Alignments for a candidate for pgmA in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas stutzeri A1501

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_011915153.1 PST_RS20675 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_000013785.1:WP_011915153.1
          Length = 554

 Score =  688 bits (1776), Expect = 0.0
 Identities = 354/552 (64%), Positives = 410/552 (74%), Gaps = 14/552 (2%)

Query: 5   PRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAI 64
           P AG+   P  L  LP LV  YYS  PDP D AQQVAFGTSGHRGS+L G+FNE HILA 
Sbjct: 5   PNAGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILAT 64

Query: 65  TQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDS-------RDRY 117
           TQAI +YR  +G  GPLF+G DTH LSEPA+VSALEVLAAN +   +D+          Y
Sbjct: 65  TQAICDYRRQEGIDGPLFMGMDTHALSEPAFVSALEVLAANGIETRIDAGCPETGGEPGY 124

Query: 118 TPTPAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKR 177
           TPTPAIS+AIL+YNRGRT  LADGIV+TPSHNPP DGG KYNP NGGPADT  T  I +R
Sbjct: 125 TPTPAISNAILSYNRGRTRGLADGIVITPSHNPPGDGGFKYNPTNGGPADTGVTKWIQER 184

Query: 178 ANEILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPL 234
           AN +L+A    VKR+   +AL+  T QR D++  YV  L  V+D+ AIR +G++   DPL
Sbjct: 185 ANALLVAGLDGVKRMDYRQALKAATTQRFDFIDAYVGGLERVIDLDAIRGSGLKFAVDPL 244

Query: 235 GGASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFG 294
           GGA V YW  IA R GL L V++ +VD T+RFM LD DG IRMDCSSP AMAGLI     
Sbjct: 245 GGAGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGTIRMDCSSPHAMAGLIE---- 300

Query: 295 NRERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVS 354
           N++R+ +A   D D DRHGIVT   GL+NPNHYLAVAIEYL+THRP W A   +GKT+VS
Sbjct: 301 NKDRFDVAFACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVS 360

Query: 355 SSIIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDG 414
           SS+IDRV AGI R+LVEVPVGFKWFVDGL+  +LGFGGEESAGASFL + G  W+TDKDG
Sbjct: 361 SSMIDRVAAGIDRRLVEVPVGFKWFVDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDG 420

Query: 415 IIMALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSAT 474
           +I+ LLAAEI AVTG  PS+RY AL   +G P Y RIDA A+REQKARL +LSA QVSA 
Sbjct: 421 LILGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAANREQKARLGKLSASQVSAK 480

Query: 475 ELAGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEV 534
           ELAG+PIT  LT APGNGAA+GGLKV TAN WFAARPSGTEDVYKIYAESF G  HL  +
Sbjct: 481 ELAGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLARI 540

Query: 535 QQTAREVVDRVI 546
           Q  A+ +VD V+
Sbjct: 541 QAEAKALVDSVL 552


Lambda     K      H
   0.318    0.135    0.401 

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: 1067
Number of extensions: 44
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: 547
Length of database: 554
Length adjustment: 36
Effective length of query: 511
Effective length of database: 518
Effective search space:   264698
Effective search space used:   264698
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_011915153.1 PST_RS20675 (alpha-D-glucose phosphate-specific phosphoglucomutase)
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.26674.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-279  912.0   0.0   6.1e-279  911.9   0.0    1.0  1  lcl|NCBI__GCF_000013785.1:WP_011915153.1  PST_RS20675 alpha-D-glucose phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011915153.1  PST_RS20675 alpha-D-glucose phosphate-specific phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  911.9   0.0  6.1e-279  6.1e-279       1     545 [.       1     552 [.       1     553 [. 0.99

  Alignments for each domain:
  == domain 1  score: 911.9 bits;  conditional E-value: 6.1e-279
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               m+i p aG+ + ++ l+++++lva yy+ +pd+ ++aq+v+fGtsGhrGs+lkg+fne hila +qa+ 
  lcl|NCBI__GCF_000013785.1:WP_011915153.1   1 MSIAPNAGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQAIC 69 
                                               7899***************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivq.......ennrytptpavshailtyn 131
                                               ++r+++Gi Gpl++G+dthalsepafvs+levlaan++e+ ++        + +ytptpa+s+ail yn
  lcl|NCBI__GCF_000013785.1:WP_011915153.1  70 DYRRQEGIDGPLFMGMDTHALSEPAFVSALEVLAANGIETRIDagcpetgGEPGYTPTPAISNAILSYN 138
                                               ******************************************988887666789*************** PP

                                 TIGR01132 132 kgkkealadGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalks 200
                                               +g++ +ladGivitpshnpp dGG+kynp nGGpa+t vtk+i++ran+ll ++l gvkr+d+ +alk+
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 139 RGRTRGLADGIVITPSHNPPGDGGFKYNPTNGGPADTGVTKWIQERANALLVAGLDGVKRMDYRQALKA 207
                                               ********************************************************************* PP

                                 TIGR01132 201 etvkekdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrf 269
                                               +t+++ d+++ yv +l  v+dl+air +gl++ vdplGGagv+yw +iae+++l l +++  vd+tfrf
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 208 ATTQRFDFIDAYVGGLERVIDLDAIRGSGLKFAVDPLGGAGVHYWPRIAERFGLPLEVLSTVVDPTFRF 276
                                               ********************************************************************* PP

                                 TIGR01132 270 mtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhr 338
                                               m ld+dG+irmdcssp+amagl+++kd++d+af+ d+d drhGivt + Gl+npnhylavaieyl++hr
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 277 MRLDWDGTIRMDCSSPHAMAGLIENKDRFDVAFACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHR 345
                                               ********************************************************************* PP

                                 TIGR01132 339 qqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvw 407
                                               ++w+ae  +Gktlvss++idrv+a ++r+lvevpvGfkwfvdGl+dgslGfGGeesaGasfl k+G +w
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 346 PGWSAEAGIGKTLVSSSMIDRVAAGIDRRLVEVPVGFKWFVDGLMDGSLGFGGEESAGASFLDKQGGAW 414
                                               ********************************************************************* PP

                                 TIGR01132 408 stdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattla 476
                                               stdkdG+il llaaeitavtGk+p++ry++l+ ++G+p+y+ridaaa+++qkarl kls+ +vsa++la
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 415 STDKDGLILGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAANREQKARLGKLSASQVSAKELA 483
                                               ********************************************************************* PP

                                 TIGR01132 477 GdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                               G++it  lt+apGngaaiGGlkv t++gwfaarpsGtedvykiyaesf+ge+hl +i+ ea+++vd+vl
  lcl|NCBI__GCF_000013785.1:WP_011915153.1 484 GQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLARIQAEAKALVDSVL 552
                                               *******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (554 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.86
//
[ok]

This GapMind analysis is from Sep 24 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