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.4524.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.07
//
[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