Alignments for a candidate for ackA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Marinobacter adhaerens HP15

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF1535 HP15_1499 acetate/propionate kinase

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__Marino:GFF1535
          Length = 398

 Score =  349 bits (896), Expect = e-101
 Identities = 189/393 (48%), Positives = 255/393 (64%), Gaps = 7/393 (1%)

Query: 6   VLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAFTAHRE 65
           VLV+NCGSSSLK A+ + Q     +S LAE  G  D+      +G +    L A   H +
Sbjct: 5   VLVVNCGSSSLKLALFNNQHRK-LVSALAERLGQSDAFAH--IDGQEGTIPLDAGAGHDQ 61

Query: 66  AVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASLAPLHN 125
           A+E  +      +   +     AIGHR+VHGGE F  +V+I  +V++ IE CA LAPLHN
Sbjct: 62  ALETLVT--AFRDLGLMTTAPSAIGHRVVHGGETFHEAVLIDGDVLKAIESCAGLAPLHN 119

Query: 126 PAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGMHGTSH 185
           P +L GIRA +A FP +PQ  VFDTAFHQT+P +A++YALP   YR+  IRRYG HGTSH
Sbjct: 120 PVNLSGIRATLAQFPDVPQTAVFDTAFHQTLPRRAFLYALPEAWYRDWGIRRYGFHGTSH 179

Query: 186 FYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMGTRCGD 245
            ++  EAA++LGK     +VI AHLGNG S+ AI+ G SVDTSMGLTPLEGLVMGTR GD
Sbjct: 180 AFMASEAARLLGKTPATTSVISAHLGNGCSITAIRDGISVDTSMGLTPLEGLVMGTRSGD 239

Query: 246 LDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGATLALDI 305
           +DP  +F  ++  G   DEV+ +LN++SGLLG+S  TND R + E    GH+ +  A+D+
Sbjct: 240 VDPG-LFDFLRSKGIAADEVHRVLNQESGLLGLSGQTNDMRSLCELADHGHEPSQTAIDV 298

Query: 306 FCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN-KAAR 364
           FC+RLA+Y+ +    L +LDA++FTGGIGENS  IRE+ +  L++  F++   LN    +
Sbjct: 299 FCFRLARYVGAMMASLSQLDALVFTGGIGENSPRIREETIRHLKLTGFELSQDLNIHHGQ 358

Query: 365 FGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKL 397
           F    + +       +VIPTNEE VIA +A +L
Sbjct: 359 FSDGHIESPDSRFPVLVIPTNEELVIAREATRL 391


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: 425
Number of extensions: 20
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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 GFF1535 HP15_1499 (acetate/propionate 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.6641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-143  464.4   0.0   1.6e-143  464.2   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1535  HP15_1499 acetate/propionate kin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1535  HP15_1499 acetate/propionate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.2   0.0  1.6e-143  1.6e-143       4     404 ..       3     392 ..       1     393 [. 0.97

  Alignments for each domain:
  == domain 1  score: 464.2 bits;  conditional E-value: 1.6e-143
                           TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 
                                           +lv+n+Gssslk al++++  +++l+s+l+er+  ++a  +   dg++++    a + h++a+++l++++  d
  lcl|FitnessBrowser__Marino:GFF1535   3 DTVLVVNCGSSSLKLALFNNQ--HRKLVSALAERLGQSDA--FAHIDGQEGTIPLDAGAGHDQALETLVTAFR-D 72 
                                         679****************99..68889********9999..677999999999******************9.6 PP

                           TIGR00016  79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFD 153
                                           ++++    ++iGHRvvhGge+f e+v+++ +vlk+i+  + lAPlHnp +l+gi+a l   + +++++ avFD
  lcl|FitnessBrowser__Marino:GFF1535  73 LGLMTTAP--SAIGHRVVHGGETFHEAVLIDGDVLKAIESCAGLAPLHNPVNLSGIRATL--AQFPDVPQTAVFD 143
                                         77776655..69**********************************************99..888999******* PP

                           TIGR00016 154 tafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGks 228
                                         tafHqt+p++a+lYalP+ +y++ g+RrYGfHGtsh +++ +aa+ll+k+ +   +i++HlGnG s++a+++G s
  lcl|FitnessBrowser__Marino:GFF1535 144 TAFHQTLPRRAFLYALPEAWYRDWGIRRYGFHGTSHAFMASEAARLLGKTPATTSVISAHLGNGCSITAIRDGIS 218
                                         *************************************************************************** PP

                           TIGR00016 229 idtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneea 303
                                         +dtsmGltPLeGlvmGtRsGd+Dp++  +l + +g ++de++++ln++sGllg+sg ++D+R + +  ++g+e +
  lcl|FitnessBrowser__Marino:GFF1535 219 VDTSMGLTPLEGLVMGTRSGDVDPGLFDFLRS-KGIAADEVHRVLNQESGLLGLSGQTNDMRSLCELADHGHEPS 292
                                         *****************************986.699*************************************** PP

                           TIGR00016 304 klAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvist 378
                                         ++A++v++ R+a+y+g+++asl++ lDa+vFtgGiGen+  +re+++++l++ G++l ++ln +  + +++ i +
  lcl|FitnessBrowser__Marino:GFF1535 293 QTAIDVFCFRLARYVGAMMASLSQ-LDALVFTGGIGENSPRIREETIRHLKLTGFELSQDLNIHHGQFSDGHIES 366
                                         **********************77.**************************************999********* PP

                           TIGR00016 379 eeskvkvlviptneelviaeDalrla 404
                                         ++s++ vlviptneelvia++a+rla
  lcl|FitnessBrowser__Marino:GFF1535 367 PDSRFPVLVIPTNEELVIAREATRLA 392
                                         **********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (398 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: 00:00:00.02
# Mc/sec: 6.91
//
[ok]

This GapMind analysis is from Sep 17 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