GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella halifaxensis HAW-EB4

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_012277679.1 SHAL_RS13495 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_000019185.1:WP_012277679.1
          Length = 398

 Score =  655 bits (1691), Expect = 0.0
 Identities = 327/398 (82%), Positives = 356/398 (89%), Gaps = 1/398 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+KLVLVLNCGSSSLKFA+IDA SGDD+ISGLAECFGLEDSRIKWK NG K+EA LGAF
Sbjct: 1   MSNKLVLVLNCGSSSLKFAVIDAISGDDQISGLAECFGLEDSRIKWKVNGQKSEASLGAF 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           TAHREAVE+ IVN+IL  HPE+AA+I+AIGHR+VHGGEKFT SVII   VI GIEDCA+L
Sbjct: 61  TAHREAVEY-IVNDILGAHPEIAAEIQAIGHRVVHGGEKFTHSVIIDESVIHGIEDCATL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQTMPEKAYIYALPYKLYRE++IRRYGM
Sbjct: 120 APLHNPAHLIGIRAAQASFPALPQVAVFDTAFHQTMPEKAYIYALPYKLYRENAIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH ++ REAA  LGKD  D N+ICAHLGNGASV AIKGGKSVDTSMGLTPLEGLVMG
Sbjct: 180 HGTSHLFISREAAAALGKDEADTNIICAHLGNGASVTAIKGGKSVDTSMGLTPLEGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGD+DPS+IFHLV +LGYTLDEV ++LNKQSGLLGISELTNDCRGIEEG+ +GHKGAT
Sbjct: 240 TRCGDVDPSVIFHLVNRLGYTLDEVESVLNKQSGLLGISELTNDCRGIEEGFENGHKGAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LAL+IFCYRLAKYIASYTVPL RLDA++FTGGIGENSNLIREKVLN L IFNF VD   N
Sbjct: 300 LALEIFCYRLAKYIASYTVPLERLDAVVFTGGIGENSNLIREKVLNSLAIFNFNVDAERN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398
            AARFG  G IT     +AMVIPTNEEWVIA+DAI+LI
Sbjct: 360 AAARFGNGGKITTDEGTVAMVIPTNEEWVIAQDAIELI 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: 602
Number of extensions: 23
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: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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_012277679.1 SHAL_RS13495 (acetate kinase)
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.2222483.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-167  541.4   0.1   6.4e-167  541.3   0.1    1.0  1  NCBI__GCF_000019185.1:WP_012277679.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012277679.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.3   0.1  6.4e-167  6.4e-167       2     404 ..       2     397 ..       1     398 [] 0.97

  Alignments for each domain:
  == domain 1  score: 541.3 bits;  conditional E-value: 6.4e-167
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                           ++k++lvln+Gssslkfa++da +++   +sgl+e++ le++rik++++g+k e+   a+++h+eav+ ++n 
  NCBI__GCF_000019185.1:WP_012277679.1   2 SNKLVLVLNCGSSSLKFAVIDAISGDDQ-ISGLAECFGLEDSRIKWKVNGQKSEASLGAFTAHREAVEYIVND 73 
                                           6799*******************99999.9******************************************* PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           +    +  +  +ei++iGHRvvhGgekft+svi++++v+++i+d + lAPlHnpa+l+gi+a+++    +  +
  NCBI__GCF_000019185.1:WP_012277679.1  74 ILG--AHPEIAAEIQAIGHRVVHGGEKFTHSVIIDESVIHGIEDCATLAPLHNPAHLIGIRAAQA--SFPALP 142
                                           **7..55999******************************************************5..556678 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           +vavFDtafHqt+pe+ay+YalPy+ly+e+ +RrYG+HGtsh +++++aa  l+k ++d n+i +HlGnGasv
  NCBI__GCF_000019185.1:WP_012277679.1 143 QVAVFDTAFHQTMPEKAYIYALPYKLYRENAIRRYGMHGTSHLFISREAAAALGKDEADTNIICAHLGNGASV 215
                                           ************************************************************************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a+k Gks+dtsmGltPLeGlvmGtR+Gd+Dp++i++l ++lg +lde+e++lnk+sGllgis+l++D+R i+
  NCBI__GCF_000019185.1:WP_012277679.1 216 TAIKGGKSVDTSMGLTPLEGLVMGTRCGDVDPSVIFHLVNRLGYTLDEVESVLNKQSGLLGISELTNDCRGIE 288
                                           ************************************************************************* PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           +  e+g++ a+lAl+++++R+akyi++y+  le  lDa+vFtgGiGen+  +re+vl++l+++ +++d e+n 
  NCBI__GCF_000019185.1:WP_012277679.1 289 EGFENGHKGATLALEIFCYRLAKYIASYTVPLER-LDAVVFTGGIGENSNLIREKVLNSLAIFNFNVDAERNA 360
                                           ********************************76.************************************** PP

                             TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           aar+g+ + i+t+e++v ++viptnee+via+Da++l+
  NCBI__GCF_000019185.1:WP_012277679.1 361 AARFGNGGKITTDEGTV-AMVIPTNEEWVIAQDAIELI 397
                                           ***********999987.689**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (398 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: 12.97
//
[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:

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