Alignments for a candidate for pgmA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Klebsiella variicola At-22

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_012968690.1 KVAR_RS18170 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= CharProtDB::CH_002452
         (546 letters)



>NCBI__GCF_000025465.1:WP_012968690.1
          Length = 546

 Score = 1058 bits (2735), Expect = 0.0
 Identities = 524/546 (95%), Positives = 536/546 (98%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MAI  RAGQPAQQSDLINVAQLTAQYYVLKPE GNAEHAVKFGTSGHRGSAARH+FNEPH
Sbjct: 1   MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEPH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAIAQAIAE+RAKNGITGPCYVGKDTHALSEPAFISVLEVL ANGVDVIVQENNGFTPT
Sbjct: 61  ILAIAQAIAEDRAKNGITGPCYVGKDTHALSEPAFISVLEVLTANGVDVIVQENNGFTPT 120

Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVE+RAN L
Sbjct: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANEL 180

Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           LA GL+GVKRISLD A+ASGHVKEQDLVQPF+EGLADIVDMAAIQKAGLTLGVDPLGGSG
Sbjct: 181 LAAGLQGVKRISLDAALASGHVKEQDLVQPFIEGLADIVDMAAIQKAGLTLGVDPLGGSG 240

Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           IEYWKRIGE+Y LNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA
Sbjct: 241 IEYWKRIGEHYKLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300

Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360
           FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGK+VAVGKTLVSSAMIDRVVN
Sbjct: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKEVAVGKTLVSSAMIDRVVN 360

Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420
           DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE
Sbjct: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420

Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480
           ITAVTGKNPQEHYNELA+RFGAPSYNRLQA+ATSAQKAALSKLSPEMVSA TLAGDPITA
Sbjct: 421 ITAVTGKNPQEHYNELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSADTLAGDPITA 480

Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540
           RLT+APGNGA+IGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRK IEKEAVEIVS
Sbjct: 481 RLTSAPGNGAAIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKLIEKEAVEIVS 540

Query: 541 EVLKNA 546
           EVLKNA
Sbjct: 541 EVLKNA 546


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: 1182
Number of extensions: 43
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: 546
Length adjustment: 35
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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_012968690.1 KVAR_RS18170 (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.30111.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1055.8   0.2          0 1055.6   0.2    1.0  1  lcl|NCBI__GCF_000025465.1:WP_012968690.1  KVAR_RS18170 alpha-D-glucose pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012968690.1  KVAR_RS18170 alpha-D-glucose phosphate-specific phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1055.6   0.2         0         0       1     546 []       1     544 [.       1     544 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1055.6 bits;  conditional E-value: 0
                                 TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavv 69 
                                               mai++raGq+aqq+dl++va+l+a+yy+lkp+ +na+++v+fGtsGhrGsa+++ fne hilaiaqa++
  lcl|NCBI__GCF_000025465.1:WP_012968690.1   1 MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEPHILAIAQAIA 69 
                                               799****************************************************************** PP

                                 TIGR01132  70 evraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkeal 138
                                               e ra++GitGp+y+Gkdthalsepaf+svlevl+an+v+vivqenn++tptpavs+ail++nk k ++l
  lcl|NCBI__GCF_000025465.1:WP_012968690.1  70 EDRAKNGITGPCYVGKDTHALSEPAFISVLEVLTANGVDVIVQENNGFTPTPAVSNAILVHNK-KGGPL 137
                                               ***************************************************************.***** PP

                                 TIGR01132 139 adGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekd 207
                                               adGivitpshnppedGGikynppnGGpa+t+vtk++e+ranell+++l+gvkr++l+ al+s++vke+d
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 138 ADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANELLAAGLQGVKRISLDAALASGHVKEQD 206
                                               ********************************************************************* PP

                                 TIGR01132 208 lvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdG 276
                                               lv+p++++lad+vd+aai+kagl+lGvdplGG+g++ywk+i+e+y+l+lt+vn++vd+tfrfm+ldkdG
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 207 LVQPFIEGLADIVDMAAIQKAGLTLGVDPLGGSGIEYWKRIGEHYKLNLTIVNDQVDQTFRFMHLDKDG 275
                                               ********************************************************************* PP

                                 TIGR01132 277 kirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaev 345
                                               +irmdcss++amagll+l+dk+dlaf+nd+d+drhGivtp +Gl+npnhylavai+yl++hr+qw++ev
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 276 AIRMDCSSECAMAGLLALRDKFDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKEV 343
                                               ****************************************.**************************** PP

                                 TIGR01132 346 avGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGi 414
                                               avGktlvssa+idrvv+dlgrklvevpvGfkwfvdGl+dgs+GfGGeesaGasflr+dGt+wstdkdGi
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 344 AVGKTLVSSAMIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGI 412
                                               ********************************************************************* PP

                                 TIGR01132 415 ilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitak 483
                                               i++llaaeitavtGknpq++y+ela+++G+p+y+r++a+atsaqka+l+klsp++vsa tlaGd+ita+
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 413 IMCLLAAEITAVTGKNPQEHYNELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSADTLAGDPITAR 481
                                               ********************************************************************* PP

                                 TIGR01132 484 ltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546
                                               lt+apGngaaiGGlkv+td+gwfaarpsGted+ykiy+esf geeh+k iekea eiv+evlk
  lcl|NCBI__GCF_000025465.1:WP_012968690.1 482 LTSAPGNGAAIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKLIEKEAVEIVSEVLK 544
                                               *************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (546 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.44
//
[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 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