLK IA+
Sbjct: 304 GVSKDTRGKTALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKVIAN 363

Query: 363 RIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAVGI 422
           RIHRLTDILA GL  KG+ + +  +FDTL  +V D  AV ARA A  +NLR D    VG+
Sbjct: 364 RIHRLTDILAAGLAAKGVTVLNTQWFDTLSFKV-DVDAVRARALAAGVNLRYDADGVVGV 422

Query: 423 TLDEATTREDVLNLFRAILGDDHGLDIDTLDKDV-ALDSRSIPASMLRDDAILTHPVFNR 481
           +L E TTR DV  LF  ILG  HGLD+  +D D+ A  S SIPA+++R++A LTHP FN 
Sbjct: 423 SLAETTTRADVAELFDIILGAGHGLDVAAIDADILAKGSSSIPAALVREEAFLTHPTFNS 482

Query: 482 YHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVDQ 541
           YHSETEMMRY+  LE KDLALN +MI LGSCTMKLNAA EMIP++WPEFA +HPFCP +Q
Sbjct: 483 YHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPSEQ 542

Query: 542 AEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIP 601
           A+GY Q+I +LSDWLV +TGYDAVCMQPNSGAQGEYAGLLAIR YHESR EGHRD+CLIP
Sbjct: 543 AQGYTQLIGELSDWLVDITGYDAVCMQPNSGAQGEYAGLLAIRKYHESRGEGHRDVCLIP 602

Query: 602 SSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVYE 661
            SAHGTNPASAQ+AGM+VVV ACDK GN+DL DLRAKA + A NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMKVVVTACDKQGNVDLDDLRAKAAEVAENLSCIMITYPSTHGVYE 662

Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
           ET+RE+C+++HQ GGQVYLDGANMNAQVG+T+PGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ETVREICDIIHQHGGQVYLDGANMNAQVGLTAPGFIGADVSHLNLHKTFAIPHGGGGPGM 722

Query: 722 GPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQA 781
           GPIGVK HLA FV GH+VV+        GAVSAAPFGSA ILPISWMYI+++G++GLKQ+
Sbjct: 723 GPIGVKKHLAPFVAGHAVVKQGIESDNNGAVSAAPFGSAGILPISWMYIKLLGSKGLKQS 782

Query: 782 SQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFG 841
           +Q A+LNANY+  +L + +PVLY GR+ R+AHECI+D+RPLKE +G++E+D+AKRL D+G
Sbjct: 783 TQTAMLNANYLTKKLSEHYPVLYRGRNDRIAHECIIDMRPLKEASGVTEMDVAKRLNDYG 842

Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAP 901
           FHAPTMSFPVAGTLM+EPTESESK ELDRFI+AM+AIRGEI RV++GEWP+++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIARVESGEWPVDNNPLANAP 902

Query: 902 HTQGELVSAW--NHPYARELAVFP--AGLNNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
           HT  +++     + PY+RELAVFP  +   NK+WPTV R+DDVYGDRNLFC+CVPMS+Y+
Sbjct: 903 HTMDDIMDPAFDSRPYSRELAVFPTESVRANKFWPTVNRIDDVYGDRNLFCACVPMSDYE 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: 2281
Number of extensions: 82
Number of successful extensions: 7
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 6938616 Sama_2719 (glycine dehydrogenase (RefSeq))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00461.hmm
# target sequence database:        /tmp/gapView.9676.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00461  [M=939]
Accession:   TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
          0 1530.5   0.1          0 1530.3   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6938616  Sama_2719 glycine dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938616  Sama_2719 glycine dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1530.3   0.1         0         0       1     939 []      18     955 ..      18     955 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1530.3 bits;  conditional E-value: 0
                         TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77 
                                       rh+Gpd+ eq+ ml+ +G+++l++l+ q+vp++irl r l+++a++ e + la ++++a+kn+++ksyiG+Gy +t 
  lcl|FitnessBrowser__SB2B:6938616  18 RHIGPDADEQQAMLNYVGAESLEDLTAQIVPESIRLGRELNVGASNGEAAGLAYIRQLADKNQVFKSYIGMGYHGTE 94 
                                       9**************************************************************************** PP

                         TIGR00461  78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.a 153
                                       +p vi+rn+lenpgwytaytpyqpei+qGrlea+lnfq++ +dltGl++a+asllde+taaaeamal++rvsk k a
  lcl|FitnessBrowser__SB2B:6938616  95 VPNVILRNVLENPGWYTAYTPYQPEIAQGRLEAILNFQQLSIDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkA 171
                                       *************************************************************************8879 PP

                         TIGR00461 154 nkfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaa 230
                                       n f+va+dv pqtl+vvktrae +g++++ + a +  ++ d++G+l qy+  +G++ d+++l  +l+ ++++v+v a
  lcl|FitnessBrowser__SB2B:6938616 172 NTFFVADDVFPQTLDVVKTRAECFGFDIVTGPAAEAANHDDLFGALFQYTNRQGQLTDFTELFAQLRAKNVIVTVGA 248
                                       ***************************************************************************** PP

