Alignments for a candidate for pgmA in Desulfuromonas acetexigens

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Desulfuromonas acetexigens

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_092053485.1 BQ4888_RS02875 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_900111775.1:WP_092053485.1
          Length = 550

 Score =  712 bits (1837), Expect = 0.0
 Identities = 353/542 (65%), Positives = 422/542 (77%), Gaps = 2/542 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA+H  AGQPA +S L N+ +L + YY  +P+  +    V FGTSGHRG+A + +FNE H
Sbjct: 1   MALHPLAGQPAPKSLLPNIPRLISDYYTRRPDPNDPAQLVAFGTSGHRGAATKQTFNEWH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI QAI + R + GI+GP ++G DTHALSEPA    LEVLA NGV+  V ++ G+TPT
Sbjct: 61  ILAIVQAICDYRKQAGISGPLFLGMDTHALSEPAHAGALEVLAGNGVETRVAKDFGYTPT 120

Query: 121 PAVSNAILVHNKKG-GPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL +N+      ADGIVITPSHNPP++GGIKYNPPNGGPADT+VT  + DRAN 
Sbjct: 121 PVISHAILAYNRGSQADQADGIVITPSHNPPDNGGIKYNPPNGGPADTDVTGWIADRANG 180

Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
            L D L+GVKR +L EA+A+   +  D V P+V  LA+++DM AI KAGL +  D LGGS
Sbjct: 181 YLRDALRGVKRFALVEALAAPTTQMHDYVTPYVADLANVIDMEAIAKAGLRIAADALGGS 240

Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
           G+ +W+ I E Y LN+ ++N   D TF FM +DKDG IRMDCSS  AMAGL+ L+DK+D+
Sbjct: 241 GLGFWRPIAEKYGLNIELINGHPDPTFSFMSVDKDGKIRMDCSSASAMAGLIQLKDKYDI 300

Query: 300 AFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRV 358
           AF NDPD+DRHGIVTP AGLMNPNHYLAVAINYLF +R  W KD AVGKTLVSS+MIDRV
Sbjct: 301 AFGNDPDFDRHGIVTPSAGLMNPNHYLAVAINYLFANRAGWRKDAAVGKTLVSSSMIDRV 360

Query: 359 VNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLA 418
              LGR L EVPVGFKWFVDGL DGS+GFGGEESAGASFLR DGT W+TDKDG I+ LLA
Sbjct: 361 AASLGRPLAEVPVGFKWFVDGLVDGSYGFGGEESAGASFLRRDGTVWTTDKDGFILALLA 420

Query: 419 AEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPI 478
           AEITAVTG++P +HY EL  RFGAP Y+R+ A ATSAQKA L KLSPEM+SA+TLAG+PI
Sbjct: 421 AEITAVTGRDPAQHYQELTARFGAPVYDRIDAVATSAQKAVLEKLSPEMISAATLAGEPI 480

Query: 479 TARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEI 538
           TA+LT AP NGA IGGLKV+T+NGWFAARPSGTE+ YKIY ESF G EH KQI++EA  I
Sbjct: 481 TAKLTRAPANGAEIGGLKVVTENGWFAARPSGTEEIYKIYAESFKGAEHLKQIQQEAQAI 540

Query: 539 VS 540
           VS
Sbjct: 541 VS 542


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: 993
Number of extensions: 42
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: 550
Length adjustment: 36
Effective length of query: 510
Effective length of database: 514
Effective search space:   262140
Effective search space used:   262140
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_092053485.1 BQ4888_RS02875 (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.9705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-289  945.7   0.2   3.9e-289  945.5   0.2    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092053485.1  BQ4888_RS02875 phosphoglucomutas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092053485.1  BQ4888_RS02875 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-depende
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  945.5   0.2  3.9e-289  3.9e-289       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 945.5 bits;  conditional E-value: 3.9e-289
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               ma++p+aGq+a+++ l ++++l++dyy+ +pd++++aq v+fGtsGhrG+a+k+tfne hilai qa+ 
  lcl|NCBI__GCF_900111775.1:WP_092053485.1   1 MALHPLAGQPAPKSLLPNIPRLISDYYTRRPDPNDPAQLVAFGTSGHRGAATKQTFNEWHILAIVQAIC 69 
                                               799****************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkeal 138
                                               ++r++ Gi+Gpl++G+dthalsepa+  +levla n+ve+ v +  +ytptp +shail+yn+g ++++
  lcl|NCBI__GCF_900111775.1:WP_092053485.1  70 DYRKQAGISGPLFLGMDTHALSEPAHAGALEVLAGNGVETRVAKDFGYTPTPVISHAILAYNRGSQADQ 138
                                               ********************************************************************* PP

                                 TIGR01132 139 adGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekd 207
                                               adGivitpshnpp++GGikynppnGGpa+t+vt +i+dran +l+d l+gvkr+ l +al++ t++ +d
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 139 ADGIVITPSHNPPDNGGIKYNPPNGGPADTDVTGWIADRANGYLRDALRGVKRFALVEALAAPTTQMHD 207
                                               ********************************************************************* PP

                                 TIGR01132 208 lvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdG 276
                                               +v+pyv+dla+v+d++ai kaglr+ +d lGG+g+++w++iaeky+l++ l+n + d+tf fm++dkdG
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 208 YVTPYVADLANVIDMEAIAKAGLRIAADALGGSGLGFWRPIAEKYGLNIELINGHPDPTFSFMSVDKDG 276
                                               ********************************************************************* PP

                                 TIGR01132 277 kirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaev 345
                                               kirmdcss  amagl++lkdkyd+afgnd+d drhGivtp++Gl+npnhylavai+yl+ +r +w ++ 
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 277 KIRMDCSSASAMAGLIQLKDKYDIAFGNDPDFDRHGIVTPSAGLMNPNHYLAVAINYLFANRAGWRKDA 345
                                               ********************************************************************* PP

                                 TIGR01132 346 avGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGi 414
                                               avGktlvss++idrv+a+lgr l evpvGfkwfvdGl+dgs+GfGGeesaGasflr+dGtvw+tdkdG 
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 346 AVGKTLVSSSMIDRVAASLGRPLAEVPVGFKWFVDGLVDGSYGFGGEESAGASFLRRDGTVWTTDKDGF 414
                                               ********************************************************************* PP

                                 TIGR01132 415 ilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitak 483
                                               ilallaaeitavtG++p q+y+el+a++G+p+y+rida+atsaqka+l+klsp+++sa+tlaG++itak
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 415 ILALLAAEITAVTGRDPAQHYQELTARFGAPVYDRIDAVATSAQKAVLEKLSPEMISAATLAGEPITAK 483
                                               ********************************************************************* PP

                                 TIGR01132 484 ltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                               lt+ap nga iGGlkv+t++gwfaarpsGte++ykiyaesfkg+ehlk+i++ea++iv+ ++
  lcl|NCBI__GCF_900111775.1:WP_092053485.1 484 LTRAPANGAEIGGLKVVTENGWFAARPSGTEEIYKIYAESFKGAEHLKQIQQEAQAIVSAAF 545
                                               **********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (550 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.69
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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