Alignments for a candidate for ackA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Escherichia coli BW25113

Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate 17189 b3115 propionate kinase/acetate kinase C, anaerobic (RefSeq)

Query= SwissProt::P11868
         (402 letters)



>FitnessBrowser__Keio:17189
          Length = 402

 Score =  794 bits (2051), Expect = 0.0
 Identities = 402/402 (100%), Positives = 402/402 (100%)

Query: 1   MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60
           MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY
Sbjct: 1   MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60

Query: 61  EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120
           EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY
Sbjct: 61  EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120

Query: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180
           ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR
Sbjct: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180

Query: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240
           YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV
Sbjct: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240

Query: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300
           DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF
Sbjct: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300

Query: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360
           VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC
Sbjct: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360

Query: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402
           GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA
Sbjct: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402


Lambda     K      H
   0.318    0.134    0.386 

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: 680
Number of extensions: 16
Number of successful extensions: 1
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: 402
Length of database: 402
Length adjustment: 31
Effective length of query: 371
Effective length of database: 371
Effective search space:   137641
Effective search space used:   137641
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 17189 b3115 (propionate kinase/acetate kinase C, anaerobic (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.4189.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-176  573.3   0.1   1.4e-176  573.1   0.1    1.0  1  lcl|FitnessBrowser__Keio:17189  b3115 propionate kinase/acetate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17189  b3115 propionate kinase/acetate kinase C, anaerobic (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.1   0.1  1.4e-176  1.4e-176       3     404 ..       4     393 ..       2     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: 573.1 bits;  conditional E-value: 1.4e-176
                       TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkki 81 
                                     + ++lv+n+Gsss+kf++lda+++e + +sg+++ i++e+a+++  ++g  +e + la++++e a+k+++ +l+k    
  lcl|FitnessBrowser__Keio:17189   4 FPVVLVINCGSSSIKFSVLDASDCEVL-MSGIADGINSENAFLS--VNG--GEPAPLAHHSYEGALKAIAFELEK---- 73 
                                     678*******************98866.*************544..555..7999*******************8.... PP

                       TIGR00016  82 lkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqti 160
                                     +++++++aliGHR++hGg+ ftes+i+tdev+++i+++s+lAPlHn+a+l+gie++++l++ ++  +vavFDt+fHqt+
  lcl|FitnessBrowser__Keio:17189  74 RNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNYANLSGIESAQQLFPGVT--QVAVFDTSFHQTM 150
                                     799******************************************************8888777..************* PP

                       TIGR00016 161 peeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLe 239
                                     + eaylY+lP+++y+elgvRrYGfHGtsh+yv+qra++lln ++dd+ l+v+HlGnGas++av+nG+s+dtsmG+tPLe
  lcl|FitnessBrowser__Keio:17189 151 APEAYLYGLPWKYYEELGVRRYGFHGTSHRYVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLE 229
                                     ******************************************************************************* PP

                       TIGR00016 240 GlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyi 318
                                     Gl+mGtRsGd+D++++s++a+++++sl ++e+++nk+sGllgisglssDlR+++++++eg+e+a+lA+k++vhRia++i
  lcl|FitnessBrowser__Keio:17189 230 GLMMGTRSGDVDFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTFVHRIARHI 308
                                     ******************************************************************************* PP

                       TIGR00016 319 gkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelvia 397
                                     + ++asl  +lD+i+FtgGiGen++ +r+lv+e+l+vlGl++d+e+nn+++s+ e+++s+e+++v ++viptnee++ia
  lcl|FitnessBrowser__Keio:17189 309 AGHAASLR-RLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSCGERIVSSENARVICAVIPTNEEKMIA 386
                                     *******5.5********************************************************************* PP

                       TIGR00016 398 eDalrla 404
                                      Da++l 
  lcl|FitnessBrowser__Keio:17189 387 LDAIHLG 393
                                     *****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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: 00:00:00.02
# Mc/sec: 7.62
//
[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:

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