Alignments for a candidate for pgmA in Rhodanobacter denitrificans 2APBS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Rhodanobacter denitrificans 2APBS1

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_015449177.1 R2APBS1_RS18975 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_000230695.2:WP_015449177.1
          Length = 548

 Score =  612 bits (1579), Expect = e-180
 Identities = 314/539 (58%), Positives = 388/539 (71%), Gaps = 2/539 (0%)

Query: 7   AGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPHILAIAQ 66
           AG+PA  S L+++ QL A Y  LKP+       V FGTSGHRGS+   SFNE HILAI+Q
Sbjct: 9   AGKPAPSSILVDIPQLLAAYADLKPDPAVPAQRVAFGTSGHRGSSLERSFNEAHILAISQ 68

Query: 67  AIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAVSNA 126
           AI E R   GI GP ++G DTHALS+PAF + LEVLAANGV  ++      TPTPAVS+A
Sbjct: 69  AICEYRRSKGIDGPLFIGADTHALSQPAFENALEVLAANGVAAMISAGGEVTPTPAVSHA 128

Query: 127 ILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLADGL 185
           ILV+NK +   LADGIVITPSHNPP++GG KYNP NGGPAD+++TK VE+RANALL  GL
Sbjct: 129 ILVYNKGRTSGLADGIVITPSHNPPDNGGFKYNPSNGGPADSDITKWVENRANALLEGGL 188

Query: 186 KGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSGIEYWK 245
           K V+R+   +A  +    E D +  +V  LA+IVD   I+ AG+ +GVDPLGG+G+ YW 
Sbjct: 189 KDVRRMPYAQARQAATTHEHDYLNSYVADLANIVDFDVIRSAGVHMGVDPLGGAGVHYWA 248

Query: 246 RIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLAFANDP 305
            I E Y L+LT+V+  VD  F FM +D DG IRMD SS+ AM  L+ L+D++D+AFA D 
Sbjct: 249 PIAERYKLDLTVVSAVVDPQFAFMSVDWDGKIRMDPSSKYAMQRLIGLKDQYDVAFACDT 308

Query: 306 DYDRHGIVT-PAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVNDLGR 364
           D+DRHG+VT  +GLM PNHYL+V I+YLF+HRPQWG   AVGKT+VS+A+IDRV   LGR
Sbjct: 309 DHDRHGVVTRSSGLMEPNHYLSVLIDYLFRHRPQWGAHAAVGKTVVSTALIDRVAKRLGR 368

Query: 365 KLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAEITAV 424
           +L E PVGFKWF  GLFDGS GFG EESAGAS LR DGT W TDKDG++  LL+AEITA 
Sbjct: 369 QLYEAPVGFKWFAPGLFDGSLGFGCEESAGASLLRRDGTAWVTDKDGLVPALLSAEITAR 428

Query: 425 TGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITARLTA 484
            GK+P E Y +L +  G P  +R+ AAAT AQKA L+KLSP+ + +  LAG+ I   L  
Sbjct: 429 EGKDPGELYAQLTRELGKPFASRVDAAATPAQKAKLAKLSPDQLKSDQLAGEKIEQVLDK 488

Query: 485 APGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVSEVL 543
           APGNGA+IGG+K +  +GWFAARPSGTE  YK+Y ESF  EEH + + KEA  IV   L
Sbjct: 489 APGNGAAIGGIKAIAASGWFAARPSGTEAIYKVYAESFKSEEHLQALLKEAQGIVDAAL 547


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: 854
Number of extensions: 42
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_015449177.1 R2APBS1_RS18975 (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.1538075.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-261  852.1   0.1   8.7e-261  851.9   0.1    1.0  1  NCBI__GCF_000230695.2:WP_015449177.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015449177.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  851.9   0.1  8.7e-261  8.7e-261       2     545 ..       4     547 ..       3     548 .] 1.00

  Alignments for each domain:
  == domain 1  score: 851.9 bits;  conditional E-value: 8.7e-261
                             TIGR01132   2 ainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraa 74 
                                           +i p+aG++a+++ l+d+++l+a+y  lkpd+  +aq+v+fGtsGhrGs+l+ +fneahilai+qa+ e+r+ 
  NCBI__GCF_000230695.2:WP_015449177.1   4 KISPLAGKPAPSSILVDIPQLLAAYADLKPDPAVPAQRVAFGTSGHRGSSLERSFNEAHILAISQAICEYRRS 76 
                                           5899********************************************************************* PP

                             TIGR01132  75 qGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitps 147
                                           +Gi Gpl+iG dthals+paf  +levlaan+v ++++     tptpavshail+ynkg++++ladGivitps
  NCBI__GCF_000230695.2:WP_015449177.1  77 KGIDGPLFIGADTHALSQPAFENALEVLAANGVAAMISAGGEVTPTPAVSHAILVYNKGRTSGLADGIVITPS 149
                                           ************************************************************************* PP

                             TIGR01132 148 hnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvv 220
                                           hnpp++GG+kynp nGGpa++++tk++e+ran+ll+ +lk v+r+++++a +++t++e+d+++ yv+dla++v
  NCBI__GCF_000230695.2:WP_015449177.1 150 HNPPDNGGFKYNPSNGGPADSDITKWVENRANALLEGGLKDVRRMPYAQARQAATTHEHDYLNSYVADLANIV 222
                                           ************************************************************************* PP

                             TIGR01132 221 dlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllk 293
                                           d+++ir+ag+++GvdplGGagv+yw +iae+y+ldlt+v+  vd+ f fm++d+dGkirmd ss+yam  l+ 
  NCBI__GCF_000230695.2:WP_015449177.1 223 DFDVIRSAGVHMGVDPLGGAGVHYWAPIAERYKLDLTVVSAVVDPQFAFMSVDWDGKIRMDPSSKYAMQRLIG 295
                                           ************************************************************************* PP

                             TIGR01132 294 lkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgr 366
                                           lkd+yd+af+ d+d drhG+vt ++Gl++pnhyl+v i+yl++hr+qw+a+ avGkt+vs+alidrv+  lgr
  NCBI__GCF_000230695.2:WP_015449177.1 296 LKDQYDVAFACDTDHDRHGVVTRSSGLMEPNHYLSVLIDYLFRHRPQWGAHAAVGKTVVSTALIDRVAKRLGR 368
                                           ************************************************************************* PP

                             TIGR01132 367 klvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydela 439
                                           +l+e pvGfkwf  Gl+dgslGfG eesaGas+lr+dGt+w tdkdG++ all+aeita  Gk+p++ y +l+
  NCBI__GCF_000230695.2:WP_015449177.1 369 QLYEAPVGFKWFAPGLFDGSLGFGCEESAGASLLRRDGTAWVTDKDGLVPALLSAEITAREGKDPGELYAQLT 441
                                           ************************************************************************* PP

                             TIGR01132 440 akyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsG 512
                                            ++G+p+ +r+daaat+aqka+l+klspd++ + +laG+ i   l kapGngaaiGG+k +++ gwfaarpsG
  NCBI__GCF_000230695.2:WP_015449177.1 442 RELGKPFASRVDAAATPAQKAKLAKLSPDQLKSDQLAGEKIEQVLDKAPGNGAAIGGIKAIAASGWFAARPSG 514
                                           ************************************************************************* PP

                             TIGR01132 513 tedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                           te +yk+yaesfk eehl+++ kea+ ivd +l
  NCBI__GCF_000230695.2:WP_015449177.1 515 TEAIYKVYAESFKSEEHLQALLKEAQGIVDAAL 547
                                           *****************************9886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 34.44
//
[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