Alignments for a candidate for ackA in Bacillus coahuilensis m4-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Bacillus coahuilensis m4-4

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_010174314.1 M44_RS13085 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000171615.1:WP_010174314.1
          Length = 396

 Score =  658 bits (1698), Expect = 0.0
 Identities = 320/394 (81%), Positives = 364/394 (92%)

Query: 1   MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60
           MSK+IAINAGSSSLKFQLFEMP ETV+TKG++ERIG+ DS+FTIS+NGEK  EVTDIPDH
Sbjct: 1   MSKVIAINAGSSSLKFQLFEMPEETVITKGIIERIGLKDSIFTISINGEKQKEVTDIPDH 60

Query: 61  AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120
            VAVKMLL+KLT  GII  L+EI+G+GHRVVHGGE FSDS ++T++ + +IE++S+LAPL
Sbjct: 61  EVAVKMLLDKLTSTGIIASLDEINGVGHRVVHGGEIFSDSAIITEDVLAKIEELSDLAPL 120

Query: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 180
           HNPANI GI+AF+  LP+V AVAVFDTAFHQ+MPE SYLYSLPYEYYEKFGIRKYGFHGT
Sbjct: 121 HNPANITGIRAFQAALPHVEAVAVFDTAFHQSMPESSYLYSLPYEYYEKFGIRKYGFHGT 180

Query: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 240
           SHKYV+ERAAELLGRP++ LRL+SCHLGNGASIAA+EGGKSIDTSMGFTPLAGV MGTRS
Sbjct: 181 SHKYVSERAAELLGRPIEQLRLLSCHLGNGASIAAIEGGKSIDTSMGFTPLAGVTMGTRS 240

Query: 241 GNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETAL 300
           GNIDPALIP+IMEKTG+TADEVL+ LNK+SG+LG+SGFSSDLRDI +AT+EGNERAE AL
Sbjct: 241 GNIDPALIPFIMEKTGKTADEVLDVLNKESGMLGVSGFSSDLRDIEQATEEGNERAELAL 300

Query: 301 EVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVR 360
           EVFA+RIHKYIGSYAARM GVDAIIFTAGIGENS  +R RVL+GLEFMGVYWDPA N VR
Sbjct: 301 EVFANRIHKYIGSYAARMCGVDAIIFTAGIGENSDVIRARVLQGLEFMGVYWDPARNKVR 360

Query: 361 GEEAFISYPHSPVKVMIIPTDEEVMIARDVVRLA 394
           GEE F++YPHSPVKV++IPTDEEVMIARDVVRLA
Sbjct: 361 GEETFVNYPHSPVKVIVIPTDEEVMIARDVVRLA 394


Lambda     K      H
   0.317    0.136    0.381 

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: 523
Number of extensions: 8
Number of successful extensions: 1
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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_010174314.1 M44_RS13085 (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.3038348.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-180  586.1   0.1   1.7e-180  586.0   0.1    1.0  1  NCBI__GCF_000171615.1:WP_010174314.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000171615.1:WP_010174314.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.0   0.1  1.7e-180  1.7e-180       4     404 ..       2     394 ..       1     395 [. 0.98

  Alignments for each domain:
  == domain 1  score: 586.0 bits;  conditional E-value: 1.7e-180
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k++ +naGssslkf+l+++ + e+v+++g++eri l+++ i+t++ +++k++e+++i+dhe avk+ll++l+
  NCBI__GCF_000171615.1:WP_010174314.1   2 SKVIAINAGSSSLKFQLFEMPE-ETVITKGIIERIGLKDS-IFTISINGEKQKEVTDIPDHEVAVKMLLDKLT 72 
                                           79*******************5.99***************.99999999************************ PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                             + i+ +l+ei+ +GHRvvhGge f++s+i+t++vl+ki+++s+lAPlHnpa+++gi+a++    l+++++v
  NCBI__GCF_000171615.1:WP_010174314.1  73 -STGIIASLDEINGVGHRVVHGGEIFSDSAIITEDVLAKIEELSDLAPLHNPANITGIRAFQ--AALPHVEAV 142
                                           .699**********************************************************..7788888** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtafHq +pe +ylY+lPy++y+++g+R+YGfHGtshkyv++raa+ll++p+++l+l++cHlGnGas++a
  NCBI__GCF_000171615.1:WP_010174314.1 143 AVFDTAFHQSMPESSYLYSLPYEYYEKFGIRKYGFHGTSHKYVSERAAELLGRPIEQLRLLSCHLGNGASIAA 215
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           ++ GksidtsmG+tPL+G+ mGtRsG+iDpa+i +++e++g+++de+ ++lnk+sG+lg+sg+ssDlRdi+++
  NCBI__GCF_000171615.1:WP_010174314.1 216 IEGGKSIDTSMGFTPLAGVTMGTRSGNIDPALIPFIMEKTGKTADEVLDVLNKESGMLGVSGFSSDLRDIEQA 288
                                           ************************************************************************* PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                           +eegne+a+lAl+v+++Ri+kyig+y+a++ g +Dai+Ft+GiGen+  +r++vl++le++G+++d+++n+  
  NCBI__GCF_000171615.1:WP_010174314.1 289 TEEGNERAELALEVFANRIHKYIGSYAARMCG-VDAIIFTAGIGENSDVIRARVLQGLEFMGVYWDPARNK-- 358
                                           ******************************77.**************************************.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404
                                            +g+e+++++++s vkv+vipt+ee++ia+D++rla
  NCBI__GCF_000171615.1:WP_010174314.1 359 VRGEETFVNYPHSPVKVIVIPTDEEVMIARDVVRLA 394
                                           9*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (396 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.83
//
[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