Alignments for a candidate for ackA in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudomonas stutzeri A1501

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011912310.1 PST_RS05740 propionate/acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_000013785.1:WP_011912310.1
          Length = 395

 Score =  382 bits (980), Expect = e-110
 Identities = 200/400 (50%), Positives = 264/400 (66%), Gaps = 5/400 (1%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS + +LV+NCGSSS+KFA+++       + GLAEC G  ++ I ++   GK   K+   
Sbjct: 1   MSARNILVINCGSSSIKFALVNEAQATFPLQGLAECIGSPEAVIHFESAAGKESVKVP-- 58

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
            A  +A    I+  +          +  IGHR+VHGGEKF  S ++  E + GIE    L
Sbjct: 59  NADHQAALAQILPRV---EDAAGGHLDGIGHRVVHGGEKFFASTLLNDETLAGIEANIQL 115

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPA+L GI AAI  FP+LPQV VFDTAFHQTMPE AY YA+P  LY++H +RRYG 
Sbjct: 116 APLHNPANLSGIHAAINLFPELPQVGVFDTAFHQTMPEHAYRYAVPDVLYKDHGVRRYGF 175

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH YV + AA++ G  V + + + AHLGNG S  A+  G+S DTSMGLTPLEGLVMG
Sbjct: 176 HGTSHRYVSKRAAELAGVPVDNSSWLVAHLGNGCSTCAVVNGESRDTSMGLTPLEGLVMG 235

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TR GD+DPS+   L K LG+ L +++N+LNK+SGL G+S L+ND R + E    GH GA 
Sbjct: 236 TRSGDVDPSLHNFLHKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLAEARQAGHPGAV 295

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LA ++FCYRLAK +A+ +  L +LD ++FTGGIGENS+ +RE+ L  L++F FK+D   N
Sbjct: 296 LAFEVFCYRLAKSLAAMSCALPQLDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEAN 355

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400
                G  G I   G+P  MV+PTNEE  IA D + L+ A
Sbjct: 356 ARCTRGVAGEIQAQGSPRVMVVPTNEERQIALDTLALLDA 395


Lambda     K      H
   0.321    0.139    0.409 

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: 499
Number of extensions: 21
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: 401
Length of database: 395
Length adjustment: 31
Effective length of query: 370
Effective length of database: 364
Effective search space:   134680
Effective search space used:   134680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_011912310.1 PST_RS05740 (propionate/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.28379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-144  468.0   0.0   1.3e-144  467.8   0.0    1.0  1  lcl|NCBI__GCF_000013785.1:WP_011912310.1  PST_RS05740 propionate/acetate k


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011912310.1  PST_RS05740 propionate/acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.8   0.0  1.3e-144  1.3e-144       2     403 ..       2     392 ..       1     394 [. 0.96

  Alignments for each domain:
  == domain 1  score: 467.8 bits;  conditional E-value: 1.3e-144
                                 TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkk 70 
                                               + + ilv+n+Gsss+kfal++ ++  +  l+gl+e+i ++ea+i   e++  ke+ k+  +dh++a+++
  lcl|NCBI__GCF_000013785.1:WP_011912310.1   2 SARNILVINCGSSSIKFALVNEAQ-ATFPLQGLAECIGSPEAVIH-FESAAGKESVKVPNADHQAALAQ 68 
                                               5678******************96.55669************666.6777788999999********** PP

                                 TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlk 139
                                               +l ++++         +++ iGHRvvhGgekf  s++++de+l++i+  ++lAPlHnpa+l+gi+a+  
  lcl|NCBI__GCF_000013785.1:WP_011912310.1  69 ILPRVED-----AAGGHLDGIGHRVVHGGEKFFASTLLNDETLAGIEANIQLAPLHNPANLSGIHAAI- 131
                                               ******4.....67899***************************************************. PP

                                 TIGR00016 140 lkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddln 208
                                                +  ++ ++v vFDtafHqt+pe+ay Ya+P  lyk++gvRrYGfHGtsh+yv++raa+l + p+d++ 
  lcl|NCBI__GCF_000013785.1:WP_011912310.1 132 -NLFPELPQVGVFDTAFHQTMPEHAYRYAVPDVLYKDHGVRRYGFHGTSHRYVSKRAAELAGVPVDNSS 199
                                               .6667788************************************************************* PP

                                 TIGR00016 209 livcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkks 277
                                                +v+HlGnG s +av nG+s dtsmGltPLeGlvmGtRsGd+Dp++ ++l++tlg  l++i ++lnk+s
  lcl|NCBI__GCF_000013785.1:WP_011912310.1 200 WLVAHLGNGCSTCAVVNGESRDTSMGLTPLEGLVMGTRSGDVDPSLHNFLHKTLGWDLAKIDNMLNKES 268
                                               ********************************************************************* PP

                                 TIGR00016 278 GllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevr 346
                                               Gl g+sgls+D+R++ ++ ++g+  a lA++v+++R+ak ++++  +l + lD++vFtgGiGen++ vr
  lcl|NCBI__GCF_000013785.1:WP_011912310.1 269 GLKGLSGLSNDMRTLAEARQAGHPGAVLAFEVFCYRLAKSLAAMSCALPQ-LDGLVFTGGIGENSSAVR 336
                                               ************************************************66.****************** PP

                                 TIGR00016 347 elvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                               e++le+l+++G+kld e n ++++g  + i   +++ +v+v+ptnee  ia D+l l
  lcl|NCBI__GCF_000013785.1:WP_011912310.1 337 ERTLEHLKLFGFKLDAEANARCTRGVAGEIQA-QGSPRVMVVPTNEERQIALDTLAL 392
                                               ******************************95.566689**************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (395 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[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