Alignments for a candidate for ackA in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Calditerrivibrio nitroreducens DSM 19672

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_013450889.1 CALNI_RS03820 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000183405.1:WP_013450889.1
          Length = 415

 Score =  456 bits (1173), Expect = e-133
 Identities = 235/400 (58%), Positives = 294/400 (73%), Gaps = 3/400 (0%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-GDEKHVIERELPDH 59
           M++L +N GSSS+KYQL + E +KV+ KGI ERIGI  S +VH V G E H  E E  DH
Sbjct: 1   MKILALNCGSSSVKYQLYDWENQKVVAKGIVERIGIGDSFIVHEVPGKETHREEYECHDH 60

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
             A+ L+++TL     GVI  + EI AVGHRVVHGGE+FK SVL+ ++V+KAIEEV  LA
Sbjct: 61  ITAINLVVHTLESPTKGVISKISEISAVGHRVVHGGEKFKRSVLITDDVVKAIEEVQHLA 120

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNP NL GI+ A K+LP VP+VA+FDTAFHQT+P+ AYLYA+PYE+YEKY +RRYGFH
Sbjct: 121 PLHNPPNLAGIRGAQKVLPDVPHVAIFDTAFHQTMPEYAYLYAVPYEWYEKYGVRRYGFH 180

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSH YVSKRAA +LGK  +E  IIT HIGNG S  A+K G  VDTSMG TPLEG VMGT
Sbjct: 181 GTSHLYVSKRAAALLGKPAKECNIITMHIGNGVSHTAIKNGVSVDTSMGLTPLEGAVMGT 240

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           R GDLDPA+P F+ ++  ++P+EM +ILNKKSG+ G++ G  +D RD+     +GD+ C 
Sbjct: 241 RCGDLDPAVPLFMQQQLNVTPKEMDNILNKKSGILGIT-GKYTDRRDVIAGGEQGDKRCH 299

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
           L LEI  YR+ KYIGAY A +  VDAIVFTAGVGEN+ + RE     LE LG+ +D +KN
Sbjct: 300 LALEIEAYRLKKYIGAYYAVLGRVDAIVFTAGVGENAWLIREKALQGLENLGIIIDFEKN 359

Query: 360 EETI-RGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
           ++T  +  E  ISTP+SRVKV V+PTNEEL+   D   I+
Sbjct: 360 KKTFSKSGETEISTPESRVKVFVIPTNEELVFIEDVVAIL 399


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: 505
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: 415
Length adjustment: 31
Effective length of query: 372
Effective length of database: 384
Effective search space:   142848
Effective search space used:   142848
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_013450889.1 CALNI_RS03820 (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.24670.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-163  527.9   0.1   8.5e-163  527.7   0.1    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013450889.1  CALNI_RS03820 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450889.1  CALNI_RS03820 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.7   0.1  8.5e-163  8.5e-163       4     403 ..       1     398 [.       1     400 [. 0.98

  Alignments for each domain:
  == domain 1  score: 527.7 bits;  conditional E-value: 8.5e-163
                                 TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkll 72 
                                               +kil ln+Gsss+k++l+d en +kv+++g+veri + +++i   + g+++++e+ + +dh +a++ ++
  lcl|NCBI__GCF_000183405.1:WP_013450889.1   1 MKILALNCGSSSVKYQLYDWEN-QKVVAKGIVERIGIGDSFIVHEVPGKETHREEYECHDHITAINLVV 68 
                                               69*******************7.7777****************************************** PP

                                 TIGR00016  73 ntlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140
                                               +tl++  k ++ + sei+++GHRvvhGgekf+ sv++td+v+k+i+++ +lAPlHnp++l gi+ ++  
  lcl|NCBI__GCF_000183405.1:WP_013450889.1  69 HTLESpTKGVISKISEISAVGHRVVHGGEKFKRSVLITDDVVKAIEEVQHLAPLHNPPNLAGIRGAQ-- 135
                                               *****9999**********************************************************.. PP

                                 TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnl 209
                                               kvl+++++va+FDtafHqt+pe aylYa+Py++y+++gvRrYGfHGtsh yv++raa ll+kp+++ n+
  lcl|NCBI__GCF_000183405.1:WP_013450889.1 136 KVLPDVPHVAIFDTAFHQTMPEYAYLYAVPYEWYEKYGVRRYGFHGTSHLYVSKRAAALLGKPAKECNI 204
                                               99******************************************************************* PP

                                 TIGR00016 210 ivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksG 278
                                               i++H+GnG s +a+knG s+dtsmGltPLeG vmGtR+Gd+Dpa+  +++++l+ + +e+ ++lnkksG
  lcl|NCBI__GCF_000183405.1:WP_013450889.1 205 ITMHIGNGVSHTAIKNGVSVDTSMGLTPLEGAVMGTRCGDLDPAVPLFMQQQLNVTPKEMDNILNKKSG 273
                                               ********************************************************************* PP

                                 TIGR00016 279 llgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevre 347
                                               +lgi+g+ +D Rd+++  e+g+++++lAl++ ++R++kyig+y a l g++DaivFt+G+Gena  +re
  lcl|NCBI__GCF_000183405.1:WP_013450889.1 274 ILGITGKYTDRRDVIAGGEQGDKRCHLALEIEAYRLKKYIGAYYAVL-GRVDAIVFTAGVGENAWLIRE 341
                                               ***********************************************.67******************* PP

                                 TIGR00016 348 lvleklevlGlkldlelnnaa.rsgkesvisteeskvkvlviptneelviaeDalrl 403
                                               ++l++le lG+ +d e+n+++ ++  e+ ist+es+vkv+viptneelv +eD++ +
  lcl|NCBI__GCF_000183405.1:WP_013450889.1 342 KALQGLENLGIIIDFEKNKKTfSKSGETEISTPESRVKVFVIPTNEELVFIEDVVAI 398
                                               *******************9988999***************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (415 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.47
//
[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 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