GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Pseudomonas simiae WCS417

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF2629 PS417_13395 phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>lcl|FitnessBrowser__WCS417:GFF2629 PS417_13395 phosphoglucomutase
          Length = 547

 Score =  639 bits (1648), Expect = 0.0
 Identities = 337/549 (61%), Positives = 399/549 (72%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA  + LVD+P LVTAYY+ +PD     Q+VAFGTSGHRG++   +FNE H
Sbjct: 1   MTISPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGNSFELSFNEWH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           +LAI+QAI  YR AQG  GPLF+G DTH LS PA  SALEVLAAN V  ++   D YTPT
Sbjct: 61  VLAISQAICLYREAQGINGPLFVGLDTHALSTPAGASALEVLAANGVHVMLAEGDEYTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PAISHAI+ YNRGRT  LADGIV+TPSHNPP  GG KYNPPNGGPADT  T  I  +ANE
Sbjct: 121 PAISHAIICYNRGRTSGLADGIVITPSHNPPQSGGYKYNPPNGGPADTHVTKWIEAKANE 180

Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L  + + VKR+  A+AL+  T  RHDYL  YV DL NV+D+ AIR A +R+G DPLGGA
Sbjct: 181 LLAKKLAGVKRITHAQALKADTTHRHDYLNTYVADLVNVIDMDAIRSADLRLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA  + L+L VVN  VDAT+RFM +D DG+IRMD SS  AM GLI    G +E
Sbjct: 241 GVRYWSAIAEHYRLNLEVVNTEVDATFRFMCVDWDGQIRMDPSSSYAMQGLI----GLKE 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ +A   D D DRHGIVTP  GLL PN+YLAV+I+YL+ +RP W A  AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPDWRADAAVGKTVVSSGL 356

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV A IGR+L EVPVGFKWF DGL   +LGFGGEESAGASFLR+DG+VW+TDKDG+I 
Sbjct: 357 IDRVAARIGRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGTVWSTDKDGLIP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ +  G  PSQ Y  L    G P   R+DA A   QKA L +LS DQV++TELA
Sbjct: 417 ALLAAEMTSRKGQDPSQIYRGLTDALGEPFAIRVDAKATPAQKALLGKLSPDQVTSTELA 476

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GE I   L+ APGN  A+GGLKV T N WFAARPSGTED+YKIYAESF G  HL ++ + 
Sbjct: 477 GESIQQILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFIGEDHLKQLVEE 536

Query: 538 AREVVDRVI 546
           A+ +VD  I
Sbjct: 537 AQVLVDGAI 545


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: 972
Number of extensions: 36
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: 547
Length of database: 547
Length adjustment: 36
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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: 52 (24.6 bits)

Align candidate GFF2629 PS417_13395 (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.5944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.5e-267  872.4   0.0   6.2e-267  872.2   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2629  PS417_13395 phosphoglucomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2629  PS417_13395 phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  872.2   0.0  6.2e-267  6.2e-267       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 872.2 bits;  conditional E-value: 6.2e-267
                           TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                         m+i p aG++a+++ l+d+++lv++yy+ +pda  ++q+v+fGtsGhrG + + +fne h+lai+qa+  +r+aq
  lcl|FitnessBrowser__WCS417:GFF2629   1 MTISPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGNSFELSFNEWHVLAISQAICLYREAQ 75 
                                         7899*********************************************************************** PP

                           TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnp 150
                                         Gi Gpl++G dthals pa  s+levlaan+v+v++ e + ytptpa+shai+ yn+g++++ladGivitpshnp
  lcl|FitnessBrowser__WCS417:GFF2629  76 GINGPLFVGLDTHALSTPAGASALEVLAANGVHVMLAEGDEYTPTPAISHAIICYNRGRTSGLADGIVITPSHNP 150
                                         *************************************************************************** PP

                           TIGR01132 151 pedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaai 225
                                         p+ GG kynppnGGpa+t+vtk+ie +anell+++l+gvkr++ ++alk++t++++d+++ yv+dl++v+d++ai
  lcl|FitnessBrowser__WCS417:GFF2629 151 PQSGGYKYNPPNGGPADTHVTKWIEAKANELLAKKLAGVKRITHAQALKADTTHRHDYLNTYVADLVNVIDMDAI 225
                                         *************************************************************************** PP

                           TIGR01132 226 rkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydl 300
                                         r+a+lrlGvdplGGagv yw  iae+y l+l +vn +vdatfrfm +d+dG+irmd ss yam gl+ lk+++d+
  lcl|FitnessBrowser__WCS417:GFF2629 226 RSADLRLGVDPLGGAGVRYWSAIAEHYRLNLEVVNTEVDATFRFMCVDWDGQIRMDPSSSYAMQGLIGLKERFDV 300
                                         *************************************************************************** PP

                           TIGR01132 301 afgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGf 375
                                         af+ d+d drhGivtp+ Gll pn ylav+i+yl+++r++w a+ avGkt+vss lidrv+a +gr+l+evpvGf
  lcl|FitnessBrowser__WCS417:GFF2629 301 AFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPDWRADAAVGKTVVSSGLIDRVAARIGRRLYEVPVGF 375
                                         *************************************************************************** PP

                           TIGR01132 376 kwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyari 450
                                         kwf dGl+dgslGfGGeesaGasflrkdGtvwstdkdG+i allaae+t+  G++p+q y  l+  +G+p+  r+
  lcl|FitnessBrowser__WCS417:GFF2629 376 KWFADGLFDGSLGFGGEESAGASFLRKDGTVWSTDKDGLIPALLAAEMTSRKGQDPSQIYRGLTDALGEPFAIRV 450
                                         *************************************************************************** PP

                           TIGR01132 451 daaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfk 525
                                         da at+aqka l klspd+v++t+laG++i   l++apGn+ aiGGlkv+t++gwfaarpsGted+ykiyaesf 
  lcl|FitnessBrowser__WCS417:GFF2629 451 DAKATPAQKALLGKLSPDQVTSTELAGESIQQILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFI 525
                                         *************************************************************************** PP

                           TIGR01132 526 geehlkeiekeaeeivdevl 545
                                         ge+hlk++ +ea+ +vd ++
  lcl|FitnessBrowser__WCS417:GFF2629 526 GEDHLKQLVEEAQVLVDGAI 545
                                         ***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (547 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.37
//
[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:

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:

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:

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, or view the source code.

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