Alignments for a candidate for ackA in Streptococcus massiliensis 4401825

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Streptococcus massiliensis 4401825

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_018371377.1 BN415_RS06580 acetate kinase

Query= BRENDA::A2RNG5
         (395 letters)



>NCBI__GCF_000341525.1:WP_018371377.1
          Length = 396

 Score =  546 bits (1407), Expect = e-160
 Identities = 269/395 (68%), Positives = 327/395 (82%), Gaps = 1/395 (0%)

Query: 1   MTKTLAVNAGSSSMKWQMYEMPEEKVLAKGLIERIGLKDSIVTVKFGEEKEERVFDIPNH 60
           M+KT+A+NAGSSS+KWQ+Y+MPEEKV+AKGLIERIGLKDSI TVK+G++K + V DI +H
Sbjct: 1   MSKTIAINAGSSSLKWQLYQMPEEKVVAKGLIERIGLKDSISTVKYGDKKHQLVLDILDH 60

Query: 61  TEAVEVLLEDLKRLKIVEEFTEITGVGHRVVAGGEIFQKSTVVTPEVLQQVKDLSALAPL 120
            +AV++LL DL  L I+ +F EITGVGHRVVAGGE F++ST+V  E L +++ LS LAPL
Sbjct: 61  VQAVKILLNDLIELGIISDFNEITGVGHRVVAGGESFKESTLVDDEALAEIEKLSELAPL 120

Query: 121 HNPANAAGIEAFLNLLPDATSVVVFDTAFHTTMPEKAFRYPLPKKYYTDYAVRKYGAHGT 180
           HNPANAAGI AF  +LPD TSV VFDTAFHTTM    + YP+P KYY DY VRKYGAHGT
Sbjct: 121 HNPANAAGIRAFKEILPDITSVAVFDTAFHTTMQPATYLYPIPVKYYEDYKVRKYGAHGT 180

Query: 181 SHMYVSQEAAKLLGKPIEETKIITAHIGNGASITAVKGGESVDTSMGFTPLAGVMMGTRT 240
           SH YV+QEAAKLLG+P+ E K+ITAHIGNG SITA   GESVDTSMGFTPLAG MMGTR+
Sbjct: 181 SHYYVAQEAAKLLGRPLSELKLITAHIGNGVSITANYHGESVDTSMGFTPLAGPMMGTRS 240

Query: 241 GEMDPSVFPYLIENDSELKDAQDVVDMMNKESGLYGVSGISSDMRDI-IAAKDTDADAKL 299
           G++DP++ PYLI+ D ELKDA DV++M+NK+SGL GVSGISSDMRDI    ++ +  A L
Sbjct: 241 GDIDPAIIPYLIQQDPELKDAADVINMLNKQSGLLGVSGISSDMRDIEDGLQEQNPKAVL 300

Query: 300 AFEMYVDRIQKFIGQYLAVLNGADALVFTAGIGENSVPVREAILSGLTWFGIEVDPEKNV 359
           A+ M++DRI+KFIGQYLAVLNGADA+VFTAG+GEN   +R  ++ GL+WFGIE+D  KNV
Sbjct: 301 AYNMFIDRIKKFIGQYLAVLNGADAIVFTAGMGENGYLMRNDVIQGLSWFGIELDLTKNV 360

Query: 360 FGVEGEISKPSSRLKVFVIPTDEELVIARDVEALK 394
           FG  G+IS P S+++V VIPTDEELVIARDVE LK
Sbjct: 361 FGATGDISTPESKVRVLVIPTDEELVIARDVERLK 395


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: 455
Number of extensions: 15
Number of successful extensions: 2
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_018371377.1 BN415_RS06580 (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.269292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     9e-157  507.9   0.0     1e-156  507.7   0.0    1.0  1  NCBI__GCF_000341525.1:WP_018371377.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341525.1:WP_018371377.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.7   0.0    1e-156    1e-156       4     403 ..       2     394 ..       1     396 [] 0.97

  Alignments for each domain:
  == domain 1  score: 507.7 bits;  conditional E-value: 1e-156
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +k + +naGssslk++l+++ + ekv+++gl+eri l+++ i+tv+ g+kk++ +l+i dh +avk lln l 
  NCBI__GCF_000341525.1:WP_018371377.1   2 SKTIAINAGSSSLKWQLYQMPE-EKVVAKGLIERIGLKDS-ISTVKYGDKKHQLVLDILDHVQAVKILLNDLI 72 
                                           68899****************6.9999*************.999***************************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                            +  i+ + +ei+ +GHRvv Gge+f+es++v+de+l++i+++selAPlHnpa++ gi+a++  ++l++   v
  NCBI__GCF_000341525.1:WP_018371377.1  73 -ELGIISDFNEITGVGHRVVAGGESFKESTLVDDEALAEIEKLSELAPLHNPANAAGIRAFK--EILPDITSV 142
                                           .7************************************************************..8999999** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtafH+t++  +ylY++P ++y++++vR+YG+HGtsh+yv+q+aakll++pl +l+li++H+GnG s++a
  NCBI__GCF_000341525.1:WP_018371377.1 143 AVFDTAFHTTMQPATYLYPIPVKYYEDYKVRKYGAHGTSHYYVAQEAAKLLGRPLSELKLITAHIGNGVSITA 215
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlg..lsldeieetlnkksGllgisglssDlRdil 293
                                              G+s+dtsmG+tPL+G +mGtRsGdiDpaii yl ++    + ++++ ++lnk+sGllg+sg+ssD+Rdi+
  NCBI__GCF_000341525.1:WP_018371377.1 216 NYHGESVDTSMGFTPLAGPMMGTRSGDIDPAIIPYLIQQDPelKDAADVINMLNKQSGLLGVSGISSDMRDIE 288
                                           ************************************98864226789************************** PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           d  +e+n +a lA+++++ Ri+k+ig+y+a l+g  DaivFt+G+Gen + +r++v+++l  +G++ldl +n 
  NCBI__GCF_000341525.1:WP_018371377.1 289 DGLQEQNPKAVLAYNMFIDRIKKFIGQYLAVLNG-ADAIVFTAGMGENGYLMRNDVIQGLSWFGIELDLTKNV 360
                                           ********************************88.9************************************9 PP

                             TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                              +g  + ist+eskv+vlvipt+eelvia+D+ rl
  NCBI__GCF_000341525.1:WP_018371377.1 361 ---FGATGDISTPESKVRVLVIPTDEELVIARDVERL 394
                                           ...99999**************************998 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 22.23
//
[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