                         TIGR00461 231 dllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqh 307
                                       d+++l+ll++pg +Gad+v+GsaqrfGvp+G+GGphaaff +kde+kr++pGri+Gvskd+ G+talr+a+qtreqh
  lcl|FitnessBrowser__SB2B:6938616 249 DIMSLVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVSKDEHKRSMPGRIIGVSKDTRGKTALRMAMQTREQH 325
                                       ***************************************************************************** PP

                         TIGR00461 308 irrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
                                       irr+ka+snictaqvllan+as yav+hGp+Glk ia+ri+rlt+ilaagl  k+  + n ++fdtl+ +v  +a  
  lcl|FitnessBrowser__SB2B:6938616 326 IRREKANSNICTAQVLLANMASFYAVFHGPQGLKVIANRIHRLTDILAAGLAAKGVTVLNTQWFDTLSFKVDVDA-- 400
                                       **********************************************************************97554.. PP

                         TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeil 457
                                        v  +a +a++nlr +  + vg++l ettt++dv +l+++++g   +gl++  ++ d+      s+pa+l r++ +l
  lcl|FitnessBrowser__SB2B:6938616 401 -VRARALAAGVNLRYDADGVVGVSLAETTTRADVAELFDIILG-AGHGLDVAAIDADILAkgssSIPAALVREEAFL 475
                                       .699999************************************.55*****9999998655666************* PP

                         TIGR00461 458 rdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaq 534
                                       +++ fn yhsete++ry++rle+kdlaln+smi lGsctmklna++em+p++wpefa++hpf+p+eq++Gy +li +
  lcl|FitnessBrowser__SB2B:6938616 476 THPTFNSYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPSEQAQGYTQLIGE 552
                                       ***************************************************************************** PP

                         TIGR00461 535 lekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeG 611
                                       l +wlv+itG+da+++qpnsGaqGeyaGl +ir+yhesrge+hr++clip+sahGtnpasa++aG+kvv+ +cdk+G
  lcl|FitnessBrowser__SB2B:6938616 553 LSDWLVDITGYDAVCMQPNSGAQGEYAGLLAIRKYHESRGEGHRDVCLIPQSAHGTNPASAQLAGMKVVVTACDKQG 629
                                       ***************************************************************************** PP

                         TIGR00461 612 nidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchln 688
                                       n+dl dl+aka + +++l+++m+typst+Gv+eet+re++di+h+ GGqvyldGanmnaqvGlt+pg++Gadv+hln
  lcl|FitnessBrowser__SB2B:6938616 630 NVDLDDLRAKAAEVAENLSCIMITYPSTHGVYEETVREICDIIHQHGGQVYLDGANMNAQVGLTAPGFIGADVSHLN 706
                                       ***************************************************************************** PP

                         TIGR00461 689 lhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlk 765
                                       lhktf+iphGGGGpgmgpigvk hlapf+ +   + vv+   es + gavsaap+Gsa ilpis+myik++G++Glk
  lcl|FitnessBrowser__SB2B:6938616 707 LHKTFAIPHGGGGPGMGPIGVKKHLAPFVAG---HAVVKQGIESDNNGAVSAAPFGSAGILPISWMYIKLLGSKGLK 780
                                       *******************************...777888889999******************************* PP

                         TIGR00461 766 kasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlm 842
                                       ++++ a+lnanyl+k+l ++y++l++gr++r+aheci+d+r+lke +g+ ++dvakrl dyGfhapt+sfpvaGtlm
  lcl|FitnessBrowser__SB2B:6938616 781 QSTQTAMLNANYLTKKLSEHYPVLYRGRNDRIAHECIIDMRPLKEASGVTEMDVAKRLNDYGFHAPTMSFPVAGTLM 857
                                       ***************************************************************************** PP

                         TIGR00461 843 veptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaew.adpysreeaaypapvlkyfk 918
                                       +epteses+ eldrfi+am+ai+ ei  v +Ge++ ++n+l naph++++ +   +   pysre a++p   ++ +k
  lcl|FitnessBrowser__SB2B:6938616 858 IEPTESESKAELDRFIEAMVAIRGEIARVESGEWPVDNNPLANAPHTMDDIMDPAFdSRPYSRELAVFPTESVRANK 934
                                       *************************************************99987661567***************** PP

                         TIGR00461 919 fwptvarlddtyGdrnlvcsc 939
                                       fwptv+r+dd+yGdrnl+c+c
  lcl|FitnessBrowser__SB2B:6938616 935 FWPTVNRIDDVYGDRNLFCAC 955
                                       ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (962 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 8.91
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory