Alignments for a candidate for galK in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Shewanella loihica PV-4

Align galactose kinase (characterized)
to candidate 5209834 Shew_2287 galactokinase (RefSeq)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__PV4:5209834
          Length = 393

 Score =  371 bits (952), Expect = e-107
 Identities = 193/387 (49%), Positives = 259/387 (66%), Gaps = 12/387 (3%)

Query: 5   EKTQSL---FANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDD 61
           E TQ+L   F  AFG  A     APGRVNLIG+HTDYN G+VLP A+D  T ++ + RDD
Sbjct: 5   ELTQALPYAFNQAFGQEAALVAYAPGRVNLIGDHTDYNLGWVLPVALDRGTSVAASQRDD 64

Query: 62  RKVRVMAADYENQLDEFSLDAPIVAHENYQ----WANYVRGVVKHLQLRNNSFG-----G 112
            +++V+A D +N+   FSLD   +A         W+NYVRG VK L       G     G
Sbjct: 65  SQIQVVARDMDNEKVSFSLDDQAMAQMPLDSVSPWSNYVRGTVKMLSAYLAETGQPPLRG 124

Query: 113 VDMVISGNVPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGI 172
             ++ISGN+P+GAGLSSSASLE+A+      L+ L +DG + A  GQ+AEN+FVGCNCGI
Sbjct: 125 ASLMISGNLPKGAGLSSSASLEMALIKAFAGLFDLKVDGIKAAQLGQQAENEFVGCNCGI 184

Query: 173 MDQLISALGKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCET 232
           MDQLISA+G+ + A+LIDC  L  K V +P G+ ++IINSN KRTLVGSEYN RREQC+ 
Sbjct: 185 MDQLISAMGEAERAMLIDCSDLAIKQVPLPAGLRLMIINSNVKRTLVGSEYNLRREQCQQ 244

Query: 233 GARFFQQPALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGE 292
            A+ F   +LR V+ E+       L+P + +R RH+++ENAR +E A AL  GD   +G 
Sbjct: 245 VAQHFGVSSLRQVSYEQLCRAEASLEPTLFRRARHVVSENARVLEMAEALSAGDNAYIGR 304

Query: 293 LMAESHASMRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAV 352
           LMA SH S+RDDF ++ P++D LVE+V  V+G  GG RMTGGGFGGC+VAL+PE  +  V
Sbjct: 305 LMAASHRSLRDDFAVSTPEVDCLVELVSEVLGMDGGARMTGGGFGGCVVALLPEHKIAEV 364

Query: 353 QQAVAEQYEAKTGIKETFYVCKPSQGA 379
           ++ +A +Y+A+TG+    Y+C+   GA
Sbjct: 365 RETIAVEYQARTGLTADIYLCQSGAGA 391


Lambda     K      H
   0.318    0.134    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: 346
Number of extensions: 10
Number of successful extensions: 4
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: 382
Length of database: 393
Length adjustment: 30
Effective length of query: 352
Effective length of database: 363
Effective search space:   127776
Effective search space used:   127776
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 5209834 Shew_2287 (galactokinase (RefSeq))
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.8002.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   8.6e-122  392.7   0.0   9.7e-122  392.5   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209834  Shew_2287 galactokinase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209834  Shew_2287 galactokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.5   0.0  9.7e-122  9.7e-122       5     385 ..      11     391 ..       7     393 .] 0.94

  Alignments for each domain:
  == domain 1  score: 392.5 bits;  conditional E-value: 9.7e-122
                        TIGR00131   5 kkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlpld 82 
                                        +F++a+++++ lv++aPGRvnliG+h+DYn g vlP+a+d +t va+ +rdd ++++++ ++dn+   ++ld++  
  lcl|FitnessBrowser__PV4:5209834  11 PYAFNQAFGQEAALVAYAPGRVNLIGDHTDYNLGWVLPVALDRGTSVAASQRDDSQIQVVARDMDNEKVSFSLDDQAM 88 
                                      568***********************************************************************9988 PP

                        TIGR00131  83 ksev....sdWanYvkgvlkvlq...eRfnsvpl.GldivisgdvPtgaGLsssaalevavaavlknlgkleldskei 152
                                      ++      s W+nYv+g++k+l        + pl G+ ++isg++P+gaGLsssa+le+a+ +    l++l++d+ + 
  lcl|FitnessBrowser__PV4:5209834  89 AQMPldsvSPWSNYVRGTVKMLSaylAETGQPPLrGASLMISGNLPKGAGLSSSASLEMALIKAFAGLFDLKVDGIKA 166
                                      766566669*************9554233334557******************************************* PP

                        TIGR00131 153 llriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeve 230
                                      ++ +q++e++fvG+ncG+mDql+s++Ge + a+l+++  L  ++v+lp  ++ l+i+n+nvk++l++seYnlRr++++
  lcl|FitnessBrowser__PV4:5209834 167 AQLGQQAENEFVGCNCGIMDQLISAMGEAERAMLIDCSDLAIKQVPLPA-GLRLMIINSNVKRTLVGSEYNLRREQCQ 243
                                      *************************************************.**************************** PP

                        TIGR00131 231 eaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasl 308
                                      + a+ + ++    +Lr v+ e+  r ea    l++   + Ra+hvvsen+Rvl+ +++l  +d   +G+Lm++s+ sl
  lcl|FitnessBrowser__PV4:5209834 244 QVAQHFGVS----SLRQVSYEQLCRAEAS---LEPTLFR-RARHVVSENARVLEMAEALSAGDNAYIGRLMAASHRSL 313
                                      *******99....9*****9999976654...5666666.************************************** PP

                        TIGR00131 309 dddyeitvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskeal 385
                                      +dd+ ++ pe+d lve++  v G  +G+R+tG+GfGGC+val+p+ ++ +vr+++a +Y++ t+l ++ ++++s+ ++
  lcl|FitnessBrowser__PV4:5209834 314 RDDFAVSTPEVDCLVELVSEVLGmDGGARMTGGGFGGCVVALLPEHKIAEVRETIAVEYQARTGLTADIYLCQSGAGA 391
                                      ***********************99************************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (393 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.15
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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