Alignments for a candidate for ackA in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Derxia gummosa DSM 723

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_028313010.1 H566_RS0121200 acetate/propionate family kinase

Query= BRENDA::P38502
         (408 letters)



>NCBI__GCF_000482785.1:WP_028313010.1
          Length = 408

 Score =  254 bits (648), Expect = 4e-72
 Identities = 159/400 (39%), Positives = 231/400 (57%), Gaps = 25/400 (6%)

Query: 3   VLVINAGSSSLKYQLIDMTN----ESALAVGLCERIGIDNSIITQKKFDGKKL------- 51
           +LVINAGSSS+K+ +         E A   G  E IG    ++  K   G+KL       
Sbjct: 4   ILVINAGSSSVKFAVFQTDGHDLREPAALHGQLEGIGGAPHLVA-KDAAGRKLADDALPH 62

Query: 52  EKLTDLPTHKD-ALEEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVE 110
           +    L T  D AL  ++  + + E G       I A+GHRVVHGG       + D+ V 
Sbjct: 63  DPAASLDTAYDTALAALLAWIGEHEVGFA-----IEAIGHRVVHGGPTHAAPVVVDDAVL 117

Query: 111 KAIKDCFELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYE 170
             +     LAPLH P N+  I A   I P    +  FDTAFH++ P  A  +ALP   +E
Sbjct: 118 AELDRYVPLAPLHQPHNLDAIRALGRIEPDAIQIACFDTAFHRSQPAVAQRFALPRR-FE 176

Query: 171 KHGVRKYGFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGF 230
             GVR+YGFHG S++Y+A R   +LG+ A+  ++I  HLGNG+S+ A+ G +SV ++MGF
Sbjct: 177 AAGVRRYGFHGLSYEYIAGRLPELLGERADG-RVIVAHLGNGASLCALHGRRSVASTMGF 235

Query: 231 TPLEGLAMGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEA 290
           + L+GL MGTR G+IDP ++ +L++ E + +  I  L+ K+SG+LGVSG+S D R L   
Sbjct: 236 SALDGLMMGTRTGAIDPGVLLYLLDTEKMDSARISRLLYKESGLLGVSGISADMRTL--L 293

Query: 291 ASKGNRKAELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGI 350
           AS     AE A+E+F Y++ + IG  +A L G DA+VFTAGIGE++A +R+R+      +
Sbjct: 294 ASDAPEAAE-AVELFCYRIAREIGSLAAALGGLDALVFTAGIGEHAAPVRERVSAACGWL 352

Query: 351 GIKIDDEKNKIRGQEIDISTPDAKVRVFVIPTNEELAIAR 390
           G+K+D E N     ++ +    + V V  IPT+EE+ IAR
Sbjct: 353 GVKLDAEAN--AAGQLRLDAAGSAVAVACIPTDEEVMIAR 390


Lambda     K      H
   0.316    0.135    0.380 

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: 415
Number of extensions: 24
Number of successful extensions: 6
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: 408
Length of database: 408
Length adjustment: 31
Effective length of query: 377
Effective length of database: 377
Effective search space:   142129
Effective search space used:   142129
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_028313010.1 H566_RS0121200 (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.1884983.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-110  354.0   0.0   5.8e-110  353.7   0.0    1.0  1  NCBI__GCF_000482785.1:WP_028313010.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028313010.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.7   0.0  5.8e-110  5.8e-110       5     400 ..       3     392 ..       1     397 [. 0.87

  Alignments for each domain:
  == domain 1  score: 353.7 bits;  conditional E-value: 5.8e-110
                             TIGR00016   5 kilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklai.......edheea 67 
                                            ilv+naGsss+kfa++++ +    e   l+g  e i  +   + +   g k   + l +       +++++a
  NCBI__GCF_000482785.1:WP_028313010.1   3 AILVINAGSSSVKFAVFQTDGhdlREPAALHGQLEGIGGAPHLVAKDAAGRKLADDALPHdpaasldTAYDTA 75 
                                           69****************9874444455788888988887776665555544433333221110001344455 PP

                             TIGR00016  68 vkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140
                                           +++ll  + +    ++    i++iGHRvvhGg +++  v+v+d vl+++ + ++lAPlH p +l++i+a+   
  NCBI__GCF_000482785.1:WP_028313010.1  76 LAALLAWIGE----HEVGFAIEAIGHRVVHGGPTHAAPVVVDDAVLAELDRYVPLAPLHQPHNLDAIRALG-- 142
                                           5555555553....566779**************************************************9.. PP

                             TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcH 213
                                            + ++a ++a+FDtafH+  p  a  +alP + ++  gvRrYGfHG+s++y++ r+ +ll+   +d ++iv+H
  NCBI__GCF_000482785.1:WP_028313010.1 143 RIEPDAIQIACFDTAFHRSQPAVAQRFALP-RRFEAAGVRRYGFHGLSYEYIAGRLPELLGE-RADGRVIVAH 213
                                           8889999***********************.567899************************9.7789****** PP

                             TIGR00016 214 lGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisgls 286
                                           lGnGas++a++  +s+  +mG+  L+Gl+mGtR+G iDp+++ yl +t+++  + i ++l k+sGllg+sg+s
  NCBI__GCF_000482785.1:WP_028313010.1 214 LGNGASLCALHGRRSVASTMGFSALDGLMMGTRTGAIDPGVLLYLLDTEKMDSARISRLLYKESGLLGVSGIS 286
                                           ************************************************************************* PP

                             TIGR00016 287 sDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlk 359
                                           +D+R++l+       ea+ A++++++Ria+ ig+ +a+l g lDa+vFt+GiGe aa vre+v  +   lG+k
  NCBI__GCF_000482785.1:WP_028313010.1 287 ADMRTLLASD---APEAAEAVELFCYRIAREIGSLAAALGG-LDALVFTAGIGEHAAPVRERVSAACGWLGVK 355
                                           ******9887...567999********************76.******************************* PP

                             TIGR00016 360 ldlelnnaarsgkesvisteeskvkvlviptneelviaeDa 400
                                           ld e n a +      +    s+v v+ ipt+ee++ia+ a
  NCBI__GCF_000482785.1:WP_028313010.1 356 LDAEANAAGQL----RLDAAGSAVAVACIPTDEEVMIARHA 392
                                           ******95444....4556788****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (408 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: 20.30
//
[ok]

This GapMind analysis is from Apr 09 2024. 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