Alignments for a candidate for pgmA in Desulfarculus baarsii DSM 2075

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Desulfarculus baarsii DSM 2075

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_013256956.1 DEBA_RS00600 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_000143965.1:WP_013256956.1
          Length = 548

 Score =  708 bits (1828), Expect = 0.0
 Identities = 352/546 (64%), Positives = 423/546 (77%), Gaps = 7/546 (1%)

Query: 4   NPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILA 63
           +P AG+PA  E L+D P LV+AYY++ P+ DD AQ+V+FGTSGHRGS+L G FNE H+LA
Sbjct: 2   HPLAGKPAPREILIDTPRLVSAYYTLRPEADDPAQRVSFGTSGHRGSSLDGAFNEAHVLA 61

Query: 64  ITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPTPAI 123
           I+QAI EYRA +G  GPLF+G DTH LS PA+V+ALEV AA  V  ++     +TPTP I
Sbjct: 62  ISQAIAEYRAGRGIDGPLFMGIDTHALSWPAFVTALEVFAAAGVTTMIQDGFGHTPTPVI 121

Query: 124 SHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANEILL 183
           SHAI+ +NRGR + LADG+V+TPSHNPP+DGG KYNPP+GGPADTA T  I  RAN+IL 
Sbjct: 122 SHAIVCHNRGRADHLADGVVITPSHNPPADGGFKYNPPHGGPADTAVTKWIEDRANQILA 181

Query: 184 -ARSMVKRLPLARALRT--AQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGASVD 240
             R   +R+  A+AL+     RHDY+G YV DL NVVD+ A+ +AG+++G DPLGG+++ 
Sbjct: 182 DGRRQARRVDFAKALKADCVVRHDYIGPYVADLANVVDLEAVAQAGLKLGVDPLGGSTLA 241

Query: 241 YWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRERYQ 300
           +W  IA R+GLDL VVNP++D T+ FMT+D DGKIRMDCSSP AMAGLI+    +R+ + 
Sbjct: 242 FWEPIARRYGLDLEVVNPVIDPTFGFMTVDKDGKIRMDCSSPQAMAGLIQ----HRQSFD 297

Query: 301 IATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSIIDR 360
           +A GND D DRHGIVT   GLLNPNHYLAVAI YL+ HRP WPAG AVGKT+VSSS+IDR
Sbjct: 298 VAFGNDPDGDRHGIVTRQAGLLNPNHYLAVAIGYLFAHRPGWPAGAAVGKTLVSSSMIDR 357

Query: 361 VVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIMALL 420
           V A +GR L EVPVGFKWFVDGLI    GFGGEESAGASFLRRDG+ WTTDKDG+IM LL
Sbjct: 358 VAAELGRPLKEVPVGFKWFVDGLIDGGYGFGGEESAGASFLRRDGAAWTTDKDGLIMDLL 417

Query: 421 AAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELAGEP 480
           AAEI A TG  P+Q Y  L   +G P Y R DAPA REQKA LA+LS + V A ELAGEP
Sbjct: 418 AAEITARTGKDPAQLYAELTQRHGDPVYQRSDAPASREQKAVLAKLSPEMVPADELAGEP 477

Query: 481 ITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQTARE 540
           I AKLT APGNGAA+GGLKV T N WFAARPSGTED+YKIYAESF+G QHL ++QQ A+E
Sbjct: 478 ILAKLTHAPGNGAAIGGLKVVTQNGWFAARPSGTEDIYKIYAESFKGRQHLAQIQQEAQE 537

