Alignments for a candidate for pgmA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Escherichia coli BW25113

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 14818 b0688 phosphoglucomutase (NCBI)

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__Keio:14818
          Length = 546

 Score = 1096 bits (2835), Expect = 0.0
 Identities = 546/546 (100%), Positives = 546/546 (100%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH
Sbjct: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT
Sbjct: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120

Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL
Sbjct: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180

Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG
Sbjct: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240

Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA
Sbjct: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300

Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360
           FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN
Sbjct: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360

Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420
           DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE
Sbjct: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420

Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480
           ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA
Sbjct: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480

Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS
Sbjct: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540

Query: 541 EVLKNA 546
           EVLKNA
Sbjct: 541 EVLKNA 546


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: 1211
Number of extensions: 50
Number of successful extensions: 1
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: 546
Length adjustment: 35
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate 14818 b0688 (phosphoglucomutase (NCBI))
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.28501.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1074.3   0.3          0 1074.2   0.3    1.0  1  lcl|FitnessBrowser__Keio:14818  b0688 phosphoglucomutase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14818  b0688 phosphoglucomutase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1074.2   0.3         0         0       1     546 []       1     544 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1074.2 bits;  conditional E-value: 0
                       TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 
                                     mai++raGq+aqq+dl++va+l+a+yy+lkp+a+na+++v+fGtsGhrGsa++++fne hilaiaqa++e+ra++GitG
  lcl|FitnessBrowser__Keio:14818   1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPHILAIAQAIAEERAKNGITG 79 
                                     89***************************************************************************** PP

                       TIGR01132  80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnppedGGiky 158
                                     p+y+Gkdthalsepaf+svlevlaan+v+vivqenn++tptpavs+ail++nk k ++ladGivitpshnppedGGiky
  lcl|FitnessBrowser__Keio:14818  80 PCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKY 157
                                     *****************************************************.************************* PP

                       TIGR01132 159 nppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGvdpl 237
                                     nppnGGpa+t+vtk++edran+ll+d+lkgvkr++l++a++s++vke+dlv+p+v++lad+vd+aai+kagl+lGvdpl
  lcl|FitnessBrowser__Keio:14818 158 NPPNGGPADTNVTKVVEDRANALLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
                                     ******************************************************************************* PP

                       TIGR01132 238 GGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtp 316
                                     GG+g++ywk+i+e+ynl+lt+vn++vd+tfrfm+ldkdG+irmdcss++amagll+l+dk+dlaf+nd+d+drhGivtp
  lcl|FitnessBrowser__Keio:14818 237 GGSGIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLAFANDPDYDRHGIVTP 315
                                     ******************************************************************************* PP

                       TIGR01132 317 dkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesa 395
                                      +Gl+npnhylavai+yl++hr+qw+++vavGktlvssa+idrvv+dlgrklvevpvGfkwfvdGl+dgs+GfGGeesa
  lcl|FitnessBrowser__Keio:14818 316 -AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESA 393
                                     .****************************************************************************** PP

                       TIGR01132 396 GasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsatt 474
                                     Gasflr+dGt+wstdkdGii++llaaeitavtGknpq++y+ela+++G+p+y+r++aaatsaqka+l+klsp++vsa+t
  lcl|FitnessBrowser__Keio:14818 394 GASFLRFDGTPWSTDKDGIIMCLLAAEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSAST 472
                                     ******************************************************************************* PP

                       TIGR01132 475 laGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                     laGd+ita+lt+apGnga+iGGlkv+td+gwfaarpsGted+ykiy+esf geeh+k+iekea eiv+evlk
  lcl|FitnessBrowser__Keio:14818 473 LAGDPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVSEVLK 544
                                     **********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (546 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: 00:00:00.03
# Mc/sec: 7.68
//
[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