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.497354.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: 25.59
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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