Alignments for a candidate for pgmA in Paucidesulfovibrio gracilis DSM 16080

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Paucidesulfovibrio gracilis DSM 16080

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_078715801.1 B5D49_RS01090 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_900167125.1:WP_078715801.1
          Length = 549

 Score =  636 bits (1641), Expect = 0.0
 Identities = 323/536 (60%), Positives = 384/536 (71%), Gaps = 2/536 (0%)

Query: 6   RAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPHILAIA 65
           R G PA  S L++   L   YY L P       AV FGTSGHRG A    FNE HILA+ 
Sbjct: 7   RPGTPAPASMLVDPEALIQAYYTLSPHPDIPGQAVSFGTSGHRGRALEGGFNEGHILAVT 66

Query: 66  QAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAVSN 125
           QA+ E RA+ G+ GP ++G DTHALSEPA  + +EVLA NGV V +Q++NG TPTP +S+
Sbjct: 67  QALCEHRARAGVNGPLFLGMDTHALSEPAQRTAIEVLAGNGVHVFIQQDNGHTPTPVISH 126

Query: 126 AILVHNKKG-GPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLADG 184
           AIL  N+ G G LADG+V+TPSHNPP DGG KYNPP+GGPA  N+T  V++RAN +L DG
Sbjct: 127 AILSWNRGGKGSLADGVVVTPSHNPPSDGGFKYNPPSGGPAGPNITGPVQERANQILRDG 186

Query: 185 LKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSGIEYW 244
           L  V+R+  + A+ S  V   D V+P+V  L ++VDM  I+ AGL +G DPLGGSG+ Y+
Sbjct: 187 LHEVRRLPYERAIQSELVHLHDYVRPYVLDLENVVDMETIRSAGLKIGADPLGGSGLAYF 246

Query: 245 KRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLAFAND 304
             I + Y L++ +VN   D  F FM LD D  IRMDCSS  AMAGL+ L+D+FD+AF ND
Sbjct: 247 DPIADLYGLDIEVVNRSTDPRFAFMPLDHDLKIRMDCSSAHAMAGLIRLKDQFDVAFGND 306

Query: 305 PDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVNDLGR 364
           PD+DRHGIVT  GLMNPNH+LAVA  +LFQ R  W +   +GKTLVSS+M+DRV   L R
Sbjct: 307 PDFDRHGIVTSQGLMNPNHFLAVACEHLFQTRTGWSRAAGLGKTLVSSSMLDRVAAHLDR 366

Query: 365 KLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAEITAV 424
            L EVPVGFKWFVDGL DGS GFGGEESAGASFLR DGT WSTDKDGIIM LLA EITA 
Sbjct: 367 TLYEVPVGFKWFVDGLLDGSLGFGGEESAGASFLRKDGTAWSTDKDGIIMDLLACEITA- 425

Query: 425 TGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITARLTA 484
           TG NP + Y  L +RFG P Y R+ A A+  QKAA  +L+P+MV+A  LAG+PI ARLT 
Sbjct: 426 TGNNPAQRYTSLTERFGEPVYARIDAPASPDQKAAFKQLTPDMVTAEHLAGEPILARLTR 485

Query: 485 APGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           APGN A IGGLKV T NGWFAARPSGTED YKIY ESFLG EH   I+ EA  IV+
Sbjct: 486 APGNNAPIGGLKVTTKNGWFAARPSGTEDIYKIYAESFLGAEHLADIQDEAKAIVN 541


Lambda     K      H
   0.316    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: 979
Number of extensions: 49
Number of successful extensions: 3
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: 546
Length of database: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_078715801.1 B5D49_RS01090 (phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

# 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/TIGR01132.hmm
# target sequence database:        /tmp/gapView.3430310.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01132  [M=546]
Accession:   TIGR01132
Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.8e-266  868.4   0.0     1e-265  868.2   0.0    1.0  1  NCBI__GCF_900167125.1:WP_078715801.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167125.1:WP_078715801.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  868.2   0.0    1e-265    1e-265       4     545 ..       5     544 ..       2     545 .. 0.99

