Alignments for a candidate for ackA in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Desulfobacter vibrioformis DSM 8776

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_035239225.1 Q366_RS12110 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000745975.1:WP_035239225.1
          Length = 401

 Score =  361 bits (926), Expect = e-104
 Identities = 191/404 (47%), Positives = 262/404 (64%), Gaps = 10/404 (2%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV------GDEKHVIER 54
           M+VLVINSGSSS+KY+L ++ G + +C G+ ERIG   S L H +      G++  +IE 
Sbjct: 1   MKVLVINSGSSSLKYKLFDLSGPRAICAGLVERIGSPESSLTHTLYPDPGPGEKTELIEI 60

Query: 55  ELPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEE 114
              +H +A++ +   L+     ++K   E+ A+GHRV  GGE FKE+ +VD   ++ I E
Sbjct: 61  -FKNHTQAIEKVAALLMAGDDPLVKSADELLAIGHRVAQGGEFFKENCIVDARAIEGIRE 119

Query: 115 VSPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIR 174
              LAPLHNPANL GI+AAM   PGVP+VAVFDT F  ++P   Y YA+P  YY  YK+R
Sbjct: 120 NIVLAPLHNPANLAGIEAAMAYFPGVPSVAVFDTLFASSLPDYVYRYALPTAYYNDYKVR 179

Query: 175 RYGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEG 234
           RYGFHG SH YV+K  A ++GK L EL  I CH+GNG+S+ AVK G C +TSMG TP  G
Sbjct: 180 RYGFHGASHAYVTKTLAGLMGKPLNELNNIVCHLGNGSSITAVKGGVCRETSMGMTPTSG 239

Query: 235 LVMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKG 294
           L+MGTR GD+DP++P ++  + G S  E+  +L+++SG+ G+     +DMRDI +A   G
Sbjct: 240 LIMGTRCGDIDPSLPAYLTSRTGKSAGEIQTVLDRESGLTGICG--MNDMRDIHKAMASG 297

Query: 295 DEWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKL 354
           D+  +L  E+  + I KYIGAY A +  +DAI FTAG+GEN    R      LE LG+ +
Sbjct: 298 DDNARLAFEMLCHGIKKYIGAYYAVLGRLDAIAFTAGIGENDTKVRAKSLEGLEHLGIIV 357

Query: 355 DKQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
           D++ N   +RGK   IST DS V+V VVPT+EE  IA   K++V
Sbjct: 358 DQEVN-AGLRGKSARISTHDSAVEVWVVPTDEEFEIATICKDLV 400


Lambda     K      H
   0.318    0.138    0.391 

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: 419
Number of extensions: 15
Number of successful extensions: 4
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: 403
Length of database: 401
Length adjustment: 31
Effective length of query: 372
Effective length of database: 370
Effective search space:   137640
Effective search space used:   137640
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_035239225.1 Q366_RS12110 (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.1427162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-137  444.3   0.0   2.2e-137  444.0   0.0    1.0  1  NCBI__GCF_000745975.1:WP_035239225.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035239225.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.0   0.0  2.2e-137  2.2e-137       4     399 ..       1     395 [.       1     400 [. 0.95

  Alignments for each domain:
  == domain 1  score: 444.0 bits;  conditional E-value: 2.2e-137
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktved....gekkeeeklaiedheeavkkll 72 
                                           +k+lv+n+Gssslk++l+d ++++  ++ glveri ++e+ ++         ++k+e +  +++h++a++k++
  NCBI__GCF_000745975.1:WP_035239225.1   1 MKVLVINSGSSSLKYKLFDLSGPRA-ICAGLVERIGSPESSLTHTLYpdpgPGEKTELIEIFKNHTQAIEKVA 72 
                                           69*******************7555.5************98887643112134666677779*********** PP

                             TIGR00016  73 ntlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvll 144
                                             l++ d+ + k+ +e+ +iGHRv++Gge f+e  iv++ ++++i++ + lAPlHnpa+l giea++     +
  NCBI__GCF_000745975.1:WP_035239225.1  73 ALLMAgDDPLVKSADELLAIGHRVAQGGEFFKENCIVDARAIEGIRENIVLAPLHNPANLAGIEAAM--AYFP 143
                                           ****999************************************************************..6777 PP

                             TIGR00016 145 kaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnG 217
                                            ++ vavFDt f   +p+  y YalP+ +y++++vRrYGfHG sh yvt+++a l++kpl++ln ivcHlGnG
  NCBI__GCF_000745975.1:WP_035239225.1 144 GVPSVAVFDTLFASSLPDYVYRYALPTAYYNDYKVRRYGFHGASHAYVTKTLAGLMGKPLNELNNIVCHLGNG 216
                                           889********************************************************************** PP

                             TIGR00016 218 asvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlR 290
                                           +s++avk G + +tsmG+tP  Gl+mGtR+GdiDp++  yl++++g+s+ ei+++l ++sGl gi g  +D+R
  NCBI__GCF_000745975.1:WP_035239225.1 217 SSITAVKGGVCRETSMGMTPTSGLIMGTRCGDIDPSLPAYLTSRTGKSAGEIQTVLDRESGLTGICG-MNDMR 288
                                           *******************************************************************.89*** PP

                             TIGR00016 291 dildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldle 363
                                           di ++++ g+++a+lA+++++h i+kyig+y a l g+lDai Ft+GiGen+++vr+++le+le lG+ +d+e
  NCBI__GCF_000745975.1:WP_035239225.1 289 DIHKAMASGDDNARLAFEMLCHGIKKYIGAYYAVL-GRLDAIAFTAGIGENDTKVRAKSLEGLEHLGIIVDQE 360
                                           ***********************************.67*********************************** PP

                             TIGR00016 364 lnnaarsgkesvisteeskvkvlviptneelviaeD 399
                                            n    +gk++ ist++s+v+v v+pt+ee  ia  
  NCBI__GCF_000745975.1:WP_035239225.1 361 VNA-GLRGKSARISTHDSAVEVWVVPTDEEFEIATI 395
                                           **9.999************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (401 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.05
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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