GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Shewanella sp. ANA-3

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 7026357 Shewana3_3499 glycine dehydrogenase (RefSeq)

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__ANA3:7026357
          Length = 962

 Score = 1350 bits (3494), Expect = 0.0
 Identities = 660/960 (68%), Positives = 796/960 (82%), Gaps = 6/960 (0%)

Query: 3   QTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPA 62
           QTL+QLE    F+ RHIGPD++QQQEMLN VGA+SL+ LT QIVP+ I+L+    +G   
Sbjct: 4   QTLTQLEQHDLFLRRHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSC 63

Query: 63  TEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQG 122
            E   +A ++ +A +N+ F SYIGMGY   Q+P VILRN+ ENPGWYTAYTPYQPE++QG
Sbjct: 64  GEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQVPNVILRNVFENPGWYTAYTPYQPEIAQG 123

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

Query: 183 TLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIV 242
           TLDVV+TRAE FGFEV+V  A + ++H+ +FG L Q     G+I D+T L +EL+++ ++
Sbjct: 184 TLDVVKTRAECFGFEVVVGPAHEAVNHE-LFGALFQYSNRFGQITDFTDLFAELRAKNVI 242

Query: 243 VSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRII 302
           V+VAADIMALVLL +PG  GAD+VFGSAQRFGVPMG+GGPHAAFF A+DE+KRSMPGRII
Sbjct: 243 VTVAADIMALVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRII 302

Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIAN 362
           GVSKD  GN ALRMAMQTREQHIRREKANSNICT+Q+LLAN+AS YAV+HGP GLK IA+
Sbjct: 303 GVSKDTRGNRALRMAMQTREQHIRREKANSNICTAQILLANMASFYAVFHGPQGLKTIAS 362

Query: 363 RIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVGI 422
           RI+R TDILAAGLQ KG+ L +  +FDT+ ++  D A V  RA AAE+NLR D    VG+
Sbjct: 363 RINRFTDILAAGLQAKGVSLVNNTWFDTISIKGLDVAAVNARALAAEMNLRFDADGIVGV 422

Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKD-VAHDSRSIQPAMLRDDEILTHPVFNR 481
           +LDETT R ++  LF+V+LG  HGLD+  LD   VA  S+SI  +++R D IL+HP FNR
Sbjct: 423 SLDETTIRTDIEALFDVILGAGHGLDVAALDAQIVAQGSQSIPASLVRQDAILSHPTFNR 482

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

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

Query: 602 ASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYE 661
            SAHGTNPASA +AGMQVVV ACDK GN+DL DL+AKA +  +NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMQVVVTACDKQGNVDLEDLKAKAAEVAENLSCIMITYPSTHGVYE 662

Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
           E+IRE+C +VHQ GGQVYLDGANMNAQVG+TSPGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ESIREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLNLHKTFAIPHGGGGPGM 722

Query: 722 GPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKA 781
           GPIGVKAHLAPFV GH VV+        GAVSAAP+GSA ILPISWMYI+++G+ GLKK+
Sbjct: 723 GPIGVKAHLAPFVAGHVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSNGLKKS 782

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

Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAP 901
           FHAPTMSFPVAGTLM+EPTESESKVELDRFIDAM++IRAEI +V+AG WP ++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAP 902

Query: 902 HIQSELV--AEWAHPYSREVAVFPAGV--ADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
           H  ++++  A  + PYSREVAVFP+     +K+WPTV R+DDVYGDRNLFC+CVP+S+Y+
Sbjct: 903 HTMADIMDPAFDSRPYSREVAVFPSAAVRTNKFWPTVNRIDDVYGDRNLFCACVPLSDYE 962


Lambda     K      H
   0.319    0.134    0.395 

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: 2277
Number of extensions: 71
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: 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 7026357 Shewana3_3499 (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.15255.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 1535.1   0.1          0 1535.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7026357  Shewana3_3499 glycine dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026357  Shewana3_3499 glycine dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1535.0   0.1         0         0       1     939 []      18     955 ..      18     955 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1535.0 bits;  conditional E-value: 0
                         TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77 
                                       rh+Gpd+++q++ml+ +G+++l++l+ q+vp++irl++ l ++ +  e e +a ++ +a++n+++ksyiG+Gyy+t+
  lcl|FitnessBrowser__ANA3:7026357  18 RHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSCGEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQ 94 
                                       9**************************************************************************** PP

                         TIGR00461  78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.a 153
                                       +p vi+rn++enpgwytaytpyqpei+qGrlea+lnfq+v +dltGl++a+asllde+taaaeamal++rvsk k a
  lcl|FitnessBrowser__ANA3:7026357  95 VPNVILRNVFENPGWYTAYTPYQPEIAQGRLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkA 171
                                       *************************************************************************8879 PP

