Alignments for a candidate for ackA in Coprobacter fastidiosus NSB1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Coprobacter fastidiosus NSB1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_022603078.1 NSB1T_RS28245 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000473955.1:WP_022603078.1
          Length = 400

 Score =  469 bits (1207), Expect = e-137
 Identities = 237/399 (59%), Positives = 299/399 (74%), Gaps = 3/399 (0%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-GDEKHVIERELPDH 59
           M+VLV+N GSSSIKY+L + + + +L +G  E+IG++GS L   +   EK ++E+++P+H
Sbjct: 1   MKVLVLNCGSSSIKYKLFDTQTKDILAQGGIEKIGLKGSFLKFTLPSGEKVILEKDIPEH 60

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
              ++ IL TL   K G IK L EI+AVGHRVVHGGE+F +SVL+D+EV   I E   +A
Sbjct: 61  TVGIEFILETLSGAKYGCIKSLDEIEAVGHRVVHGGEKFNQSVLIDKEVKAKIIECIDIA 120

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNPANL GI A  K+LP VP VAVFDTAFHQT+P+ AY+YA+PYE YEKY IRRYGFH
Sbjct: 121 PLHNPANLKGIDAVEKILPKVPQVAVFDTAFHQTMPKHAYMYALPYEMYEKYGIRRYGFH 180

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSHRYVS+RA E LG   E  +IITCHIGNG S+ A+K GK +DTSMG TP+EGL+MGT
Sbjct: 181 GTSHRYVSRRACEFLGVPYENQRIITCHIGNGGSITAIKDGKSIDTSMGLTPVEGLMMGT 240

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           R GD+D     FIMEKE +    +  ++NKKSGV G+S G SSDMR+IE A  +G+E  K
Sbjct: 241 RCGDVDAGALSFIMEKENLDAHGLSTLVNKKSGVMGIS-GVSSDMREIEAAIAQGNERAK 299

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
           L L++YDYRIAKYIGAY A + GVD IVFT GVGEN  +TR  VC  LEF+GVK+D++ N
Sbjct: 300 LALQMYDYRIAKYIGAYTAVLGGVDIIVFTGGVGENQTVTRATVCRQLEFMGVKIDEELN 359

Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
             TI GKE  +S PDS+VKV+V+PT+EE MIA DT+ I+
Sbjct: 360 -STIHGKEADLSAPDSKVKVVVIPTDEEYMIASDTQAIL 397


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: 542
Number of extensions: 24
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: 400
Length adjustment: 31
Effective length of query: 372
Effective length of database: 369
Effective search space:   137268
Effective search space used:   137268
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_022603078.1 NSB1T_RS28245 (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.553256.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-165  536.4   1.2   2.2e-165  536.2   1.2    1.0  1  NCBI__GCF_000473955.1:WP_022603078.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000473955.1:WP_022603078.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.2   1.2  2.2e-165  2.2e-165       4     402 ..       1     395 [.       1     398 [. 0.98

  Alignments for each domain:
  == domain 1  score: 536.2 bits;  conditional E-value: 2.2e-165
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k+lvln+Gsss+k++l+d++ ++ +l++g +e+i l+++++k    +++k   +++i++h+ +++++l+tl 
  NCBI__GCF_000473955.1:WP_022603078.1   1 MKVLVLNCGSSSIKYKLFDTQ-TKDILAQGGIEKIGLKGSFLKFTLPSGEKVILEKDIPEHTVGIEFILETLS 72 
                                           69******************9.699******************999999************************ PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                             +   +k+l+ei+++GHRvvhGgekf++sv++++ev +ki + +++APlHnpa+l+gi+av   k+l+k+++
  NCBI__GCF_000473955.1:WP_022603078.1  73 GaKYGCIKSLDEIEAVGHRVVHGGEKFNQSVLIDKEVKAKIIECIDIAPLHNPANLKGIDAVE--KILPKVPQ 143
                                           88999**********************************************************..99****** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqt+p++ay+YalPy++y+++g+RrYGfHGtsh+yv++ra + l+ p ++ ++i+cH+GnG+s++
  NCBI__GCF_000473955.1:WP_022603078.1 144 VAVFDTAFHQTMPKHAYMYALPYEMYEKYGIRRYGFHGTSHRYVSRRACEFLGVPYENQRIITCHIGNGGSIT 216
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+k+GksidtsmGltP+eGl+mGtR+Gd+D +++s+++e+++l ++ + +++nkksG++gisg+ssD+R+i++
  NCBI__GCF_000473955.1:WP_022603078.1 217 AIKDGKSIDTSMGLTPVEGLMMGTRCGDVDAGALSFIMEKENLDAHGLSTLVNKKSGVMGISGVSSDMREIEA 289
                                           ************************************************************************* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           ++++gne+aklAl++y +Riakyig+y+a l g +D ivFtgG+Gen++  r+ v+++le++G+k+d+eln  
  NCBI__GCF_000473955.1:WP_022603078.1 290 AIAQGNERAKLALQMYDYRIAKYIGAYTAVLGG-VDIIVFTGGVGENQTVTRATVCRQLEFMGVKIDEELNS- 360
                                           *******************************76.*************************************9. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalr 402
                                           + +gke+ +s ++skvkv+vipt+ee +ia D+  
  NCBI__GCF_000473955.1:WP_022603078.1 361 TIHGKEADLSAPDSKVKVVVIPTDEEYMIASDTQA 395
                                           999*****************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.22
//
[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