Alignments for a candidate for pgmA in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Collimonas arenae Ter10

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_061533694.1 CAter10_RS12735 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_001584165.1:WP_061533694.1
          Length = 552

 Score =  600 bits (1546), Expect = e-176
 Identities = 315/545 (57%), Positives = 379/545 (69%), Gaps = 2/545 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAI   AG+PA  S L+NV +L + YY   P+   A   V FGTSGHRG++   SFNE H
Sbjct: 1   MAISPLAGKPAPSSILVNVPRLVSAYYTEVPDPTLAAQRVAFGTSGHRGTSFEASFNEWH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           +LAI+QAI   RA+ GI GP ++G DTHALS PA  S LEVLAANGV+V++  ++ +TPT
Sbjct: 61  VLAISQAICAYRAERGINGPLFLGVDTHALSVPACASALEVLAANGVEVMLSLDDEYTPT 120

Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           PAVS AIL HN+ +   LADGIVITPSHNPPE GG KYNPPNGG ADT VT  +E +AN 
Sbjct: 121 PAVSLAILTHNRGRSSGLADGIVITPSHNPPESGGFKYNPPNGGAADTVVTAWIEAKANE 180

Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
            LA GL GVKR+S+++A+        D +  +V  L  ++DM  I+ A + LGVDPLGG+
Sbjct: 181 YLAAGLYGVKRMSVEKALKLATTHRYDFLGSYVNQLDQVIDMEVIRGANIHLGVDPLGGA 240

Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
           G+ YW RIG+ Y LNL +V+ +VD TFRFM +D DG IRMD SS  AM  L+ +  ++D+
Sbjct: 241 GVHYWARIGDQYKLNLAVVSSEVDPTFRFMTVDWDGRIRMDPSSSYAMQRLIDMNGRYDI 300

Query: 300 AFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRV 358
           AFA D D+DRHGIV  + GL+  NHYLAVAI+YLFQHRPQW  D  VGKT+VSS +ID V
Sbjct: 301 AFACDTDHDRHGIVANSVGLLPANHYLAVAIDYLFQHRPQWSMDAGVGKTVVSSQIIDLV 360

Query: 359 VNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLA 418
              L R+L E P GFKWF DGL +GS GF GEESAGASFLR DGT W+TDKDG+I  LLA
Sbjct: 361 CTRLKRRLYETPAGFKWFADGLCEGSLGFCGEESAGASFLRLDGTVWTTDKDGLIPGLLA 420

Query: 419 AEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPI 478
           AE+TA TG +P + Y  L    G P   R++A AT+AQK  LS LSP+ V  S LAG+ I
Sbjct: 421 AEMTARTGHDPGQLYRLLTSELGEPVSTRVEARATAAQKKMLSALSPQQVQCSELAGEKI 480

Query: 479 TARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEI 538
              L  APGN A IGGLKV+ D GWFAARPSGTED YKIY ES  GEEH   I  EA  I
Sbjct: 481 QHILANAPGNNAPIGGLKVVADGGWFAARPSGTEDIYKIYAESMRGEEHLSHIVTEAQAI 540

Query: 539 VSEVL 543
           V   L
Sbjct: 541 VDAAL 545


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: 872
Number of extensions: 43
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: 552
Length adjustment: 36
Effective length of query: 510
Effective length of database: 516
Effective search space:   263160
Effective search space used:   263160
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: 53 (25.0 bits)

Align candidate WP_061533694.1 CAter10_RS12735 (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.1376627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-253  827.1   0.0   3.3e-253  826.9   0.0    1.0  1  NCBI__GCF_001584165.1:WP_061533694.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584165.1:WP_061533694.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  826.9   0.0  3.3e-253  3.3e-253       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 826.9 bits;  conditional E-value: 3.3e-253
                             TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 
                                           mai p+aG++a+++ l++v++lv++yy+  pd+  aaq+v+fGtsGhrG++ +++fne h+lai+qa+  +ra
  NCBI__GCF_001584165.1:WP_061533694.1   1 MAISPLAGKPAPSSILVNVPRLVSAYYTEVPDPTLAAQRVAFGTSGHRGTSFEASFNEWHVLAISQAICAYRA 73 
                                           799********************************************************************** PP

                             TIGR01132  74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146
                                           ++Gi Gpl++G dthals pa  s+levlaan+vev+++  + ytptpavs ailt+n+g++++ladGivitp
  NCBI__GCF_001584165.1:WP_061533694.1  74 ERGINGPLFLGVDTHALSVPACASALEVLAANGVEVMLSLDDEYTPTPAVSLAILTHNRGRSSGLADGIVITP 146
                                           ************************************************************************* PP

                             TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219
                                           shnppe GG+kynppnGG a+t vt +ie +ane+l+++l gvkr+++ekalk +t+++ d++  yv++l +v
  NCBI__GCF_001584165.1:WP_061533694.1 147 SHNPPESGGFKYNPPNGGAADTVVTAWIEAKANEYLAAGLYGVKRMSVEKALKLATTHRYDFLGSYVNQLDQV 219
                                           ************************************************************************* PP

                             TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292
                                           +d+++ir a+++lGvdplGGagv+yw +i+++y+l+l++v+ +vd+tfrfmt+d+dG+irmd ss yam  l+
  NCBI__GCF_001584165.1:WP_061533694.1 220 IDMEVIRGANIHLGVDPLGGAGVHYWARIGDQYKLNLAVVSSEVDPTFRFMTVDWDGRIRMDPSSSYAMQRLI 292
                                           ************************************************************************* PP

                             TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365
                                            ++ +yd+af+ d+d drhGiv+ ++Gll  nhylavai+yl++hr+qw+ +  vGkt+vss +id v + l 
  NCBI__GCF_001584165.1:WP_061533694.1 293 DMNGRYDIAFACDTDHDRHGIVANSVGLLPANHYLAVAIDYLFQHRPQWSMDAGVGKTVVSSQIIDLVCTRLK 365
                                           ************************************************************************* PP

                             TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438
                                           r+l+e p Gfkwf dGl +gslGf GeesaGasflr dGtvw+tdkdG+i  llaae+ta tG++p+q y  l
  NCBI__GCF_001584165.1:WP_061533694.1 366 RRLYETPAGFKWFADGLCEGSLGFCGEESAGASFLRLDGTVWTTDKDGLIPGLLAAEMTARTGHDPGQLYRLL 438
                                           ************************************************************************* PP

                             TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511
                                           ++++G+p+ +r++a at+aqk++l+ lsp++v  ++laG+ i   l++apGn+a iGGlkv++d gwfaarps
  NCBI__GCF_001584165.1:WP_061533694.1 439 TSELGEPVSTRVEARATAAQKKMLSALSPQQVQCSELAGEKIQHILANAPGNNAPIGGLKVVADGGWFAARPS 511
                                           ************************************************************************* PP

                             TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           Gted+ykiyaes++geehl +i +ea++ivd +l
  NCBI__GCF_001584165.1:WP_061533694.1 512 GTEDIYKIYAESMRGEEHLSHIVTEAQAIVDAAL 545
                                           *******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (552 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: 00:00:00.01
# Mc/sec: 18.59
//
[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 2024 update 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