Alignments for a candidate for galK in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Lacinutrix algicola AKS293

Align Galactokinase (EC 2.7.1.6) (characterized)
to candidate WP_055436940.1 ASC41_RS12270 galactokinase

Query= reanno::Pedo557:CA265_RS06125
         (383 letters)



>NCBI__GCF_001418085.1:WP_055436940.1
          Length = 386

 Score =  314 bits (805), Expect = 2e-90
 Identities = 162/381 (42%), Positives = 244/381 (64%), Gaps = 10/381 (2%)

Query: 4   QHLKNTFKKLFNAEPILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDDEIH 63
           + +K +FK+ F  +P++V SPGRIN+IGEHTDYN GF  PAAI+K I +AISK   +   
Sbjct: 7   KEVKQSFKEHFRTKPLIVFSPGRINLIGEHTDYNDGFAFPAAINKGIALAISKSTSNVSS 66

Query: 64  LFS---ESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLGA 120
           +++   E    FD + I  L   +  W NY++G+  +L+  G Q+G F+    G++P GA
Sbjct: 67  VYALNKEEIYAFDTTKIKPLV--DGGWRNYVIGVVAELQMLGKQIGSFDSVFAGNIPGGA 124

Query: 121 GLSSSAAVECATGFALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQ 180
           G+SSSAA+E +  + L+ LF L +++  + L++QKAE  FAGV CGIMDQ+AS+FG K  
Sbjct: 125 GMSSSAALENSFVYGLNDLFDLGLTKHQMILVSQKAEHNFAGVKCGIMDQYASMFGIKKS 184

Query: 181 AIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYPNV 240
           A++LDCR+++     +    YKL+L+N+NVKH L++SAYN RR  CE+      +   ++
Sbjct: 185 ALLLDCRTVESEPYKIDFKDYKLMLINSNVKHDLSESAYNDRREVCER-----VSELLHL 239

Query: 241 STLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFETHE 300
             LRD     L+     +  E Y K  +V+ E  R+   +E ++  +++ALG L++++HE
Sbjct: 240 DALRDASKEDLDRIKTDISEEDYQKALYVINENNRVKQFSEAIKKDDIEALGDLLYQSHE 299

Query: 301 GLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSSKY 360
           GLS +Y+VSCKELDFLV+  K    VLGARMMGGGFGGCTIN+VK+++     +E++ K+
Sbjct: 300 GLSTNYKVSCKELDFLVDRAKENTNVLGARMMGGGFGGCTINLVKKDEFKKFKKEVAKKF 359

Query: 361 LLQFGLKLDSYTVQTDNGTSL 381
              F      Y+V+   GT +
Sbjct: 360 RATFEYDCSVYSVKLSRGTQI 380


Lambda     K      H
   0.319    0.136    0.393 

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: 412
Number of extensions: 20
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: 383
Length of database: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_055436940.1 ASC41_RS12270 (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.985521.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.9e-90  287.7   0.5    7.9e-90  287.5   0.5    1.0  1  NCBI__GCF_001418085.1:WP_055436940.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055436940.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.5   0.5   7.9e-90   7.9e-90       2     384 ..       7     377 ..       6     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 287.5 bits;  conditional E-value: 7.9e-90
                             TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklae 74 
                                           +evk+ F + + +kp l+v++PGR+nliGeh+DYndg+ +P ai+ ++++a+ +   +  s+++ n + ++  
  NCBI__GCF_001418085.1:WP_055436940.1   7 KEVKQSFKEHFRTKP-LIVFSPGRINLIGEHTDYNDGFAFPAAINKGIALAISKSTSNVSSVYALNKE-EI-- 75 
                                           68999******9998.6789**********************************************99.33.. PP

                             TIGR00131  75 rkldlpldksev.sdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkle 146
                                           + +d+   k  v   W nYv gv+ +lq   ++++  +d v+ g++P gaG+sssaale      l++l++l 
  NCBI__GCF_001418085.1:WP_055436940.1  76 YAFDTTKIKPLVdGGWRNYVIGVVAELQMLGKQIG-SFDSVFAGNIPGGAGMSSSAALENSFVYGLNDLFDLG 147
                                           445555444444267*****************999.9************************************ PP

                             TIGR00131 147 ldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlap 219
                                           l++++++l  qk+e +f Gv cG+mDq as +G ++ all+++r+++ +p k++  +  l+++n+nvk++l +
  NCBI__GCF_001418085.1:WP_055436940.1 148 LTKHQMILVSQKAEHNFAGVKCGIMDQYASMFGIKKSALLLDCRTVESEPYKIDFKDYKLMLINSNVKHDLSE 220
                                           ************************************************************************* PP

                             TIGR00131 220 seYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkde 292
                                           s Yn Rr+ +e   + l+      aLrD ++e+ +r +   t ++++ + q+a +v+ en+Rv +  +++k++
  NCBI__GCF_001418085.1:WP_055436940.1 221 SAYNDRREVCERVSELLHLD----ALRDASKEDLDRIK---TDISEE-DYQKALYVINENNRVKQFSEAIKKD 285
                                           *****************999....***********655...555555.4459********************* PP

                             TIGR00131 293 dlkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCtvalvpnenvekvrkalaek 365
                                           d++ lG L+ +s++ l  +y +++ e+d lv  ++    + G+R+ G+GfGGCt++lv++++ +k++k +a+k
  NCBI__GCF_001418085.1:WP_055436940.1 286 DIEALGDLLYQSHEGLSTNYKVSCKELDFLVDRAKENTNVLGARMMGGGFGGCTINLVKKDEFKKFKKEVAKK 358
                                           ************************************************************************* PP

                             TIGR00131 366 Yekktdlklefavivskea 384
                                           + ++ +   + + ++ +++
  NCBI__GCF_001418085.1:WP_055436940.1 359 FRATFEYDCSVYSVKLSRG 377
                                           9999888777777766665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 15.40
//
[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