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 acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_097070243.1 CRO22_RS11210 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_900217815.1:WP_097070243.1
          Length = 412

 Score =  374 bits (959), Expect = e-108
 Identities = 195/392 (49%), Positives = 269/392 (68%), Gaps = 2/392 (0%)

Query: 3   VLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERELPDHEEA 62
           +L+IN GSSS+KYQL   +  KVL  GI  +IG       H VG        E  +H +A
Sbjct: 2   ILIINCGSSSLKYQLYTPDLAKVLASGIVAKIGEPEGYAEHFVGRRGERRHSETANHHDA 61

Query: 63  LKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAPLH 122
             +++  L+  + GV++    I A+GHRVVHGG  F  SVLVD+ V++A+ + +  APLH
Sbjct: 62  FGVMMEALLSPEYGVLECPGAITAIGHRVVHGGAIFFGSVLVDDCVIQALHDCAHFAPLH 121

Query: 123 NPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHGTS 182
           NPAN++GI+ A +  PG PNVAVFDTAFHQT+P KA+LYA+P+E    + IRRYGFHGTS
Sbjct: 122 NPANIVGIEEARRAFPGAPNVAVFDTAFHQTVPPKAHLYALPFELSTAHGIRRYGFHGTS 181

Query: 183 HRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTRSG 242
            RYVS+ AAE+L + +E L ++ CH+GNG ++ A+  GK VDT++GF    G+ MGTR+G
Sbjct: 182 CRYVSQTAAELLNRPIEALSMVVCHLGNGVTLDAIDGGKSVDTTIGFGTFSGVAMGTRAG 241

Query: 243 DLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKLVL 302
           D DPAI F ++++ G+S  ++ +I  +KSG+ GLS G S+DMR+I  AA KG+  C+L L
Sbjct: 242 DFDPAIIFHLVKELGMSLDQVEEICYRKSGLLGLS-GLSNDMREICTAAEKGNTRCQLAL 300

Query: 303 EIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNEET 362
           E++ Y+I K IGAYAAAM G+DA+VFTAG+GENS   R  +C+ + FLG+++D + N   
Sbjct: 301 EVFTYQIRKTIGAYAAAMGGIDALVFTAGIGENSAEIRARICADIGFLGIEIDPRLN-AA 359

Query: 363 IRGKEGIISTPDSRVKVLVVPTNEELMIARDT 394
            RG +  IS   +RV  LVVPT+EE MIA DT
Sbjct: 360 ARGGDPNISAAGARVATLVVPTDEERMIAIDT 391


Lambda     K      H
   0.318    0.138    0.391 

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: 424
Number of extensions: 12
Number of successful extensions: 3
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: 403
Length of database: 412
Length adjustment: 31
Effective length of query: 372
Effective length of database: 381
Effective search space:   141732
Effective search space used:   141732
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_097070243.1 CRO22_RS11210 (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.880716.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-144  466.3   0.0   4.1e-144  466.2   0.0    1.0  1  NCBI__GCF_900217815.1:WP_097070243.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900217815.1:WP_097070243.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.2   0.0  4.1e-144  4.1e-144       6     404 ..       2     395 ..       1     396 [. 0.97

  Alignments for each domain:
  == domain 1  score: 466.2 bits;  conditional E-value: 4.1e-144
                             TIGR00016   6 ilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk. 77 
                                           il++n+Gssslk++l+      kvl+sg+v +i  +e        g ++e+ + ++++h+ a   ++++l + 
  NCBI__GCF_900217815.1:WP_097070243.1   2 ILIINCGSSSLKYQLYTPD-LAKVLASGIVAKIGEPEG-YAEHFVGRRGERRHSETANHHDAFGVMMEALLSp 72 
                                           9***************998.68999**********999.55678899************************99 PP

                             TIGR00016  78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150
                                           +  +l+    i++iGHRvvhGg  f  sv+v+d v+++++d +++APlHnpa++ gie++      + a+nva
  NCBI__GCF_900217815.1:WP_097070243.1  73 EYGVLECPGAITAIGHRVVHGGAIFFGSVLVDDCVIQALHDCAHFAPLHNPANIVGIEEAR--RAFPGAPNVA 143
                                           9************************************************************..6667789*** PP

                             TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                           vFDtafHqt+p +a+lYalP++l + +g+RrYGfHGts +yv+q+aa+lln+p++ l ++vcHlGnG  + a+
  NCBI__GCF_900217815.1:WP_097070243.1 144 VFDTAFHQTVPPKAHLYALPFELSTAHGIRRYGFHGTSCRYVSQTAAELLNRPIEALSMVVCHLGNGVTLDAI 216
                                           ************************************************************************* PP

                             TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296
                                             Gks+dt++G+    G++mGtR+Gd Dpaii++l ++lg+sld++ee+  +ksGllg+sgls+D+R+i  + 
  NCBI__GCF_900217815.1:WP_097070243.1 217 DGGKSVDTTIGFGTFSGVAMGTRAGDFDPAIIFHLVKELGMSLDQVEEICYRKSGLLGLSGLSNDMREICTAA 289
                                           ************************************************************************* PP

                             TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369
                                           e+gn +++lAl+v+++ i+k ig+y+a++ g +Da+vFt+GiGen+ae+r++++ ++ +lG+++d+ ln  a 
  NCBI__GCF_900217815.1:WP_097070243.1 290 EKGNTRCQLALEVFTYQIRKTIGAYAAAMGG-IDALVFTAGIGENSAEIRARICADIGFLGIEIDPRLNA-AA 360
                                           *****************************76.*************************************9.77 PP

                             TIGR00016 370 sgkesvisteeskvkvlviptneelviaeDalrla 404
                                           +g +  is   ++v  lv+pt+ee +ia D++ l+
  NCBI__GCF_900217815.1:WP_097070243.1 361 RGGDPNISAAGARVATLVVPTDEERMIAIDTVALT 395
                                           889999*************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (412 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.07
//
[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