Alignments for a candidate for pgmA in Chlorobium phaeobacteroides BS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Chlorobium phaeobacteroides BS1

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_012474608.1 CPHAMN1_RS05900 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_000020545.1:WP_012474608.1
          Length = 548

 Score =  614 bits (1584), Expect = e-180
 Identities = 312/550 (56%), Positives = 399/550 (72%), Gaps = 6/550 (1%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           M I   AG+  +Q  L+N+  L   ++ L P+    EH V FGTSGHRGS+   SFNEPH
Sbjct: 1   MTISPFAGKLPEQEMLVNIPHLVTAFFALSPDPSVDEHRVAFGTSGHRGSSFSCSFNEPH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI QAI   R K GI GP ++G DTHALSEPAF   LEVLAAN V+V++  +  FTPT
Sbjct: 61  ILAITQAICMYRMKEGIDGPLFLGMDTHALSEPAFAVALEVLAANEVEVMIAGDERFTPT 120

Query: 121 PAVSNAILVHNK---KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRA 177
           PAVS+AIL  N+   KG  LADGI++TPSHNPP DGGIKYNPP+GGPA ++VT  +ED+A
Sbjct: 121 PAVSHAILTWNRNRRKG--LADGILLTPSHNPPGDGGIKYNPPHGGPAGSHVTSWIEDKA 178

Query: 178 NALLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLG 237
           N LL   L+ V R+  ++A+++   +  D    ++E L +++DM  I ++G+TLGVDPLG
Sbjct: 179 NELLEQKLREVHRVPFEKALSAPATRTYDYPGRYIEDLGNVLDMEGISESGITLGVDPLG 238

Query: 238 GSGIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKF 297
           G+G+ YW+RI E Y LNL I+N  +D TFRFM +D+DG IRMD SS   M  L+A +D+F
Sbjct: 239 GAGVAYWERIAEQYALNLAILNTTIDPTFRFMSVDRDGKIRMDPSSPYTMQPLIAQKDRF 298

Query: 298 DLAFANDPDYDRHGIVT-PAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMID 356
           D++FA D DYDRHGIVT  +GL+ PNH+L+V I YLFQ+R +W +   +GKTLVSS+MID
Sbjct: 299 DISFACDTDYDRHGIVTGSSGLLQPNHFLSVCIEYLFQNRQEWPESAMIGKTLVSSSMID 358

Query: 357 RVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCL 416
           RV   +GR++ EVPVGFKWFV+GL +GS GF GEESAGASFLR +GT W+TDKDG I  L
Sbjct: 359 RVGARMGRRVYEVPVGFKWFVEGLLNGSLGFAGEESAGASFLRKNGTVWTTDKDGFIPAL 418

Query: 417 LAAEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGD 476
           L+AEITA  GK+P E Y  L +  G P Y+R+ A+A+   KA L +LSPE V    LAG+
Sbjct: 419 LSAEITAQRGKDPGEIYKGLTQELGEPVYSRIDASASPEDKAKLKELSPEHVRLEELAGE 478

Query: 477 PITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAV 536
            I + +T APGNGASIGGLKV+T+NGWFAARPSGTE+ YKIY ESFLG +H  +I  EA 
Sbjct: 479 KIQSIVTDAPGNGASIGGLKVVTENGWFAARPSGTENIYKIYAESFLGGDHLDRILVEAQ 538

Query: 537 EIVSEVLKNA 546
           E+V++ L+ A
Sbjct: 539 EVVADALEGA 548


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: 863
Number of extensions: 28
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: 546
Length of database: 548
Length adjustment: 36
Effective length of query: 510
Effective length of database: 512
Effective search space:   261120
Effective search space used:   261120
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 WP_012474608.1 CPHAMN1_RS05900 (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.29499.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-262  856.4   0.0   4.3e-262  856.2   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474608.1  CPHAMN1_RS05900 alpha-D-glucose 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474608.1  CPHAMN1_RS05900 alpha-D-glucose phosphate-specific phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  856.2   0.0  4.3e-262  4.3e-262       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 856.2 bits;  conditional E-value: 4.3e-262
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               m+i p aG+ ++qe l+++++lv++++ l pd+   +++v+fGtsGhrGs+   +fne hilai+qa+ 
  lcl|NCBI__GCF_000020545.1:WP_012474608.1   1 MTISPFAGKLPEQEMLVNIPHLVTAFFALSPDPSVDEHRVAFGTSGHRGSSFSCSFNEPHILAITQAIC 69 
                                               7899***************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkeal 138
                                                +r ++Gi Gpl++G+dthalsepaf  +levlaan+vev++   +r+tptpavshailt+n+ ++++l
  lcl|NCBI__GCF_000020545.1:WP_012474608.1  70 MYRMKEGIDGPLFLGMDTHALSEPAFAVALEVLAANEVEVMIAGDERFTPTPAVSHAILTWNRNRRKGL 138
                                               ********************************************************************* PP

                                 TIGR01132 139 adGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekd 207
                                               adGi++tpshnpp dGGikynpp+GGpa ++vt +ied+anell+++l+ v+r+++ekal +  +++ d
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 139 ADGILLTPSHNPPGDGGIKYNPPHGGPAGSHVTSWIEDKANELLEQKLREVHRVPFEKALSAPATRTYD 207
                                               ********************************************************************* PP

                                 TIGR01132 208 lvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdG 276
                                               +  +y++dl +v+d++ i ++g++lGvdplGGagv yw++iae+y l+l+++n ++d+tfrfm++d+dG
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 208 YPGRYIEDLGNVLDMEGISESGITLGVDPLGGAGVAYWERIAEQYALNLAILNTTIDPTFRFMSVDRDG 276
                                               ********************************************************************* PP

                                 TIGR01132 277 kirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaev 345
                                               kirmd sspy+m  l++ kd++d++f+ d+d+drhGivt ++Gll+pnh+l+v+ieyl+++rq+w+++ 
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 277 KIRMDPSSPYTMQPLIAQKDRFDISFACDTDYDRHGIVTGSSGLLQPNHFLSVCIEYLFQNRQEWPESA 345
                                               ********************************************************************* PP

                                 TIGR01132 346 avGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGi 414
                                                +Gktlvss++idrv+a +gr+++evpvGfkwfv+Gll+gslGf GeesaGasflrk+Gtvw+tdkdG 
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 346 MIGKTLVSSSMIDRVGARMGRRVYEVPVGFKWFVEGLLNGSLGFAGEESAGASFLRKNGTVWTTDKDGF 414
                                               ********************************************************************* PP

                                 TIGR01132 415 ilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitak 483
                                               i all+aeita+ Gk+p++ y+ l++++G+p+y+rida+a++++ka+lk lsp++v  ++laG+ i + 
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 415 IPALLSAEITAQRGKDPGEIYKGLTQELGEPVYSRIDASASPEDKAKLKELSPEHVRLEELAGEKIQSI 483
                                               ********************************************************************* PP

                                 TIGR01132 484 ltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                               +t apGnga+iGGlkv+t++gwfaarpsGte++ykiyaesf g +hl +i  ea+e+v ++l
  lcl|NCBI__GCF_000020545.1:WP_012474608.1 484 VTDAPGNGASIGGLKVVTENGWFAARPSGTENIYKIYAESFLGGDHLDRILVEAQEVVADAL 545
                                               **********************************************************9887 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.07
//
[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