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

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_012277819.1 SHAL_RS14195 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_000019185.1:WP_012277819.1
          Length = 402

 Score =  597 bits (1538), Expect = e-175
 Identities = 297/402 (73%), Positives = 347/402 (86%), Gaps = 5/402 (1%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAK---- 56
           MS+K VLVLNCGSSSLKFA+IDA SG+D +SGL+ECFGLED+ IKWK   G+ E+K    
Sbjct: 1   MSNKYVLVLNCGSSSLKFAVIDAISGEDLLSGLSECFGLEDACIKWKTRVGQQESKHQES 60

Query: 57  LGAFTAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIED 116
           LGAF+AH EA+ + IV+ ILA HP L  QI A+GHR+VHGGE+F+ SVII  EV+QGIE 
Sbjct: 61  LGAFSAHTEAMAY-IVDTILAAHPTLKQQILAVGHRVVHGGEQFSGSVIINDEVLQGIEA 119

Query: 117 CASLAPLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIR 176
           CA+LAPLHNPAH+IGI AA  +FPQL Q+ VFDTAFHQTMP+KA+IYALPY+LYREHSIR
Sbjct: 120 CATLAPLHNPAHIIGILAAKVAFPQLAQIAVFDTAFHQTMPQKAFIYALPYQLYREHSIR 179

Query: 177 RYGMHGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEG 236
           R+GMHGTSH Y+C+ AAK LG  V+D+N+I AHLGNGASV AIK G SVDTSMG+TPLEG
Sbjct: 180 RFGMHGTSHRYICQTAAKTLGIAVEDLNLISAHLGNGASVTAIKAGISVDTSMGMTPLEG 239

Query: 237 LVMGTRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGH 296
           +VMGTRCGDLDPSIIF+LV+ LGY+L EV +++NKQSGLLGISELTNDCRGIEEG+ +GH
Sbjct: 240 VVMGTRCGDLDPSIIFYLVQNLGYSLKEVEDMMNKQSGLLGISELTNDCRGIEEGHANGH 299

Query: 297 KGATLALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVD 356
           KGA+LALDIFCYRLAKYIASYTVPLGR+DA++FTGGIGENS LIR+KV+ LL IFNFK+D
Sbjct: 300 KGASLALDIFCYRLAKYIASYTVPLGRIDALVFTGGIGENSALIRQKVIELLSIFNFKLD 359

Query: 357 DILNKAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398
              N AARFGQQG IT    P+AMVIPTNEEWVIA+DA+KLI
Sbjct: 360 RQRNLAARFGQQGQITADTGPVAMVIPTNEEWVIAQDALKLI 401


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: 546
Number of extensions: 21
Number of successful extensions: 3
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: 402
Length adjustment: 31
Effective length of query: 370
Effective length of database: 371
Effective search space:   137270
Effective search space used:   137270
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_012277819.1 SHAL_RS14195 (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.497829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-160  519.2   0.1   3.5e-160  519.1   0.1    1.0  1  NCBI__GCF_000019185.1:WP_012277819.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012277819.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.1   0.1  3.5e-160  3.5e-160       2     404 ..       2     401 ..       1     402 [] 0.95

  Alignments for each domain:
  == domain 1  score: 519.1 bits;  conditional E-value: 3.5e-160
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktv....edgekkeeeklaiedheeavkk 70 
                                           ++k +lvln+Gssslkfa++da ++e + lsgl e++ le+a ik++    ++++k++e   a+++h+ea++ 
  NCBI__GCF_000019185.1:WP_012277819.1   2 SNKYVLVLNCGSSSLKFAVIDAISGEDL-LSGLSECFGLEDACIKWKtrvgQQESKHQESLGAFSAHTEAMAY 73 
                                           6789*******************87776.9****************942222334456677899********* PP

                             TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143
                                           +++t+ +  +  +++++i ++GHRvvhGge+f+ svi++devl++i+  + lAPlHnpa+++gi a++ ++  
  NCBI__GCF_000019185.1:WP_012277819.1  74 IVDTILA--AHPTLKQQILAVGHRVVHGGEQFSGSVIINDEVLQGIEACATLAPLHNPAHIIGILAAKVAF-- 142
                                           ******7..559999*****************************************************555.. PP

                             TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216
                                           ++  ++avFDtafHqt+p++a++YalPy+ly+e+ +Rr+G+HGtsh+y+ q+aak+l+ +++dlnli++HlGn
  NCBI__GCF_000019185.1:WP_012277819.1 143 PQLAQIAVFDTAFHQTMPQKAFIYALPYQLYREHSIRRFGMHGTSHRYICQTAAKTLGIAVEDLNLISAHLGN 215
                                           5556********************************************************************* PP

                             TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289
                                           Gasv+a+k G s+dtsmG+tPLeG+vmGtR+Gd+Dp+ii+yl ++lg sl+e+e+++nk+sGllgis+l++D+
  NCBI__GCF_000019185.1:WP_012277819.1 216 GASVTAIKAGISVDTSMGMTPLEGVVMGTRCGDLDPSIIFYLVQNLGYSLKEVEDMMNKQSGLLGISELTNDC 288
                                           ************************************************************************* PP

                             TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362
                                           R i++  ++g++ a+lAl+++++R+akyi++y+  l g++Da+vFtgGiGen+a +r++v+e l ++ +kld 
  NCBI__GCF_000019185.1:WP_012277819.1 289 RGIEEGHANGHKGASLALDIFCYRLAKYIASYTVPL-GRIDALVFTGGIGENSALIRQKVIELLSIFNFKLDR 360
                                           ************************************.67********************************** PP

                             TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           ++n aar+g+++ i+ + + v ++viptnee+via+Dal+l+
  NCBI__GCF_000019185.1:WP_012277819.1 361 QRNLAARFGQQGQITADTGPV-AMVIPTNEEWVIAQDALKLI 401
                                           ***************777766.789**************996 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.15
//
[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:

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