Alignments for a candidate for pgmA in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Moritella dasanensis ArB 0140

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_017219954.1 A923_RS0101930 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_000276805.1:WP_017219954.1
          Length = 545

 Score =  691 bits (1783), Expect = 0.0
 Identities = 347/544 (63%), Positives = 410/544 (75%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA+H RAGQ AQ SDL N+  L + YY+ KP+       V FGTSGHRG+A   SFNE H
Sbjct: 1   MAVHPRAGQKAQNSDLCNIPALVSHYYINKPDVTKIAERVAFGTSGHRGNAFASSFNEDH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI+QAIAE R + GITGP ++GKDTHALSEPA ISV+EVL ANGVDV VQ ++GFTPT
Sbjct: 61  ILAISQAIAEYRVEQGITGPLFIGKDTHALSEPANISVIEVLIANGVDVRVQADDGFTPT 120

Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           P +S+AIL HN      ADGIVITPSHNPP+DGGIKYNPP+GGPAD++VTK++E+RAN +
Sbjct: 121 PVISHAILAHNGHSDIQADGIVITPSHNPPQDGGIKYNPPHGGPADSDVTKIIENRANDI 180

Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           +A+ L  VKRIS   A  S H +E D V+ +V  L +++++ AI  AG+ +GVD LGGSG
Sbjct: 181 IAERLVAVKRISFAIATESAHYQEIDYVEAYVADLENVLNLKAISDAGIKIGVDTLGGSG 240

Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
             YW  I   YNL++T+VND+VD +F FM LDKDG IRMDCSS  AMA L++L+D FD+A
Sbjct: 241 FAYWDVIAAKYNLDITVVNDRVDPSFSFMCLDKDGKIRMDCSSPYAMASLISLKDDFDIA 300

Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360
             NDPDYDRHGIVT +GLMNPNHYLAVAI YLF HR  W  +  VGKTLVSS+MIDRV  
Sbjct: 301 IGNDPDYDRHGIVTKSGLMNPNHYLAVAIQYLFTHRTNWPVNAKVGKTLVSSSMIDRVAA 360

Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420
            + R L EVPVGFKWFV+GL    F FGGEESAGASFLR DGT W+TDKDGII+ LL+AE
Sbjct: 361 KIERPLCEVPVGFKWFVEGLHTAEFAFGGEESAGASFLRKDGTVWTTDKDGIILALLSAE 420

Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480
           I AVTGK+P + Y EL + FG+P YNR+ A A+  +KA LS LSPE+V A TLAG+ ITA
Sbjct: 421 ILAVTGKDPAQLYAELTEEFGSPVYNRIDAPASFEEKAILSNLSPELVQAKTLAGETITA 480

Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           +LT APGN   IGGLKV T+NGWFAARPSGTE  YKIY ESF  E H   I  EA EIVS
Sbjct: 481 KLTNAPGNDGKIGGLKVTTENGWFAARPSGTEAIYKIYAESFKDEAHLALILSEAQEIVS 540

Query: 541 EVLK 544
             LK
Sbjct: 541 AALK 544


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: 900
Number of extensions: 31
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: 545
Length adjustment: 35
Effective length of query: 511
Effective length of database: 510
Effective search space:   260610
Effective search space used:   260610
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_017219954.1 A923_RS0101930 (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.2109096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-281  919.7   1.6   2.8e-281  919.6   1.6    1.0  1  NCBI__GCF_000276805.1:WP_017219954.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017219954.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  919.6   1.6  2.8e-281  2.8e-281       1     546 []       1     544 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 919.6 bits;  conditional E-value: 2.8e-281
                             TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 
                                           ma++praGqkaq++dl ++++lv++yy  kpd  + a++v+fGtsGhrG a  ++fne hilai+qa++e+r 
  NCBI__GCF_000276805.1:WP_017219954.1   1 MAVHPRAGQKAQNSDLCNIPALVSHYYINKPDVTKIAERVAFGTSGHRGNAFASSFNEDHILAISQAIAEYRV 73 
                                           89*********************************************************************** PP

                             TIGR01132  74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146
                                           +qGitGpl+iGkdthalsepa +sv+evl+an+v+v vq  +++tptp +shail++n  +++ +adGivitp
  NCBI__GCF_000276805.1:WP_017219954.1  74 EQGITGPLFIGKDTHALSEPANISVIEVLIANGVDVRVQADDGFTPTPVISHAILAHNG-HSDIQADGIVITP 145
                                           **********************************************************6.999********** PP

                             TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219
                                           shnpp+dGGikynpp+GGpa+++vtk+ie+ran+++++rl +vkr++++ a +s++ +e d+v+ yv+dl +v
  NCBI__GCF_000276805.1:WP_017219954.1 146 SHNPPQDGGIKYNPPHGGPADSDVTKIIENRANDIIAERLVAVKRISFAIATESAHYQEIDYVEAYVADLENV 218
                                           ************************************************************************* PP

                             TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292
                                           ++l+ai +ag+++Gvd lGG+g  yw+ ia+kynld+t+vn+ vd++f fm ldkdGkirmdcsspyama+l+
  NCBI__GCF_000276805.1:WP_017219954.1 219 LNLKAISDAGIKIGVDTLGGSGFAYWDVIAAKYNLDITVVNDRVDPSFSFMCLDKDGKIRMDCSSPYAMASLI 291
                                           ************************************************************************* PP

                             TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365
                                            lkd +d+a+gnd+d+drhGivt  +Gl+npnhylavai+yl++hr +w+ +  vGktlvss++idrv+a+++
  NCBI__GCF_000276805.1:WP_017219954.1 292 SLKDDFDIAIGNDPDYDRHGIVTK-SGLMNPNHYLAVAIQYLFTHRTNWPVNAKVGKTLVSSSMIDRVAAKIE 363
                                           ***********************9.9*********************************************** PP

                             TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438
                                           r l+evpvGfkwfv+Gl  +++ fGGeesaGasflrkdGtvw+tdkdGiilall+aei+avtGk+p q y el
  NCBI__GCF_000276805.1:WP_017219954.1 364 RPLCEVPVGFKWFVEGLHTAEFAFGGEESAGASFLRKDGTVWTTDKDGIILALLSAEILAVTGKDPAQLYAEL 436
                                           ************************************************************************* PP

                             TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511
                                           ++++G+p+y+rida+a+ ++ka l++lsp+ v a+tlaG++itaklt+apGn+  iGGlkvtt++gwfaarps
  NCBI__GCF_000276805.1:WP_017219954.1 437 TEEFGSPVYNRIDAPASFEEKAILSNLSPELVQAKTLAGETITAKLTNAPGNDGKIGGLKVTTENGWFAARPS 509
                                           ************************************************************************* PP

                             TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                           Gte +ykiyaesfk+e+hl  i +ea+eiv+ +lk
  NCBI__GCF_000276805.1:WP_017219954.1 510 GTEAIYKIYAESFKDEAHLALILSEAQEIVSAALK 544
                                           *******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (545 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: 21.13
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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