                         TIGR00461 154 nkfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaa 230
                                       n f+va+dv pqtl+vvktrae +g+ev+v+ a++  ++ +++G+l qy+   G+i d+++l  el+ ++++v+vaa
  lcl|FitnessBrowser__ANA3:7026357 172 NIFFVADDVFPQTLDVVKTRAECFGFEVVVGPAHEAVNH-ELFGALFQYSNRFGQITDFTDLFAELRAKNVIVTVAA 247
                                       9*********************************98765.89*********************************** PP

                         TIGR00461 231 dllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqh 307
                                       d++al+ll++pg +Gad+v+GsaqrfGvp+G+GGphaaff ++de+kr++pGri+Gvskd+ Gn alr+a+qtreqh
  lcl|FitnessBrowser__ANA3:7026357 248 DIMALVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRIIGVSKDTRGNRALRMAMQTREQH 324
                                       ***************************************************************************** PP

                         TIGR00461 308 irrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
                                       irr+ka+snictaq+llan+as yav+hGp+Glk ia ri r+t+ilaagl+ k+ +l n+t+fdt++++  + aa 
  lcl|FitnessBrowser__ANA3:7026357 325 IRREKANSNICTAQILLANMASFYAVFHGPQGLKTIASRINRFTDILAAGLQAKGVSLVNNTWFDTISIKGLDVAA- 400
                                       **********************************************************************998888. PP

                         TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeil 457
                                        v+ +a +ae+nlr +  + vg++ldett + d++ l++v++g   +gl++  l+ ++      s+pa l r+d il
  lcl|FitnessBrowser__ANA3:7026357 401 -VNARALAAEMNLRFDADGIVGVSLDETTIRTDIEALFDVILG-AGHGLDVAALDAQIVAqgsqSIPASLVRQDAIL 475
                                       .9*****************************************.55*******99987544666************* PP

                         TIGR00461 458 rdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaq 534
                                        ++ fnry sete++ry++rleskdlaln smi lGsctmklna++em+p++wpefa++hpf+p +q++Gy +li +
  lcl|FitnessBrowser__ANA3:7026357 476 SHPTFNRYQSETEMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQAKGYTQLIEE 552
                                       ***************************************************************************** PP

                         TIGR00461 535 lekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeG 611
                                       l +wlv++tG+da+++qpnsGaqGeyaGl +ir+yhesrge hrniclip+sahGtnpasa++aG++vv+ +cdk+G
  lcl|FitnessBrowser__ANA3:7026357 553 LSSWLVNVTGYDAVCIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIPQSAHGTNPASAQLAGMQVVVTACDKQG 629
                                       ***************************************************************************** PP

                         TIGR00461 612 nidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchln 688
                                       n+dl+dlkaka + +++l+++m+typst+Gv+ee+ire+++ivh+ GGqvyldGanmnaqvGltspg++Gadv+hln
  lcl|FitnessBrowser__ANA3:7026357 630 NVDLEDLKAKAAEVAENLSCIMITYPSTHGVYEESIREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLN 706
                                       ***************************************************************************** PP

                         TIGR00461 689 lhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlk 765
                                       lhktf+iphGGGGpgmgpigvk+hlapf+ +   + vv+   es + gavsaapyGsa ilpis+myik++G++Glk
  lcl|FitnessBrowser__ANA3:7026357 707 LHKTFAIPHGGGGPGMGPIGVKAHLAPFVAG---HVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSNGLK 780
                                       *******************************...67788889999******************************** PP

                         TIGR00461 766 kasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlm 842
                                       k+++ a+lnany++k+l ++y++lf+gr++rvaheci+dlr++ke +g+ ++d+akrl dyGfhapt+sfpvaGtlm
  lcl|FitnessBrowser__ANA3:7026357 781 KSTQTALLNANYVMKKLSEHYPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYGFHAPTMSFPVAGTLM 857
                                       ***************************************************************************** PP

                         TIGR00461 843 veptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaew.adpysreeaaypapvlkyfk 918
                                       +epteses++eldrfidam++i++ei +v aGe+++++n+l+naph++ + +   +   pysre+a++p + ++ +k
  lcl|FitnessBrowser__ANA3:7026357 858 IEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAPHTMADIMDPAFdSRPYSREVAVFPSAAVRTNK 934
                                       *************************************************99987661567***************** PP

                         TIGR00461 919 fwptvarlddtyGdrnlvcsc 939
                                       fwptv+r+dd+yGdrnl+c+c
  lcl|FitnessBrowser__ANA3:7026357 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 8.58
//
[ok]

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

Links

Downloads

Related tools

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:

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