GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella amazonensis SB2B

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 6937325 Sama_1495 acetate kinase (RefSeq)

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__SB2B:6937325
          Length = 399

 Score =  672 bits (1733), Expect = 0.0
 Identities = 332/398 (83%), Positives = 362/398 (90%), Gaps = 1/398 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+ LVLVLNCGSSSLKFAI+DA +GD+KISGLAECFGLE++RIKWK  G K+EA LGAF
Sbjct: 1   MSNTLVLVLNCGSSSLKFAILDATNGDEKISGLAECFGLENARIKWKLRGEKHEASLGAF 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           +AHREAVE+ IVN IL   PEL  Q+ AIGHRIVHGGEKFT SVII   V++GIEDCASL
Sbjct: 61  SAHREAVEY-IVNKILVNEPELKGQLIAIGHRIVHGGEKFTHSVIIDDAVLKGIEDCASL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQ+MP++AYIYALPYKLYREH IRRYGM
Sbjct: 120 APLHNPAHLIGIRAAQASFPSLPQVAVFDTAFHQSMPDRAYIYALPYKLYREHGIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V REAAK LGKDV D NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG
Sbjct: 180 HGTSHLFVSREAAKALGKDVNDTNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGDLDPSII+HLV QLGYTLDEVNNL+NKQSGLLGISELTNDCRGIEEGY +GHKGAT
Sbjct: 240 TRCGDLDPSIIYHLVHQLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LAL+IFCYRLAKYIASYTVPLGRLDAI+FTGGIGENS+LIREKVLNLLEIF F+VD   N
Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAIVFTGGIGENSDLIREKVLNLLEIFKFEVDSERN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398
           KAARFG QGVIT+ G+PIAMVIPTNEEWVIAED+++L+
Sbjct: 360 KAARFGNQGVITKEGSPIAMVIPTNEEWVIAEDSLRLV 397


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: 610
Number of extensions: 24
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 6937325 Sama_1495 (acetate kinase (RefSeq))
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.10727.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.9e-169  548.6   0.0   4.4e-169  548.4   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937325  Sama_1495 acetate kinase (RefSeq


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937325  Sama_1495 acetate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.4   0.0  4.4e-169  4.4e-169       2     404 ..       2     397 ..       1     398 [. 0.97

  Alignments for each domain:
  == domain 1  score: 548.4 bits;  conditional E-value: 4.4e-169
                         TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 
                                       +++++lvln+Gssslkfa+lda+n++++ +sgl+e++ le+arik++  gek+e+   a+++h+eav+ ++n++  +
  lcl|FitnessBrowser__SB2B:6937325   2 SNTLVLVLNCGSSSLKFAILDATNGDEK-ISGLAECFGLENARIKWKLRGEKHEASLGAFSAHREAVEYIVNKILVN 77 
                                       6789************************.9********************************************975 PP

                         TIGR00016  79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDta 155
                                       +   +++ ++ +iGHR+vhGgekft+svi++d vlk+i+d ++lAPlHnpa+l+gi+a++     ++ ++vavFDta
  lcl|FitnessBrowser__SB2B:6937325  78 E--PELKGQLIAIGHRIVHGGEKFTHSVIIDDAVLKGIEDCASLAPLHNPAHLIGIRAAQ--ASFPSLPQVAVFDTA 150
                                       5..999******************************************************..6667778******** PP

                         TIGR00016 156 fHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidts 232
                                       fHq +p++ay+YalPy+ly+e+g+RrYG+HGtsh +v+++aak l+k ++d n+i +HlGnGasv+avk Gks+dts
  lcl|FitnessBrowser__SB2B:6937325 151 FHQSMPDRAYIYALPYKLYREHGIRRYGMHGTSHLFVSREAAKALGKDVNDTNVICAHLGNGASVTAVKGGKSVDTS 227
                                       ***************************************************************************** PP

                         TIGR00016 233 mGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkv 309
                                       mGltPLeGlvmGtR+Gd+Dp+ii +l ++lg +lde+++++nk+sGllgis+l++D+R i++ ++eg++ a+lAl++
  lcl|FitnessBrowser__SB2B:6937325 228 MGLTPLEGLVMGTRCGDLDPSIIYHLVHQLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGATLALEI 304
                                       ***************************************************************************** PP

                         TIGR00016 310 yvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvl 386
                                       +++R+akyi++y+  l g+lDaivFtgGiGen+  +re+vl+ le++ +++d+e+n+aar+g+++vi++e ++  ++
  lcl|FitnessBrowser__SB2B:6937325 305 FCYRLAKYIASYTVPL-GRLDAIVFTGGIGENSDLIREKVLNLLEIFKFEVDSERNKAARFGNQGVITKE-GSPIAM 379
                                       ****************.67************************************************955.555689 PP

                         TIGR00016 387 viptneelviaeDalrla 404
                                       viptnee+viaeD+lrl+
  lcl|FitnessBrowser__SB2B:6937325 380 VIPTNEEWVIAEDSLRLV 397
                                       9**************996 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.43
//
[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