Alignments for a candidate for pgmA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas stutzeri RCH2

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF39 Psest_0039 phosphoglucomutase, alpha-D-glucose phosphate-specific

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__psRCH2:GFF39
          Length = 554

 Score =  686 bits (1771), Expect = 0.0
 Identities = 353/550 (64%), Positives = 410/550 (74%), Gaps = 14/550 (2%)

Query: 7   AGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAITQ 66
           AG+   P  L  LP LV  YYS  PDP D AQQVAFGTSGHRGS+L G+FNE HILA TQ
Sbjct: 7   AGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQ 66

Query: 67  AIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDS-------RDRYTP 119
           AI +YR  +G  GPLF+G DTH LSEPA++SALEVLAAN +   +D+          YTP
Sbjct: 67  AICDYRRQEGIDGPLFMGMDTHALSEPAFISALEVLAANGIETRIDAGCAETGGEPGYTP 126

Query: 120 TPAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRAN 179
           TPAIS+AIL+YNRGRT  LADGIV+TPSHNPP DGG KYNP NGGPADT  T  I +RAN
Sbjct: 127 TPAISNAILSYNRGRTSGLADGIVITPSHNPPGDGGFKYNPTNGGPADTGVTKWIQERAN 186

Query: 180 EILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGG 236
            +L+A    VKR+   +AL+  T QR D++  YV  L  V+D+ AIR +G++   DPLGG
Sbjct: 187 ALLVAGLEGVKRMDYRQALKATTTQRFDFIDAYVGGLERVIDLDAIRGSGLKFAVDPLGG 246

Query: 237 ASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNR 296
           A V YW  IA R GL L V++ +VD T+RFM LD DGKIRMDCSSP AMAGLI     N+
Sbjct: 247 AGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGKIRMDCSSPHAMAGLIE----NK 302

Query: 297 ERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSS 356
           +R+ +A   D D DRHGIVT   GL+NPNHYLAVAIEYL+THRP W A   +GKT+VSSS
Sbjct: 303 DRFDVAFACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVSSS 362

Query: 357 IIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGII 416
           +IDRV AGI R+LVEVPVGFKWFVDGL+  +LGFGGEESAGASFL + G  W+TDKDG+I
Sbjct: 363 MIDRVAAGIERRLVEVPVGFKWFVDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDGLI 422

Query: 417 MALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATEL 476
           + LLAAEI AVTG  PS+RY AL   +G P Y RIDA A+REQKARL +LSA QVSA EL
Sbjct: 423 LGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAANREQKARLGKLSASQVSAKEL 482

Query: 477 AGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQ 536
           AG+PIT  LT APGNGAA+GGLKV TAN WFAARPSGTEDVYKIYAESF G  HL  +Q 
Sbjct: 483 AGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLKRIQA 542

Query: 537 TAREVVDRVI 546
            A+ +VD V+
Sbjct: 543 EAKALVDSVL 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: 1048
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 GFF39 Psest_0039 (phosphoglucomutase, alpha-D-glucose phosphate-specific)
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.18309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.2e-280  914.6   0.0     1e-279  914.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF39  Psest_0039 phosphoglucomutase, a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF39  Psest_0039 phosphoglucomutase, alpha-D-glucose phosphate-specific
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  914.4   0.0    1e-279    1e-279       1     545 [.       1     552 [.       1     553 [. 0.99

  Alignments for each domain:
  == domain 1  score: 914.4 bits;  conditional E-value: 1e-279
                         TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGi 77 
                                       m+i + aG+ + ++ l+++++lva yy+ +pd+ ++aq+v+fGtsGhrGs+lkg+fne hila +qa+ ++r+++Gi
  lcl|FitnessBrowser__psRCH2:GFF39   1 MSIAANAGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQAICDYRRQEGI 77 
                                       678899*********************************************************************** PP

                         TIGR01132  78 tGplyiGkdthalsepafvsvlevlaanqvevivq.......ennrytptpavshailtynkgkkealadGivitps 147
                                        Gpl++G+dthalsepaf+s+levlaan++e+ ++        + +ytptpa+s+ail yn+g++++ladGivitps
  lcl|FitnessBrowser__psRCH2:GFF39  78 DGPLFMGMDTHALSEPAFISALEVLAANGIETRIDagcaetgGEPGYTPTPAISNAILSYNRGRTSGLADGIVITPS 154
                                       **********************************988886666789******************************* PP

                         TIGR01132 148 hnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaa 224
                                       hnpp dGG+kynp nGGpa+t vtk+i++ran+ll ++l+gvkr+d+ +alk++t+++ d+++ yv +l  v+dl+a
  lcl|FitnessBrowser__psRCH2:GFF39 155 HNPPGDGGFKYNPTNGGPADTGVTKWIQERANALLVAGLEGVKRMDYRQALKATTTQRFDFIDAYVGGLERVIDLDA 231
                                       ***************************************************************************** PP

                         TIGR01132 225 irkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydla 301
                                       ir +gl++ vdplGGagv+yw +iae+++l l +++  vd+tfrfm ld+dGkirmdcssp+amagl+++kd++d+a
  lcl|FitnessBrowser__psRCH2:GFF39 232 IRGSGLKFAVDPLGGAGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGKIRMDCSSPHAMAGLIENKDRFDVA 308
                                       ***************************************************************************** PP

                         TIGR01132 302 fgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwf 378
                                       f+ d+d drhGivt + Gl+npnhylavaieyl++hr++w+ae  +Gktlvss++idrv+a ++r+lvevpvGfkwf
  lcl|FitnessBrowser__psRCH2:GFF39 309 FACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVSSSMIDRVAAGIERRLVEVPVGFKWF 385
                                       ***************************************************************************** PP

                         TIGR01132 379 vdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaat 455
                                       vdGl+dgslGfGGeesaGasfl k+G +wstdkdG+il llaaeitavtGk+p++ry++l+ ++G+p+y+ridaaa+
  lcl|FitnessBrowser__psRCH2:GFF39 386 VDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDGLILGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAAN 462
                                       ***************************************************************************** PP

                         TIGR01132 456 saqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlke 532
                                       ++qkarl kls+ +vsa++laG++it  lt+apGngaaiGGlkv t++gwfaarpsGtedvykiyaesf+ge+hlk+
  lcl|FitnessBrowser__psRCH2:GFF39 463 REQKARLGKLSASQVSAKELAGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLKR 539
                                       ***************************************************************************** PP

                         TIGR01132 533 iekeaeeivdevl 545
                                       i+ ea+++vd+vl
  lcl|FitnessBrowser__psRCH2:GFF39 540 IQAEAKALVDSVL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.69
//
[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