Alignments for a candidate for ackA in Rhodobacter maris JA276

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Rhodobacter maris JA276

Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_097070675.1 CRO22_RS13420 acetate/propionate family kinase

Query= SwissProt::P11868
         (402 letters)



>NCBI__GCF_900217815.1:WP_097070675.1
          Length = 389

 Score =  247 bits (631), Expect = 4e-70
 Identities = 157/393 (39%), Positives = 225/393 (57%), Gaps = 30/393 (7%)

Query: 7   VLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSYEG---- 62
           +L +N GSSS+K  + D S    L +   D + +  A L +   E   L    +      
Sbjct: 5   ILTLNAGSSSLKLGLFDES-LAPLATAHVDRLGAPEASLKLTDAEGRKLPSEGFSADDFA 63

Query: 63  ----ALKAI--AFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAP 116
               AL++   AF  +   L   +  IGHRI HGG    E   +T+ ++D++ R++P AP
Sbjct: 64  THTLALRSALSAFRADLPGLE--ITGIGHRIVHGGIQHAEPEPVTEVLMDHLERLTPFAP 121

Query: 117 LHNYANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHG 176
           LH   NL+G+ +A + FPGV  +A FDT+FH+        Y LP  YYE+ GVRRYGFHG
Sbjct: 122 LHQPHNLAGVRAAIEAFPGVANIACFDTAFHRGHPFVEDTYALPRSYYEK-GVRRYGFHG 180

Query: 177 TSHRYVSQRAHSLLNLAEDD---SGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMM 233
            S+ Y+      +L   E +     +VVAHLG+GASICA+RNGQS+  +MG + L GL M
Sbjct: 181 LSYAYID----GVLAAEEPELRAGRVVVAHLGSGASICAIRNGQSIACTMGFSTLSGLPM 236

Query: 234 GTRSGDVDFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERA 293
           GTR+G++D G + ++  Q      ++  ++ K SGL G+SG+S+D+R L  A  E H R 
Sbjct: 237 GTRAGELDAGVVLYLMDQEKMDAAEITELLFKRSGLWGMSGVSNDMRTL-VASKEPHARE 295

Query: 294 QLAIKTFVHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEM 353
             AI  F HR++R IA   A++  LD +IF GG+GENS+L+R  V   L   G+EID+E 
Sbjct: 296 --AIDYFCHRVSREIASLGAAMGGLDALIFCGGVGENSALVREDVCATLGWAGVEIDSE- 352

Query: 354 NNRSNSCGERIVSSENARVICAVIPTNEEKMIA 386
              +N+   R +S+   RV   VIPTNEE +IA
Sbjct: 353 ---ANAAHAREIST--GRVAVRVIPTNEEIVIA 380


Lambda     K      H
   0.318    0.134    0.386 

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: 399
Number of extensions: 16
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: 402
Length of database: 389
Length adjustment: 31
Effective length of query: 371
Effective length of database: 358
Effective search space:   132818
Effective search space used:   132818
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_097070675.1 CRO22_RS13420 (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.3436150.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-106  340.6   0.0   6.1e-106  340.4   0.0    1.0  1  NCBI__GCF_900217815.1:WP_097070675.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900217815.1:WP_097070675.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.4   0.0  6.1e-106  6.1e-106       4     400 ..       3     383 ..       1     388 [. 0.90

  Alignments for each domain:
  == domain 1  score: 340.4 bits;  conditional E-value: 6.1e-106
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeek....laiedheeavkkll 72 
                                           + il lnaGssslk  l+d +     l+ + v+r+  +ea +k    +++k   +     +++ h+ a++  l
  NCBI__GCF_900217815.1:WP_097070675.1   3 RAILTLNAGSSSLKLGLFDES--LAPLATAHVDRLGAPEASLKLTDAEGRKLPSEgfsaDDFATHTLALRSAL 73 
                                           679****************99..56789************988776555555443111145566667777766 PP

                             TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145
                                           +++ +    +    ei+ iGHR+vhGg +++e   vt+  ++++++++++APlH p +l g++a+ +++  + 
  NCBI__GCF_900217815.1:WP_097070675.1  74 SAFRA----DLPGLEITGIGHRIVHGGIQHAEPEPVTEVLMDHLERLTPFAPLHQPHNLAGVRAAIEAF--PG 140
                                           66665....456779***************************************************555..55 PP

                             TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218
                                           + n+a+FDtafH+  p     YalP+s+y+ +gvRrYGfHG+s+ y+   +a     +l   +++v+HlG Ga
  NCBI__GCF_900217815.1:WP_097070675.1 141 VANIACFDTAFHRGHPFVEDTYALPRSYYE-KGVRRYGFHGLSYAYIDGVLAAEEP-ELRAGRVVVAHLGSGA 211
                                           66***********************99886.69**************998887654.48999*********** PP

                             TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291
                                           s++a++nG+si  +mG+  L Gl mGtR+G++D +++ yl++++++ ++ei+e+l k+sGl g+sg+s+D+R+
  NCBI__GCF_900217815.1:WP_097070675.1 212 SICAIRNGQSIACTMGFSTLSGLPMGTRAGELDAGVVLYLMDQEKMDAAEITELLFKRSGLWGMSGVSNDMRT 284
                                           ************************************************************************* PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           +++ k   + +a+ A++ ++hR+ + i++  a++ g lDa++F gG+Gen+a vre+v+ +l   G+++d+e 
  NCBI__GCF_900217815.1:WP_097070675.1 285 LVASK---EPHAREAIDYFCHRVSREIASLGAAMGG-LDALIFCGGVGENSALVREDVCATLGWAGVEIDSEA 353
                                           **998...5569**********************76.************************************ PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDa 400
                                           n      + + is   ++v v viptnee+via+ a
  NCBI__GCF_900217815.1:WP_097070675.1 354 NA----AHAREIS--TGRVAVRVIPTNEEIVIARAA 383
                                           99....6677898..6899999**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (389 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: 25.36
//
[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