Alignments for a candidate for pgmA in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Collimonas pratensis Ter91

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_061939910.1 CPter91_RS10350 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>NCBI__GCF_001584185.1:WP_061939910.1
          Length = 556

 Score =  617 bits (1592), Expect = 0.0
 Identities = 322/549 (58%), Positives = 387/549 (70%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA    LVD+P LV+AYY+  PDP+   Q+VAFGTSGHRGS+   +FNE H
Sbjct: 1   MKISPLAGKPAPSALLVDVPKLVSAYYTNVPDPEVAEQRVAFGTSGHRGSSFDCSFNEAH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           +LAI+QAI  YR+ QG +GPLFIG DTH LS  A  SA+EVLAAN V  ++   D YTPT
Sbjct: 61  VLAISQAICAYRSKQGISGPLFIGIDTHALSIAACASAVEVLAANGVDIMLAEGDEYTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PA+SHAI+ YNRGR   LADGIV+TPSHNPP DGG+KYNPPNGG ADT  T  I   AN 
Sbjct: 121 PAVSHAIIKYNRGRQSGLADGIVITPSHNPPEDGGVKYNPPNGGAADTDITGWIEAAANA 180

Query: 181 ILLARSM-VKRLPLARALRTAQRH--DYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L A    VKR+PL +ALR A  H  DYL  YVD+L  V+D+A IR+AGV +G DPLGGA
Sbjct: 181 LLRAGLKDVKRMPLQKALRLASTHRYDYLNTYVDELDQVIDMALIRDAGVHLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  I+ R+ L+L+VV+  VD T+RFMT+D DG+IRMD SS  AM  L+    G ++
Sbjct: 241 GVHYWQRISERYQLNLSVVSEEVDPTFRFMTVDWDGRIRMDPSSSYAMQRLL----GMKD 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           RY IA   D D DRHGIVT   GLL  NHYLAV I+YL+ HR  WP    +GKTVVSS I
Sbjct: 297 RYDIAFACDTDHDRHGIVTRSAGLLPANHYLAVMIDYLFQHRSQWPQAAGIGKTVVSSQI 356

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDR+   + R+L EVP GFKWF  GL   +LGFGGEESAGA+F R DGSVWTTDKDG++ 
Sbjct: 357 IDRIATRLKRRLYEVPAGFKWFAPGLSDGSLGFGGEESAGATFQRLDGSVWTTDKDGLVP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAEI A  G  P + Y  LA E G P   R++A A   QK  LA LS  Q+ +TELA
Sbjct: 417 ALLAAEITARGGRDPGEVYRRLASELGDPLSTRVEASATPAQKKMLAALSPQQIQSTELA 476

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GE I   ++ APGN AA+GG++VTTA  WFAARPSGTED+YKIYAESF G +HL  + Q 
Sbjct: 477 GEKIQDIISKAPGNDAAIGGVRVTTAGGWFAARPSGTEDIYKIYAESFHGAEHLQRIVQE 536

Query: 538 AREVVDRVI 546
           A+ +VD  +
Sbjct: 537 AQAIVDAAL 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: 943
Number of extensions: 32
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: 556
Length adjustment: 36
Effective length of query: 511
Effective length of database: 520
Effective search space:   265720
Effective search space used:   265720
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_061939910.1 CPter91_RS10350 (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.2651944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-257  841.7   0.1   1.3e-257  841.5   0.1    1.0  1  NCBI__GCF_001584185.1:WP_061939910.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584185.1:WP_061939910.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.5   0.1  1.3e-257  1.3e-257       1     545 [.       1     545 [.       1     546 [. 1.00

  Alignments for each domain:
  == domain 1  score: 841.5 bits;  conditional E-value: 1.3e-257
                             TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 
                                           m+i p+aG++a++  l+dv+klv++yy+  pd+e a+q+v+fGtsGhrGs+   +fneah+lai+qa+  +r+
  NCBI__GCF_001584185.1:WP_061939910.1   1 MKISPLAGKPAPSALLVDVPKLVSAYYTNVPDPEVAEQRVAFGTSGHRGSSFDCSFNEAHVLAISQAICAYRS 73 
                                           7899********************************************************************* PP

                             TIGR01132  74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146
                                           +qGi+Gpl+iG dthals  a  s++evlaan+v++++ e + ytptpavshai+ yn+g++++ladGivitp
  NCBI__GCF_001584185.1:WP_061939910.1  74 KQGISGPLFIGIDTHALSIAACASAVEVLAANGVDIMLAEGDEYTPTPAVSHAIIKYNRGRQSGLADGIVITP 146
                                           ************************************************************************* PP

                             TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219
                                           shnppedGG+kynppnGG a+t++t +ie  an+ll+++lk vkr++l+kal+ + +++ d+++ yvd+l +v
  NCBI__GCF_001584185.1:WP_061939910.1 147 SHNPPEDGGVKYNPPNGGAADTDITGWIEAAANALLRAGLKDVKRMPLQKALRLASTHRYDYLNTYVDELDQV 219
                                           ************************************************************************* PP

                             TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292
                                           +d+a ir+ag++lGvdplGGagv+yw++i+e+y+l+l++v+e+vd+tfrfmt+d+dG+irmd ss yam  ll
  NCBI__GCF_001584185.1:WP_061939910.1 220 IDMALIRDAGVHLGVDPLGGAGVHYWQRISERYQLNLSVVSEEVDPTFRFMTVDWDGRIRMDPSSSYAMQRLL 292
                                           ************************************************************************* PP

                             TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365
                                            +kd+yd+af+ d+d drhGivt ++Gll  nhylav i+yl++hr qw++   +Gkt+vss +idr+++ l 
  NCBI__GCF_001584185.1:WP_061939910.1 293 GMKDRYDIAFACDTDHDRHGIVTRSAGLLPANHYLAVMIDYLFQHRSQWPQAAGIGKTVVSSQIIDRIATRLK 365
                                           ************************************************************************* PP

                             TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438
                                           r+l+evp Gfkwf  Gl dgslGfGGeesaGa+f r dG+vw+tdkdG++ allaaeita  G++p++ y  l
  NCBI__GCF_001584185.1:WP_061939910.1 366 RRLYEVPAGFKWFAPGLSDGSLGFGGEESAGATFQRLDGSVWTTDKDGLVPALLAAEITARGGRDPGEVYRRL 438
                                           ************************************************************************* PP

                             TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511
                                           a+++Gdp+ +r++a+at+aqk++l+ lsp+++ +t+laG+ i   ++kapGn+aaiGG++vtt+ gwfaarps
  NCBI__GCF_001584185.1:WP_061939910.1 439 ASELGDPLSTRVEASATPAQKKMLAALSPQQIQSTELAGEKIQDIISKAPGNDAAIGGVRVTTAGGWFAARPS 511
                                           ************************************************************************* PP

                             TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           Gted+ykiyaesf+g+ehl++i +ea++ivd +l
  NCBI__GCF_001584185.1:WP_061939910.1 512 GTEDIYKIYAESFHGAEHLQRIVQEAQAIVDAAL 545
                                           ******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (556 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 0.03s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.76
//
[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