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.28753.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  lcl|FitnessBrowser__MR1:202039  SO2915 acetate kinase (NCBI ptt 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202039  SO2915 acetate kinase (NCBI ptt file)
   #    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 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkk 80 
                                     ++k++lvln+Gssslkfa++da++++   +sgl+e++ le++rik++ +gek+e+   a+++h+eav++++n++ +   
  lcl|FitnessBrowser__MR1:202039   2 SNKLVLVLNCGSSSLKFAVIDAQTGDDQ-ISGLAECFGLEDSRIKWKINGEKHESSLGAFTAHREAVEFIVNKILA--G 77 
                                     6799********************9999.9*********************************************7..5 PP

                       TIGR00016  81 ilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqt 159
                                       ++ ++i+++GHR+vhGgekft svi++++v+k+i++ s+lAPlHnpa+l+gi+a++     +k ++vavFDtafHq 
  lcl|FitnessBrowser__MR1:202039  78 QPELAAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSLAPLHNPAHLIGIRAAM--ASFPKLPQVAVFDTAFHQS 154
                                     59********************************************************..6677889************ PP

                       TIGR00016 160 ipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPL 238
                                     +pe++++YalPy+ly+e+g+RrYG+HGtsh +v+++aak+l kpl++ n+i +HlGnGasv+avk Gks+dtsmGltPL
  lcl|FitnessBrowser__MR1:202039 155 MPERSFIYALPYKLYREHGIRRYGMHGTSHLFVSREAAKVLKKPLAETNVICAHLGNGASVTAVKGGKSVDTSMGLTPL 233
                                     ******************************************************************************* PP

                       TIGR00016 239 eGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiaky 317
                                     eGlvmGtR+GdiDp+ii +l ++lg +l+e+++++nk+sGllgis+l++D+R i++ +++g++ a+lAl+++++R+aky
  lcl|FitnessBrowser__MR1:202039 234 EGLVMGTRCGDIDPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGATLALEIFCYRLAKY 312
                                     ******************************************************************************* PP

                       TIGR00016 318 igkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelvi 396
                                     i++y+  l g+lDa+vFtgGiGen+  +re+vl+ l+++ +++d+e+n+aar+gk+++i+ ++s+v ++viptnee+vi
  lcl|FitnessBrowser__MR1:202039 313 IASYTVPL-GRLDAVVFTGGIGENSDIIREKVLNMLQIFNFHVDSERNKAARFGKKGIITADNSTV-AMVIPTNEEWVI 389
                                     ********.67*************************************************999987.689********* PP

                       TIGR00016 397 aeDalrla 404
                                     aeD+++l+
  lcl|FitnessBrowser__MR1:202039 390 AEDSIKLI 397
                                     *****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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.11
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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