Alignments for a candidate for gcvP in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Sinorhizobium meliloti 1021

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate SMc02049 SMc02049 glycine dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
         (950 letters)



>FitnessBrowser__Smeli:SMc02049
          Length = 954

 Score = 1180 bits (3053), Expect = 0.0
 Identities = 576/936 (61%), Positives = 707/936 (75%), Gaps = 6/936 (0%)

Query: 15  RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAT 74
           RHIGP   +   ML  +G+ SL+AL    +P SI+  + L     ++E +AL  ++  A 
Sbjct: 21  RHIGPSPAEMDEMLKVVGYPSLDALIDDTVPPSIRQRTPLAWGAPMTEREALDKLRETAN 80

Query: 75  KNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISD 134
           +N+   + IGQGYYGT TP  I RN+LENPAWYTAYTPYQPEISQGRLEALLN+QT++ D
Sbjct: 81  RNRKLVSLIGQGYYGTITPPVIQRNILENPAWYTAYTPYQPEISQGRLEALLNYQTMVCD 140

Query: 135 LTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQTLDVLRTRAEPLGI 194
           LTGL +ANASLLDEATAAAEAM   +R++K+K   AFF   +CHPQT+ +L+TRAEPLG 
Sbjct: 141 LTGLDVANASLLDEATAAAEAMAIAERVAKSKAK-AFFIDENCHPQTIALLKTRAEPLGW 199

Query: 195 DVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVLT 254
            +V+GD  E  D    FGA+ QYP + G V D+  L  + H   A+ AVAAD LAL +L 
Sbjct: 200 QIVLGDPFEDLDAAGVFGAIFQYPGTYGHVRDFSGLIAKLHGQGAIAAVAADPLALALLK 259

Query: 255 APGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGNPALRL 314
           +PGE GAD+AIGS QRFGVP+G+GGPHAAY + KDA+KR MPGRLVGVSVD  GN A RL
Sbjct: 260 SPGEMGADIAIGSTQRFGVPVGYGGPHAAYMAVKDAYKRSMPGRLVGVSVDARGNRAYRL 319

Query: 315 AMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAILAKGLS 374
           ++QTREQHIRREKATSNICTAQVLLA +ASMYAV+HGP G+  IA  VH  T  LA GL 
Sbjct: 320 SLQTREQHIRREKATSNICTAQVLLAVMASMYAVFHGPDGIKAIAQSVHQKTVRLAMGLE 379

Query: 375 ALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQADVET 434
            LG +VE   FFDT+TV+ G     +   A A+ +NLR +   R+G+SLDE +    +E 
Sbjct: 380 KLGYTVEPDVFFDTITVEVGKLQGIILKAAVAEEVNLRKIGTTRIGISLDERSRPVTLEA 439

Query: 435 LWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKLADK 494
           +W          DF          +P  L+R S  L+HP+F+   +E+E+ RY+R+LAD+
Sbjct: 440 VWRAFGG-----DFKVEEFEPDYRLPQELLRTSAYLTHPIFHMNRAESEMTRYMRRLADR 494

Query: 495 DLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLCA 554
           DLALDR MIPLGSCTMKLNA +EM+P+TW EF  +HPF PA+Q+ GYQ L ++L   LCA
Sbjct: 495 DLALDRAMIPLGSCTMKLNATAEMLPITWPEFSEIHPFVPADQALGYQHLIEDLSQKLCA 554

Query: 555 ATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMAGMR 614
            TGYD++S+QPN+G+QGEYAGLLAIRAYH + G + RD+CLIP+SAHGTNPA+AQMAGM+
Sbjct: 555 ITGYDAISMQPNSGAQGEYAGLLAIRAYHIANGNEHRDVCLIPTSAHGTNPASAQMAGMK 614

Query: 615 VVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNGGQV 674
           VVV      G +D++D RAKA ++ + L+  MITYPSTHGVFEE +RE+C ++H +GGQV
Sbjct: 615 VVVVKVSDAGEIDMDDFRAKAEQYADTLSCCMITYPSTHGVFEENVREVCEVVHKHGGQV 674