Query: 541 VVDRVI 546
           +V + +
Sbjct: 538 IVGQAL 543


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: 1103
Number of extensions: 58
Number of successful extensions: 4
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 WP_013256956.1 DEBA_RS00600 (phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent))
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.2516811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-284  929.8   0.0   2.6e-284  929.6   0.0    1.0  1  NCBI__GCF_000143965.1:WP_013256956.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013256956.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  929.6   0.0  2.6e-284  2.6e-284       3     545 ..       1     543 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 929.6 bits;  conditional E-value: 2.6e-284
                             TIGR01132   3 inpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                           ++p+aG++a++e l+d ++lv++yy+l+p+a+++aq+v+fGtsGhrGs+l g+fneah+lai+qa++e+ra +
  NCBI__GCF_000143965.1:WP_013256956.1   1 MHPLAGKPAPREILIDTPRLVSAYYTLRPEADDPAQRVSFGTSGHRGSSLDGAFNEAHVLAISQAIAEYRAGR 73 
                                           79*********************************************************************** PP

                             TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpsh 148
                                           Gi Gpl++G dthals pafv++lev+aa +v +++q+  ++tptp +shai+ +n+g+ ++ladG+vitpsh
  NCBI__GCF_000143965.1:WP_013256956.1  74 GIDGPLFMGIDTHALSWPAFVTALEVFAAAGVTTMIQDGFGHTPTPVISHAIVCHNRGRADHLADGVVITPSH 146
                                           ************************************************************************* PP

                             TIGR01132 149 nppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvd 221
                                           npp dGG+kynpp+GGpa+t+vtk+iedran++l+d+ ++ +r+d++kalk++ v ++d++ pyv+dla+vvd
  NCBI__GCF_000143965.1:WP_013256956.1 147 NPPADGGFKYNPPHGGPADTAVTKWIEDRANQILADGRRQARRVDFAKALKADCVVRHDYIGPYVADLANVVD 219
                                           ************************************************************************* PP

                             TIGR01132 222 laairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllkl 294
                                           l+a+ +agl+lGvdplGG+++ +w++ia++y+ldl +vn+ +d+tf fmt+dkdGkirmdcssp+amagl++ 
  NCBI__GCF_000143965.1:WP_013256956.1 220 LEAVAQAGLKLGVDPLGGSTLAFWEPIARRYGLDLEVVNPVIDPTFGFMTVDKDGKIRMDCSSPQAMAGLIQH 292
                                           ************************************************************************* PP

                             TIGR01132 295 kdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrk 367
                                           ++ +d+afgnd+d+drhGivt ++Gllnpnhylavai yl+ hr++w+a  avGktlvss++idrv+a+lgr 
  NCBI__GCF_000143965.1:WP_013256956.1 293 RQSFDVAFGNDPDGDRHGIVTRQAGLLNPNHYLAVAIGYLFAHRPGWPAGAAVGKTLVSSSMIDRVAAELGRP 365
                                           ************************************************************************* PP

                             TIGR01132 368 lvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaa 440
                                           l evpvGfkwfvdGl+dg +GfGGeesaGasflr+dG++w+tdkdG+i++llaaeita tGk+p q y el++
  NCBI__GCF_000143965.1:WP_013256956.1 366 LKEVPVGFKWFVDGLIDGGYGFGGEESAGASFLRRDGAAWTTDKDGLIMDLLAAEITARTGKDPAQLYAELTQ 438
                                           ************************************************************************* PP

                             TIGR01132 441 kyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGt 513
                                           ++Gdp+y+r da+a+++qka+l+klsp++v a +laG++i aklt+apGngaaiGGlkv+t++gwfaarpsGt
  NCBI__GCF_000143965.1:WP_013256956.1 439 RHGDPVYQRSDAPASREQKAVLAKLSPEMVPADELAGEPILAKLTHAPGNGAAIGGLKVVTQNGWFAARPSGT 511
                                           ************************************************************************* PP

                             TIGR01132 514 edvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           ed+ykiyaesfkg +hl +i++ea+eiv ++l
  NCBI__GCF_000143965.1:WP_013256956.1 512 EDIYKIYAESFKGRQHLAQIQQEAQEIVGQAL 543
                                           ****************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.22
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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