  Alignments for each domain:
  == domain 1  score: 868.2 bits;  conditional E-value: 1e-265
                             TIGR01132   4 npraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqG 76 
                                           +pr G +a+++ l+d  +l+++yy+l p+++ + q+v+fGtsGhrG al+g fne hila++qa+ e+ra+ G
  NCBI__GCF_900167125.1:WP_078715801.1   5 QPRPGTPAPASMLVDPEALIQAYYTLSPHPDIPGQAVSFGTSGHRGRALEGGFNEGHILAVTQALCEHRARAG 77 
                                           6899********************************************************************* PP

                             TIGR01132  77 itGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshn 149
                                           + Gpl++G+dthalsepa+ +++evla n+v+v++q+ n++tptp +shail +n+g k++ladG+v+tpshn
  NCBI__GCF_900167125.1:WP_078715801.1  78 VNGPLFLGMDTHALSEPAQRTAIEVLAGNGVHVFIQQDNGHTPTPVISHAILSWNRGGKGSLADGVVVTPSHN 150
                                           ************************************************************************* PP

                             TIGR01132 150 ppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdl 222
                                           pp+dGG+kynpp+GGpa +++t  +++ran++l+d+l+ v+rl++e+a++se+v+ +d+v+pyv dl +vvd+
  NCBI__GCF_900167125.1:WP_078715801.1 151 PPSDGGFKYNPPSGGPAGPNITGPVQERANQILRDGLHEVRRLPYERAIQSELVHLHDYVRPYVLDLENVVDM 223
                                           ************************************************************************* PP

                             TIGR01132 223 aairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklk 295
                                           ++ir+agl++G+dplGG+g+ y+++ia+ y+ld+ +vn + d+ f fm ld+d kirmdcss +amagl++lk
  NCBI__GCF_900167125.1:WP_078715801.1 224 ETIRSAGLKIGADPLGGSGLAYFDPIADLYGLDIEVVNRSTDPRFAFMPLDHDLKIRMDCSSAHAMAGLIRLK 296
                                           ************************************************************************* PP

                             TIGR01132 296 dkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrkl 368
                                           d++d+afgnd+d drhGivt  +Gl+npnh+lava e+l++ r +w+    +Gktlvss+++drv+a+l+r l
  NCBI__GCF_900167125.1:WP_078715801.1 297 DQFDVAFGNDPDFDRHGIVTS-QGLMNPNHFLAVACEHLFQTRTGWSRAAGLGKTLVSSSMLDRVAAHLDRTL 368
                                           ********************9.*************************************************** PP

                             TIGR01132 369 vevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaak 441
                                           +evpvGfkwfvdGlldgslGfGGeesaGasflrkdGt+wstdkdGii++lla eita tG+np qry  l+++
  NCBI__GCF_900167125.1:WP_078715801.1 369 YEVPVGFKWFVDGLLDGSLGFGGEESAGASFLRKDGTAWSTDKDGIIMDLLACEITA-TGNNPAQRYTSLTER 440
                                           *******************************************************98.9************** PP

                             TIGR01132 442 yGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGte 514
                                           +G+p+yarida+a+++qka++k+l+pd+v+a++laG++i a+lt+apGn+a iGGlkvtt++gwfaarpsGte
  NCBI__GCF_900167125.1:WP_078715801.1 441 FGEPVYARIDAPASPDQKAAFKQLTPDMVTAEHLAGEPILARLTRAPGNNAPIGGLKVTTKNGWFAARPSGTE 513
                                           ************************************************************************* PP

                             TIGR01132 515 dvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           d+ykiyaesf g+ehl +i++ea++iv+ ++
  NCBI__GCF_900167125.1:WP_078715801.1 514 DIYKIYAESFLGAEHLADIQDEAKAIVNAAF 544
                                           ***************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (549 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.13
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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