Alignments for a candidate for ackA in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudovibrio axinellae Ad2

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_068006986.1 PsAD2_RS14055 acetate/propionate family kinase

Query= curated2:B8EIS2
         (404 letters)



>NCBI__GCF_001623255.1:WP_068006986.1
          Length = 388

 Score =  342 bits (876), Expect = 1e-98
 Identities = 178/386 (46%), Positives = 254/386 (65%), Gaps = 15/386 (3%)

Query: 7   TLNAGSSSIKFALFREGLTQEGSAKELTPMAIGLAEMVGEERRITVHDGAGAKIYEVKRT 66
           TLN GSSS+KF+L++     E           G  E +G   ++ +       I +V+R 
Sbjct: 6   TLNTGSSSVKFSLYKAHDKPEFYIS-------GSIECLGPSAKLKMQ----TPIEQVRR- 53

Query: 67  EHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTDEVLKYLHTLI 126
             +    HA A+  I +  +     + VV  GHR+VHGG  +  P  +T +V+  L  LI
Sbjct: 54  -ELGPIDHASAVPAIFSALEPFLKGSSVVGIGHRIVHGGRSFFEPTELTPKVMDELEQLI 112

Query: 127 PLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRRFYDEGVRRYG 186
           PLAPLH+PY++A I  A++ +P   Q+ CFDTAFH  H F ND FA+PR FY+EGVRRYG
Sbjct: 113 PLAPLHQPYSLATIQAAKQVFPDALQIGCFDTAFHAGHSFPNDAFAIPRHFYEEGVRRYG 172

Query: 187 FHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLPMG 246
           FHGLS++ I   +R+     A  R+V+AHLGNGASMCA+ +G S+++S GF+A+DGLPMG
Sbjct: 173 FHGLSFDAICNEMRDRYSQVANERLVIAHLGNGASMCAVNNGHSISASTGFSAVDGLPMG 232

Query: 247 TRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEAADTLEAQQAI 306
           TRCG+LDPGV+LYLMQEKK+S  EI  ++YR SGL GLSG+S DMR+LE ++   A +AI
Sbjct: 233 TRCGRLDPGVMLYLMQEKKLSPEEIETIIYRRSGLLGLSGISSDMRDLEESNDPFAIEAI 292

Query: 307 EYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGVELDRSANSAN 366
           +Y+ ++ RRE+  +AA L+GIDA++F  G+GENS  VR ++ + + ++G+ +D+  N+ N
Sbjct: 293 DYYCYQARREVATMAASLEGIDALIFSAGVGENSALVRSKICQPLAFLGITIDQKKNTVN 352

Query: 367 AEVISSERSRTRVFVIPTDEEGMIAR 392
           A  I +     RVF++ TDEE +I R
Sbjct: 353 APEIGT--GPVRVFIVATDEEQVIVR 376


Lambda     K      H
   0.322    0.137    0.404 

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: 428
Number of extensions: 22
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: 404
Length of database: 388
Length adjustment: 31
Effective length of query: 373
Effective length of database: 357
Effective search space:   133161
Effective search space used:   133161
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_068006986.1 PsAD2_RS14055 (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.2562315.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-105  337.0   0.0   7.5e-105  336.9   0.0    1.0  1  NCBI__GCF_001623255.1:WP_068006986.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_068006986.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9   0.0  7.5e-105  7.5e-105       8     401 ..       6     379 ..       1     383 [. 0.94

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 7.5e-105
                             TIGR00016   8 vlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkk 80 
                                            ln+Gsss+kf+l++a++  +  +sg +e++  + +   ++++  ++ + +l   dh++av +++++l+    
  NCBI__GCF_001623255.1:WP_068006986.1   6 TLNTGSSSVKFSLYKAHDKPEFYISGSIECLGPSAK--LKMQTPIEQVRRELGPIDHASAVPAIFSALEP--- 73 
                                           69****************98999*******997776..45667778888889999**************6... PP

                             TIGR00016  81 ilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFD 153
                                              + s++  iGHR+vhGg +f e + +t +v+++++++++lAPlH p  l +i+a++  +v ++a ++ +FD
  NCBI__GCF_001623255.1:WP_068006986.1  74 -FLKGSSVVGIGHRIVHGGRSFFEPTELTPKVMDELEQLIPLAPLHQPYSLATIQAAK--QVFPDALQIGCFD 143
                                           .55678999*************************************************..7788899****** PP

                             TIGR00016 154 tafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknG 226
                                           tafH     ++  +a+P+++y+e gvRrYGfHG+s+  + +++ +   + +++ +l+++HlGnGas++av+nG
  NCBI__GCF_001623255.1:WP_068006986.1 144 TAFHAGHSFPNDAFAIPRHFYEE-GVRRYGFHGLSFDAICNEMRDRYSQ-VANERLVIAHLGNGASMCAVNNG 214
                                           ******999999*****998865.9*********************999.9999******************* PP

                             TIGR00016 227 ksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeeg 299
                                           +si  s G+  ++Gl mGtR+G +Dp+++ yl+++++ls +eie+++ ++sGllg+sg+ssD+Rd+++     
  NCBI__GCF_001623255.1:WP_068006986.1 215 HSISASTGFSAVDGLPMGTRCGRLDPGVMLYLMQEKKLSPEEIETIIYRRSGLLGLSGISSDMRDLEESN--- 284
                                           ******************************************************************9988... PP

                             TIGR00016 300 neeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgk 372
                                           +  a  A++ y++  ++ +++++asleg +Da++F +G+Gen+a vr ++++ l++lG+ +d+++n+     +
  NCBI__GCF_001623255.1:WP_068006986.1 285 DPFAIEAIDYYCYQARREVATMAASLEG-IDALIFSAGVGENSALVRSKICQPLAFLGITIDQKKNT----VN 352
                                           566899********************99.*************************************9....45 PP

                             TIGR00016 373 esvisteeskvkvlviptneelviaeDal 401
                                              i    + v+v+++ t+ee vi++ ++
  NCBI__GCF_001623255.1:WP_068006986.1 353 APEIG--TGPVRVFIVATDEEQVIVRAVA 379
                                           55666..689***************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (388 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: 00:00:00.01
# Mc/sec: 10.99
//
[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 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