Alignments for a candidate for ackA in Pedobacter arcticus A12

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pedobacter arcticus A12

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_017258803.1 B176_RS0110675 acetate/propionate family kinase

Query= BRENDA::A2RNG5
         (395 letters)



>NCBI__GCF_000302595.1:WP_017258803.1
          Length = 400

 Score =  254 bits (648), Expect = 4e-72
 Identities = 157/390 (40%), Positives = 226/390 (57%), Gaps = 17/390 (4%)

Query: 5   LAVNAGSSSMKWQMYEMPEE-KVLAKGLIERIGLKDSIVTVKFGEEKEERVFDIP--NHT 61
           L +N GSSS+K+ +YE+ E    L  G +E I    + +        +    DIP  NHT
Sbjct: 10  LTINGGSSSIKYALYEIKEPLNQLLSGEMEGIWSGQAQLHFTHANGVKNHHIDIPVTNHT 69

Query: 62  EAVEVLLEDLKRLKIVEEFTEITGVGHRVVAGGEIFQKSTV---VTPEVLQQVKDLSALA 118
           EA E L   L++     E+ ++T +GHR+V G     K T    +T E L Q+K +SA  
Sbjct: 70  EAAEWLFNWLQK---ETEYIKVTAIGHRIVQG----MKHTAPEKITDEFLAQLKAISAFD 122

Query: 119 PLHNPANAAGIEAFLNLLPDATSVVVFDTAFHTTMPEKAFRYPLPKKYYTDYAVRKYGAH 178
           P H PA    IE F    PD   V  FDT FHT+MP  A   P+P+KY  +  +++YG H
Sbjct: 123 PEHLPAEIELIEVFRKRYPDVDQVACFDTYFHTSMPAIAKLVPIPRKY-RNKGIKRYGFH 181

Query: 179 GTSHMYVSQEAAKLLGKPIEETKIITAHIGNGASITAVKGGESVDTSMGFTPLAGVMMGT 238
           G S+ Y+ QE  ++ G    + KII AH+G+GAS+ A+K G+S+DTSMGFTP +G+ M T
Sbjct: 182 GLSYAYLLQEFERIAGTEKSKGKIIVAHLGSGASMVAIKNGKSIDTSMGFTPASGLTMST 241

Query: 239 RTGEMDPSVFPYLIENDSELKDAQDVVDMMNKESGLYGVSGISSDMRDIIAAKDTDADAK 298
           RTG++DP V  YL +   +L  AQ    M+N ESGL  +SG ++DM+ ++  +  D+ A 
Sbjct: 242 RTGDLDPGVAWYL-QQFEKLSPAQ-FNHMVNHESGLLAISGTTADMQQLLKIQQQDSRAT 299

Query: 299 LAFEMYVDRIQKFIGQYLAVLNGADALVFTAGIGENSVPVREAILSGLTWFGIEVDPEKN 358
            A + +  +  K+IG + AVL G D L+F+ GIGE+S  VR  I  GL + GIE+D   N
Sbjct: 300 EAVDFFCYQCIKWIGAFTAVLGGLDTLIFSGGIGEHSPEVRSKICDGLEFLGIELDEVHN 359

Query: 359 VFGVEGEISKPSSRLKVFVIPTDEELVIAR 388
           +      IS   SR  V+++ T+EEL+IA+
Sbjct: 360 MNNTT-IISTEKSRTPVYMMHTNEELMIAQ 388


Lambda     K      H
   0.315    0.134    0.372 

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: 373
Number of extensions: 19
Number of successful extensions: 5
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: 395
Length of database: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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_017258803.1 B176_RS0110675 (acetate/propionate family 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.1972517.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-114  368.2   0.0   2.9e-114  367.9   0.0    1.0  1  NCBI__GCF_000302595.1:WP_017258803.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000302595.1:WP_017258803.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.9   0.0  2.9e-114  2.9e-114       5     399 ..       8     389 ..       5     395 .. 0.94

  Alignments for each domain:
  == domain 1  score: 367.9 bits;  conditional E-value: 2.9e-114
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktv.edgekkeeeklaiedheeavkkllntlk 76 
                                            +l +n Gsss+k+al++ +++ + llsg +e i + +a++     +g k++++   +++h+ea + l+n l+
  NCBI__GCF_000302595.1:WP_017258803.1   8 CLLTINGGSSSIKYALYEIKEPLNQLLSGEMEGIWSGQAQLHFThANGVKNHHIDIPVTNHTEAAEWLFNWLQ 80 
                                           5899*******************************9988876652667777788899**************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                           k     +e  ++++iGHR+v+G  k+t    +tde l+++k is + P H pae+e ie +   k  +++ +v
  NCBI__GCF_000302595.1:WP_017258803.1  81 K----ETEYIKVTAIGHRIVQGM-KHTAPEKITDEFLAQLKAISAFDPEHLPAEIELIEVFR--KRYPDVDQV 146
                                           8....578889**********86.67888899******************************..8999999** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           a+FDt fH+ +p  a l ++P + y+++g++rYGfHG+s+ y+ q+ +++ + +  + ++iv+HlG Gas+ a
  NCBI__GCF_000302595.1:WP_017258803.1 147 ACFDTYFHTSMPAIAKLVPIP-RKYRNKGIKRYGFHGLSYAYLLQEFERIAGTEKSKGKIIVAHLGSGASMVA 218
                                           *********************.66899********************************************** PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           +knGksidtsmG+tP  Gl m tR+Gd+Dp++  yl++ ++ls ++ ++++n +sGll+isg ++D+ ++l+ 
  NCBI__GCF_000302595.1:WP_017258803.1 219 IKNGKSIDTSMGFTPASGLTMSTRTGDLDPGVAWYLQQFEKLSPAQFNHMVNHESGLLAISGTTADMQQLLKI 291
                                           **********************************************************************987 PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                           + +++ +a+ A++ +++   k+ig+++a l g lD+++F gGiGe + evr +++++le+lG++ld+  n   
  NCBI__GCF_000302595.1:WP_017258803.1 292 Q-QQDSRATEAVDFFCYQCIKWIGAFTAVLGG-LDTLIFSGGIGEHSPEVRSKICDGLEFLGIELDEVHNM-- 360
                                           7.7788************************76.*********************************98888.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeD 399
                                             ++ ++iste+s++ v++++tneel+ia+ 
  NCBI__GCF_000302595.1:WP_017258803.1 361 --NNTTIISTEKSRTPVYMMHTNEELMIAQL 389
                                           ..7899**********************985 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.75
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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