Query: 675 YIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLPGHA 734
           Y+DGANMNAMVGL  PG  G DVSHLNLHKTFCIPHGGGGPG+GPIGVKSHLAPFLPGH 
Sbjct: 675 YLDGANMNAMVGLSRPGDIGSDVSHLNLHKTFCIPHGGGGPGMGPIGVKSHLAPFLPGHP 734

Query: 735 QMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEEHYPVL 794
           Q +  EGAV AAPFGSASILPI+W Y  MMGG GL +A+++AILNANY++ RL+  Y VL
Sbjct: 735 QTDGHEGAVSAAPFGSASILPISWSYCLMMGGEGLTQATKVAILNANYVAARLKGAYDVL 794

Query: 795 YTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIEPTESE 854
           Y  + G VAHECI+D RPL +S+G++VDDVAKRLID GFHAPTMS+PVAGTLMIEPTESE
Sbjct: 795 YKSAKGRVAHECIIDTRPLAESAGVTVDDVAKRLIDCGFHAPTMSWPVAGTLMIEPTESE 854

Query: 855 SKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVGEWSHPYSREQAVYP 914
           +K ELDRFCDAM+ IREE RA+E+G +DK +NPLKNAPHT ++LVG+W  PYSREQA +P
Sbjct: 855 TKAELDRFCDAMLAIREEARAIEDGRMDKVNNPLKNAPHTVEDLVGDWDRPYSREQACFP 914

Query: 915 VASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
             +    KYW PV RVDNV+GDRNLVC CP IESYA
Sbjct: 915 PGAFRVDKYWSPVNRVDNVYGDRNLVCTCPPIESYA 950


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: 2248
Number of extensions: 80
Number of successful extensions: 4
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: 950
Length of database: 954
Length adjustment: 44
Effective length of query: 906
Effective length of database: 910
Effective search space:   824460
Effective search space used:   824460
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 SMc02049 SMc02049 (glycine dehydrogenase)
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.29897.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 1463.9   0.0          0 1463.7   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02049  SMc02049 glycine dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02049  SMc02049 glycine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1463.7   0.0         0         0       1     939 []      21     943 ..      21     943 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1463.7 bits;  conditional E-value: 0
                           TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyya 75 
                                         rh+Gp++ae+ +mlk +G+ +l+ali++ vp++ir+++pl  +ap +e eal +l++ a++n+k+ s iG+Gyy+
  lcl|FitnessBrowser__Smeli:SMc02049  21 RHIGPSPAEMDEMLKVVGYPSLDALIDDTVPPSIRQRTPLAWGAPMTEREALDKLRETANRNRKLVSLIGQGYYG 95 
                                         9************************************************************************** PP

                           TIGR00461  76 tilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvsk 150
                                         ti+ppviqrn+lenp wytaytpyqpeisqGrlealln+qt+v dltGl+vanasllde+taaaeama++ rv+k
  lcl|FitnessBrowser__Smeli:SMc02049  96 TITPPVIQRNILENPAWYTAYTPYQPEISQGRLEALLNYQTMVCDLTGLDVANASLLDEATAAAEAMAIAERVAK 170
                                         *************************************************************************** PP

                           TIGR00461 151 kkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkal 225
                                         +ka++f++++++hpqt+ ++ktraeplg +++ +d  +  +a  v+G++ qyp+t G++ d+  li +l+ + a+
  lcl|FitnessBrowser__Smeli:SMc02049 171 SKAKAFFIDENCHPQTIALLKTRAEPLGWQIVLGDPFEDLDAAGVFGAIFQYPGTYGHVRDFSGLIAKLHGQGAI 245
                                         *************************************************************************** PP

                           TIGR00461 226 vsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrla 300
                                          +vaad+lal+ll++pg++Gadi++Gs+qrfGvp+GyGGphaa++avkd ykr++pGr+vGvs da Gn a rl+
  lcl|FitnessBrowser__Smeli:SMc02049 246 AAVAADPLALALLKSPGEMGADIAIGSTQRFGVPVGYGGPHAAYMAVKDAYKRSMPGRLVGVSVDARGNRAYRLS 320
                                         *************************************************************************** PP

