Alignments for a candidate for ackA in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Psychromonas ingrahamii 37

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011771022.1 PING_RS14235 acetate kinase

Query= BRENDA::P63411
         (400 letters)



>NCBI__GCF_000015285.1:WP_011771022.1
          Length = 402

 Score =  563 bits (1452), Expect = e-165
 Identities = 283/403 (70%), Positives = 330/403 (81%), Gaps = 5/403 (1%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60
           MS+KL+LVLNCGSSSLKFAIID   G+E LSGLAEC HL +AR+KWK++G+K  A LG G
Sbjct: 1   MSNKLILVLNCGSSSLKFAIIDMSTGEEKLSGLAECLHLDDARMKWKLEGAKGSADLGIG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120
           AAH EALN+IVN IL+ +PEL   L AIGHRIVHGGEK+T SVVI + VIQGI+D  S A
Sbjct: 61  AAHEEALNYIVNEILSNQPELKENLFAIGHRIVHGGEKFTQSVVITDQVIQGIEDCVSLA 120

Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180
           PLHNPAHL+GI  A  +F  L   NVAVFDTAFHQTMPEE++LYALPY LY+E G+RRYG
Sbjct: 121 PLHNPAHLVGIRAAQHAFAGLP--NVAVFDTAFHQTMPEEAFLYALPYKLYREKGIRRYG 178

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
            HGTSH Y++ EAA +LNKPVEELNII CHLGNGGSV AI+NGK VDTSMG+TPLEGLVM
Sbjct: 179 MHGTSHLYISLEAAGILNKPVEELNIINCHLGNGGSVCAIKNGKSVDTSMGMTPLEGLVM 238

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTR GDIDPA+IFHL+D LG S+ +IN MLTKESGLLGLTE TSDCR+VEDNY T   AK
Sbjct: 239 GTRCGDIDPAVIFHLYDELGYSMAEINTMLTKESGLLGLTEKTSDCRFVEDNYDTDPAAK 298

Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RAMD+YC+RLAKYI SYTA +DGRLDAVVFTGGIGEN+A +REL+L +L +LGF+V+ + 
Sbjct: 299 RAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRELTLARLSLLGFKVNQQE 358

Query: 361 NLAARFGKS---GFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLA RFGKS   G I + G+  A+VI TNEE +IA+D   L +
Sbjct: 359 NLANRFGKSSNQGIITEPGSTVAMVIQTNEEWIIARDTLALVS 401


Lambda     K      H
   0.318    0.134    0.384 

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: 506
Number of extensions: 10
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: 400
Length of database: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
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_011771022.1 PING_RS14235 (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.3606148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-171  556.5   0.0   1.7e-171  556.3   0.0    1.0  1  NCBI__GCF_000015285.1:WP_011771022.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015285.1:WP_011771022.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.3   0.0  1.7e-171  1.7e-171       2     404 ..       2     400 ..       1     401 [. 0.95

  Alignments for each domain:
  == domain 1  score: 556.3 bits;  conditional E-value: 1.7e-171
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                           ++k+ilvln+Gssslkfa++d++++e++ lsgl+e+++l++ar+k++ +g k++++    ++heea++ ++n+
  NCBI__GCF_000015285.1:WP_011771022.1   2 SNKLILVLNCGSSSLKFAIIDMSTGEEK-LSGLAECLHLDDARMKWKLEGAKGSADLGIGAAHEEALNYIVNE 73 
                                           6799************************.9******************************************* PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           + +++   ++++++ +iGHR+vhGgekft+sv++td+v+++i+d ++lAPlHnpa+l gi+a+++       +
  NCBI__GCF_000015285.1:WP_011771022.1  74 ILSNQ--PELKENLFAIGHRIVHGGEKFTQSVVITDQVIQGIEDCVSLAPLHNPAHLVGIRAAQH--AFAGLP 142
                                           **755..999******************************************************5..555667 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           nvavFDtafHqt+peea+lYalPy+ly+e+g+RrYG+HGtsh y++ +aa +lnkp+++ln+i cHlGnG+sv
  NCBI__GCF_000015285.1:WP_011771022.1 143 NVAVFDTAFHQTMPEEAFLYALPYKLYREKGIRRYGMHGTSHLYISLEAAGILNKPVEELNIINCHLGNGGSV 215
                                           ************************************************************************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a+knGks+dtsmG+tPLeGlvmGtR+GdiDpa+i++l+++lg s++ei+++l+k+sGllg+++++sD+R ++
  NCBI__GCF_000015285.1:WP_011771022.1 216 CAIKNGKSVDTSMGMTPLEGLVMGTRCGDIDPAVIFHLYDELGYSMAEINTMLTKESGLLGLTEKTSDCRFVE 288
                                           ************************************************************************* PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           d++ +++  ak+A+++y++R+akyi++y+a+l+g+lDa+vFtgGiGen+a +rel+l +l +lG+k++++ n 
  NCBI__GCF_000015285.1:WP_011771022.1 289 DNY-DTDPAAKRAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRELTLARLSLLGFKVNQQENL 360
                                           ***.8999****************************************************************9 PP

                             TIGR00016 367 aarsgkes...visteeskvkvlviptneelviaeDalrla 404
                                           a r+gk+s   +i+ e +++ ++vi+tnee++ia+D+l l+
  NCBI__GCF_000015285.1:WP_011771022.1 361 ANRFGKSSnqgIIT-EPGSTVAMVIQTNEEWIIARDTLALV 400
                                           98777654221566.555566899************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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: 27.45
//
[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