Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N2E3

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate AO353_24665 AO353_24665 phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24665
          Length = 548

 Score =  643 bits (1658), Expect = 0.0
 Identities = 338/549 (61%), Positives = 397/549 (72%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA  E LVD+P LVTAYY+ +PD     Q+VAFGTSGHRGS+   +FNE H
Sbjct: 1   MTLSPFAGKPAPVELLVDIPRLVTAYYTGQPDASVSTQRVAFGTSGHRGSSFELSFNEWH 60

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

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PAISHAIL YNRGRT  LADGIV+TPSHNPP  GG KYNP NGGPADT  T  I  +ANE
Sbjct: 121 PAISHAILCYNRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANE 180

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

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

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

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV   + R+L EVPVGFKWF DGL   +LGFGGEESAGASFLR+DG VW+TDKDG+I 
Sbjct: 357 IDRVAKRLNRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGGVWSTDKDGLIP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ A TG  PSQ Y AL  E G P   R+DA A+ EQKA L +LS DQV +T+LA
Sbjct: 417 ALLAAEMTARTGRDPSQAYRALTDELGEPFSVRVDAKANPEQKALLGKLSPDQVKSTQLA 476

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

Query: 538 AREVVDRVI 546
           A+ +VD  I
Sbjct: 537 AQTLVDSAI 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: 938
Number of extensions: 35
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: 548
Length adjustment: 36
Effective length of query: 511
Effective length of database: 512
Effective search space:   261632
Effective search space used:   261632
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 AO353_24665 AO353_24665 (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.19584.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-269  879.0   0.0   6.3e-269  878.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665  AO353_24665 phosphoglucomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665  AO353_24665 phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  878.8   0.0  6.3e-269  6.3e-269       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 878.8 bits;  conditional E-value: 6.3e-269
                                     TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaia 65 
                                                   m++ p aG++a+ e l+d+++lv++yy+ +pda  ++q+v+fGtsGhrGs+ + +fne h+lai+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665   1 MTLSPFAGKPAPVELLVDIPRLVTAYYTGQPDASVSTQRVAFGTSGHRGSSFELSFNEWHVLAIS 65 
                                                   678899*********************************************************** PP

                                     TIGR01132  66 qavvevraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailty 130
                                                   qa+  +r+aqGi Gpl++G dthals pa  s+levlaan+v v++ e + ytptpa+shail y
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665  66 QAICLYREAQGIDGPLFVGIDTHALSTPAGASALEVLAANGVTVMIAEGDEYTPTPAISHAILCY 130
                                                   ***************************************************************** PP

                                     TIGR01132 131 nkgkkealadGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldle 195
                                                   n+g++++ladGivitpshnpp+ GG kynp nGGpa+t++tk+ie +anell+++l+gvkr+++e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 131 NRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANELLANKLAGVKRISYE 195
                                                   ***************************************************************** PP

                                     TIGR01132 196 kalksetvkekdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvn 260
                                                   +alk++t++++d+++ yv+dl++v+d++air a+lrlGvdplGGagv yw  iae+y l+l +vn
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 196 QALKASTTHRHDYLNTYVADLVNVIDFDAIRGANLRLGVDPLGGAGVRYWSAIAEHYRLNLEVVN 260
                                                   ***************************************************************** PP

                                     TIGR01132 261 eavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnh 325
                                                    +vd+tfrfm++d+dG+irmd ss yam gl+ lk+++d+af+ d+d drhGivtp+ Gll pn 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 261 TQVDPTFRFMSVDWDGQIRMDPSSSYAMQGLIGLKERFDVAFACDPDHDRHGIVTPSGGLLAPNN 325
                                                   ***************************************************************** PP

                                     TIGR01132 326 ylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfG 390
                                                   ylav+i+yl+++r+qw a+ avGkt+vss lidrv+  l+r+l+evpvGfkwf dGl+dgslGfG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 326 YLAVSIDYLFQNRPQWRADAAVGKTVVSSGLIDRVAKRLNRRLYEVPVGFKWFADGLFDGSLGFG 390
                                                   ***************************************************************** PP

                                     TIGR01132 391 GeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaat 455
                                                   GeesaGasflrkdG vwstdkdG+i allaae+ta tG++p+q y +l+ ++G+p+  r+da a+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 391 GEESAGASFLRKDGGVWSTDKDGLIPALLAAEMTARTGRDPSQAYRALTDELGEPFSVRVDAKAN 455
                                                   ***************************************************************** PP

                                     TIGR01132 456 saqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiy 520
                                                   ++qka l klspd+v +t+laG+ai + l+kapGn+ aiGGlkv+t++gwfaarpsGted+ykiy
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 456 PEQKALLGKLSPDQVKSTQLAGEAIQSILSKAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIY 520
                                                   ***************************************************************** PP

                                     TIGR01132 521 aesfkgeehlkeiekeaeeivdevl 545
                                                   aesf g++hlk++ +ea+ +vd+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_24665 521 AESFIGDDHLKQLVSEAQTLVDSAI 545
                                                   *********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (548 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.44
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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