                           TIGR00461 301 lqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtlt 375
                                         lqtreqhirr+katsnictaqvlla++as+yav+hGp G+k ia+ +++ t+ la+gl++ +y ++ + +fdt+t
  lcl|FitnessBrowser__Smeli:SMc02049 321 LQTREQHIRREKATSNICTAQVLLAVMASMYAVFHGPDGIKAIAQSVHQKTVRLAMGLEKLGYTVEPDVFFDTIT 395
                                         *************************************************************************** PP

                           TIGR00461 376 vevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpael 450
                                         vevg+  +  +lkaa + e+nlr + +t +gi+lde      ++ +++ + g d   +++ee++ d++  +p+el
  lcl|FitnessBrowser__Smeli:SMc02049 396 VEVGKLQG-IILKAAVAEEVNLRKIGTTRIGISLDERSRPVTLEAVWRAFGG-D---FKVEEFEPDYR--LPQEL 463
                                         ****9888.99***************************************99.5...999***99996..9**** PP

                           TIGR00461 451 lrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqv 525
                                         lr++ +l++++f++  +e+e+ ry+ rl  +dlal+++miplGsctmklnataemlpitwpef+eihpf pa+q+
  lcl|FitnessBrowser__Smeli:SMc02049 464 LRTSAYLTHPIFHMNRAESEMTRYMRRLADRDLALDRAMIPLGSCTMKLNATAEMLPITWPEFSEIHPFVPADQA 538
                                         *************************************************************************** PP

                           TIGR00461 526 eGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGl 600
                                          Gy++li +l ++l+ itG+dais+qpnsGaqGeyaGl +ir yh ++g+ehr++clip+sahGtnpasa+maG+
  lcl|FitnessBrowser__Smeli:SMc02049 539 LGYQHLIEDLSQKLCAITGYDAISMQPNSGAQGEYAGLLAIRAYHIANGNEHRDVCLIPTSAHGTNPASAQMAGM 613
                                         *************************************************************************** PP

                           TIGR00461 601 kvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGlt 675
                                         kvv+vk  + G+id+ d++akae+++d l++ m+typst+Gvfee +rev+++vh+ GGqvyldGanmna vGl+
  lcl|FitnessBrowser__Smeli:SMc02049 614 KVVVVKVSDAGEIDMDDFRAKAEQYADTLSCCMITYPSTHGVFEENVREVCEVVHKHGGQVYLDGANMNAMVGLS 688
                                         *************************************************************************** PP

                           TIGR00461 676 spgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilp 750
                                         +pgd+G+dv+hlnlhktf+iphGGGGpgmgpigvkshlapflp++          ++ + gavsaap+Gsasilp
  lcl|FitnessBrowser__Smeli:SMc02049 689 RPGDIGSDVSHLNLHKTFCIPHGGGGPGMGPIGVKSHLAPFLPGHPQ--------TDGHEGAVSAAPFGSASILP 755
                                         ********************************************543........345679************** PP

                           TIGR00461 751 isymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlld 825
                                         is+ y  mmG eGl++a++vailnany+a+rlk ay++l+++ ++rvaheci+d r+l e ag+ + dvakrl+d
  lcl|FitnessBrowser__Smeli:SMc02049 756 ISWSYCLMMGGEGLTQATKVAILNANYVAARLKGAYDVLYKSAKGRVAHECIIDTRPLAESAGVTVDDVAKRLID 830
                                         *************************************************************************** PP

                           TIGR00461 826 yGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewad 900
                                          Gfhapt+s+pvaGtlm+eptese++ eldrf+dam+ai+ee+ a+  G++++ +n+lknaph++++l v++w  
  lcl|FitnessBrowser__Smeli:SMc02049 831 CGFHAPTMSWPVAGTLMIEPTESETKAELDRFCDAMLAIREEARAIEDGRMDKVNNPLKNAPHTVEDL-VGDWDR 904
                                         ***************************************************************99985.79**** PP

                           TIGR00461 901 pysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
                                         pysre+a++p +  +  k+w  v+r+d++yGdrnlvc+c
  lcl|FitnessBrowser__Smeli:SMc02049 905 PYSREQACFPPGAFRVDKYWSPVNRVDNVYGDRNLVCTC 943
                                         **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (954 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 12.73
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources