Alignments for a candidate for ackA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Shewanella oneidensis MR-1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 202039 SO2915 acetate kinase (NCBI ptt file)

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__MR1:202039
          Length = 399

 Score =  677 bits (1746), Expect = 0.0
 Identities = 332/399 (83%), Positives = 370/399 (92%), Gaps = 1/399 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+KLVLVLNCGSSSLKFA+IDAQ+GDD+ISGLAECFGLEDSRIKWK NG K+E+ LGAF
Sbjct: 1   MSNKLVLVLNCGSSSLKFAVIDAQTGDDQISGLAECFGLEDSRIKWKINGEKHESSLGAF 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           TAHREAVEF IVN ILA  PELAAQI+A+GHRIVHGGEKFTRSVII   VI+GIE+C+SL
Sbjct: 61  TAHREAVEF-IVNKILAGQPELAAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAHLIGIRAA+ASFP+LPQV VFDTAFHQ+MPE+++IYALPYKLYREH IRRYGM
Sbjct: 120 APLHNPAHLIGIRAAMASFPKLPQVAVFDTAFHQSMPERSFIYALPYKLYREHGIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V REAAKVL K + + NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG
Sbjct: 180 HGTSHLFVSREAAKVLKKPLAETNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGD+DPSII+HLV QLGYTL+EVNNL+NKQSGLLGISELTNDCRGIEEGY DGHKGAT
Sbjct: 240 TRCGDIDPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LAL+IFCYRLAKYIASYTVPLGRLDA++FTGGIGENS++IREKVLN+L+IFNF VD   N
Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAVVFTGGIGENSDIIREKVLNMLQIFNFHVDSERN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLIT 399
           KAARFG++G+IT   + +AMVIPTNEEWVIAED+IKLIT
Sbjct: 360 KAARFGKKGIITADNSTVAMVIPTNEEWVIAEDSIKLIT 398


Lambda     K      H
   0.321    0.139    0.409 

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: 617
Number of extensions: 17
Number of successful extensions: 2
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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 202039 SO2915 (acetate kinase (NCBI ptt file))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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/TIGR00016.hmm
# target sequence database:        /tmp/gapView.1805723.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   5.7e-170  551.3   0.2   6.5e-170  551.1   0.2    1.0  1  FitnessBrowser__MR1:202039  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__MR1:202039  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.1   0.2  6.5e-170  6.5e-170       2     404 ..       2     397 ..       1     398 [. 0.98

  Alignments for each domain:
  == domain 1  score: 551.1 bits;  conditional E-value: 6.5e-170
                   TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkkilke 84 
                                 ++k++lvln+Gssslkfa++da++++   +sgl+e++ le++rik++ +gek+e+   a+++h+eav++++n++ +     ++
  FitnessBrowser__MR1:202039   2 SNKLVLVLNCGSSSLKFAVIDAQTGDDQ-ISGLAECFGLEDSRIKWKINGEKHESSLGAFTAHREAVEFIVNKILA--GQPEL 81 
                                 6799********************9999.9*********************************************7..559** PP

                   TIGR00016  85 lseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqtipeeaylY 167
                                  ++i+++GHR+vhGgekft svi++++v+k+i++ s+lAPlHnpa+l+gi+a++     +k ++vavFDtafHq +pe++++Y
  FitnessBrowser__MR1:202039  82 AAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSLAPLHNPAHLIGIRAAM--ASFPKLPQVAVFDTAFHQSMPERSFIY 162
                                 ******************************************************..6677889******************** PP

                   TIGR00016 168 alPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdi 250
                                 alPy+ly+e+g+RrYG+HGtsh +v+++aak+l kpl++ n+i +HlGnGasv+avk Gks+dtsmGltPLeGlvmGtR+Gdi
  FitnessBrowser__MR1:202039 163 ALPYKLYREHGIRRYGMHGTSHLFVSREAAKVLKKPLAETNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMGTRCGDI 245
                                 *********************************************************************************** PP

                   TIGR00016 251 DpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaiv 333
                                 Dp+ii +l ++lg +l+e+++++nk+sGllgis+l++D+R i++ +++g++ a+lAl+++++R+akyi++y+  l g+lDa+v
  FitnessBrowser__MR1:202039 246 DPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGATLALEIFCYRLAKYIASYTVPL-GRLDAVV 327
                                 ***************************************************************************.67***** PP

                   TIGR00016 334 FtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                 FtgGiGen+  +re+vl+ l+++ +++d+e+n+aar+gk+++i+ ++s+v ++viptnee+viaeD+++l+
  FitnessBrowser__MR1:202039 328 FTGGIGENSDIIREKVLNMLQIFNFHVDSERNKAARFGKKGIITADNSTV-AMVIPTNEEWVIAEDSIKLI 397
                                 ********************************************999987.689**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (399 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: 22.95
//
[ok]

This GapMind analysis is from Apr 09 2024. 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