Alignments for a candidate for galK in Paludibacter propionicigenes WB4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Paludibacter propionicigenes WB4

Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate WP_013445644.1 PALPR_RS10695 galactokinase

Query= curated2:Q8RHD0
         (389 letters)



>NCBI__GCF_000183135.1:WP_013445644.1
          Length = 386

 Score =  355 bits (910), Expect = e-102
 Identities = 185/367 (50%), Positives = 240/367 (65%), Gaps = 3/367 (0%)

Query: 22  FFSPGRVNLIGEHTDYNGGFVFPCALDFGTYAVVKKREDKTFKMYSKNFENLGIIEFNLD 81
           +FSPGRVNLIGEHTDYNGG VFPCAL FGTY ++ K + K     S N     II    D
Sbjct: 22  YFSPGRVNLIGEHTDYNGGSVFPCALSFGTYLLLAKNDKKVINFKSLNQPE--IISLGFD 79

Query: 82  NLIYDKKDDWANYPKGVIKTFLDRNYKIDSGFDVLFFGNIPNGAGLSSSASIEVLTAVIL 141
            L       W NYP GVI  F+ R   I  G+D+L +GN+PNGAGLSSSA++EV+TA   
Sbjct: 80  QLTTPLDKSWVNYPLGVIAQFVKRGVAITEGYDILIWGNVPNGAGLSSSAALEVVTAYAF 139

Query: 142 KDLFKLDVDIIEMVKMCQVAENKFIGVNSGIMDQFAVGMGKKDNAILLDCNTLKYEYVPV 201
            D  +   +   + ++ Q +E++F  VN GIMDQFA   G KD+AI L+C+TL++E VPV
Sbjct: 140 NDQLETGFNRTVLAQIGQKSEHEFALVNCGIMDQFASANGAKDHAIHLNCDTLEFELVPV 199

Query: 202 KLVNMSIVIANTNKKRGLADSKYNERRTSCEEAVKVLNNNEVNIKYLGELTVTEFEKVKH 261
           KL  + I+I+NT+    L    YN+R   C+ AV+ LN     +KYL ELT  EF+ ++ 
Sbjct: 200 KLEGVKILISNTHSPHKLDSGAYNQRVAECKLAVEQLNKVRP-LKYLAELTEAEFKSIES 258

Query: 262 YITDEEQLKRATHAVTENERAKIAVEFLKKDDIAEFGKLMNKSHTSLRDDYEVTGLELDS 321
            ITD    KRA H V E +R   AV+ LK  D+  FG+LMN SH SLRDDYEVTG ELD+
Sbjct: 259 AITDPVAHKRARHVVGEVQRTSDAVKALKAGDLTLFGQLMNASHVSLRDDYEVTGPELDT 318

Query: 322 LVEAAWEEKGTVGSRMTGAGFGGCTVSIVENDYVDSFIKNVGKKYKEKTGLEASFYIANI 381
           +   AW+  G +GSRMTG GFGGCTVS+V+++ +D+FIK VG  Y+ K G++  FYIA I
Sbjct: 319 MAAEAWKIDGVIGSRMTGGGFGGCTVSLVKDEAIDTFIKEVGAAYEAKIGIKPEFYIAEI 378

Query: 382 GDGAGKV 388
           G+GA K+
Sbjct: 379 GNGACKI 385


Lambda     K      H
   0.317    0.137    0.389 

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: 414
Number of extensions: 10
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: 389
Length of database: 386
Length adjustment: 30
Effective length of query: 359
Effective length of database: 356
Effective search space:   127804
Effective search space used:   127804
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: 50 (23.9 bits)

Align candidate WP_013445644.1 PALPR_RS10695 (galactokinase)
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

# 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/TIGR00131.hmm
# target sequence database:        /tmp/gapView.2334522.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00131  [M=388]
Accession:   TIGR00131
Description: gal_kin: galactokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-115  369.5   0.0   1.1e-114  369.3   0.0    1.0  1  NCBI__GCF_000183135.1:WP_013445644.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183135.1:WP_013445644.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.3   0.0  1.1e-114  1.1e-114       2     386 ..       4     383 ..       3     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 369.3 bits;  conditional E-value: 1.1e-114
                             TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklae 74 
                                           +e+k++F say++ ++ v ++PGRvnliGeh+DYn+gsv+P+a+ ++t++  ++ d k ++  + n  +++  
  NCBI__GCF_000183135.1:WP_013445644.1   4 QELKSAFQSAYGKTAEAVYFSPGRVNLIGEHTDYNGGSVFPCALSFGTYLLLAKNDKKVINFKSLNQ-PEIIS 75 
                                           6899**************************************************9999999999996.69999 PP

                             TIGR00131  75 rkldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgklel 147
                                             +d+  +  + + W nY+ gv+ ++ +R  ++  G di+i g+vP+gaGLsssaalev+ a   ++  ++  
  NCBI__GCF_000183135.1:WP_013445644.1  76 LGFDQLTTPLD-KSWVNYPLGVIAQFVKRGVAITEGYDILIWGNVPNGAGLSSSAALEVVTAYAFNDQLETGF 147
                                           ****9888888.99************************************************77775555555 PP

                             TIGR00131 148 dskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlaps 220
                                           + +  ++ +qk e +f  vncG+mDq+as+ G +dha+ +++++L+ + v++   ++ ++i nt  +++l ++
  NCBI__GCF_000183135.1:WP_013445644.1 148 NRTVLAQIGQKSEHEFALVNCGIMDQFASANGAKDHAIHLNCDTLEFELVPVKLEGVKILISNTHSPHKLDSG 220
                                           67789999*********************************************99****************** PP

                             TIGR00131 221 eYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkded 293
                                            Yn R+ e++ a+++l+k      L +++e+ef+      ++++  v+++Ra+hvv e +R+ +avk+lk +d
  NCBI__GCF_000183135.1:WP_013445644.1 221 AYNQRVAECKLAVEQLNKVRPLKYLAELTEAEFK---SIESAITDPVAHKRARHVVGEVQRTSDAVKALKAGD 290
                                           *******************99*************...6667788888888*********************** PP

                             TIGR00131 294 lkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCtvalvpnenvekvrkalaekY 366
                                           l+ +G+Lmn+s+ sl+ddye+t pe+d+    +++ +G+iGsR+tG+GfGGCtv+lv++e +++++k ++  Y
  NCBI__GCF_000183135.1:WP_013445644.1 291 LTLFGQLMNASHVSLRDDYEVTGPELDTMAAEAWKIDGVIGSRMTGGGFGGCTVSLVKDEAIDTFIKEVGAAY 363
                                           ************************************************************************* PP

                             TIGR00131 367 ekktdlklefavivskealg 386
                                           e+k ++k ef+++++++++ 
  NCBI__GCF_000183135.1:WP_013445644.1 364 EAKIGIKPEFYIAEIGNGAC 383
                                           ***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (386 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: 16.23
//
[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