Alignments for a candidate for ackA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudomonas stutzeri RCH2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF3154 Psest_3213 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__psRCH2:GFF3154
          Length = 395

 Score =  384 bits (987), Expect = e-111
 Identities = 204/401 (50%), Positives = 269/401 (67%), Gaps = 7/401 (1%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS + +LV+NCGSSS+KFA+++       + GLAEC G  ++ I ++   GK   K+   
Sbjct: 1   MSARNILVINCGSSSIKFALVNEAQATFPLQGLAECIGSPEAVIHFESAAGKESVKVPN- 59

Query: 61  TAHREAVEFFIVNNILAEHPELAA-QIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCAS 119
             H+ A+       IL    E A   +  IGHR+VHGGEKF  S ++  E + GIE    
Sbjct: 60  ADHQAALA-----QILPRVEEAAGGHLDGIGHRVVHGGEKFFASSLLNDETLAGIEANIQ 114

Query: 120 LAPLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYG 179
           LAPLHNPA+L GI AAI  FP+LPQV VFDTAFHQTMPE AY YA+P  LY+EH +RRYG
Sbjct: 115 LAPLHNPANLSGIHAAINLFPELPQVGVFDTAFHQTMPEHAYRYAVPDVLYKEHGVRRYG 174

Query: 180 MHGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVM 239
            HGTSH +V + AA++ G  V++ + + AHLGNG S  A+  G+S DTSMGLTPLEGLVM
Sbjct: 175 FHGTSHRFVSKRAAEMAGVPVENSSWLVAHLGNGCSTCAVVNGESRDTSMGLTPLEGLVM 234

Query: 240 GTRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGA 299
           GTR GD+DPS+   L K LG+ L +++N+LNK+SGL G+S L+ND R + +  + GH GA
Sbjct: 235 GTRSGDVDPSLHNFLNKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLADARNAGHPGA 294

Query: 300 TLALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDIL 359
            LA D+FCYRLAK +A+ +  L +LD ++FTGGIGENS+ +RE+ L  L++F FK+D   
Sbjct: 295 VLAFDVFCYRLAKSLAAMSCALPQLDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEA 354

Query: 360 NKAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400
           N     G  G I  AG+P  MV+PTNEE  IA D + L+ A
Sbjct: 355 NARCTRGVAGEIQAAGSPRIMVVPTNEERQIALDTLALLDA 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: 487
Number of extensions: 19
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 GFF3154 Psest_3213 (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.7681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-143  464.9   0.0   1.1e-143  464.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3154  Psest_3213 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3154  Psest_3213 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.7   0.0  1.1e-143  1.1e-143       2     403 ..       2     392 ..       1     394 [. 0.95

  Alignments for each domain:
  == domain 1  score: 464.7 bits;  conditional E-value: 1.1e-143
                           TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                         + + ilv+n+Gsss+kfal++ ++  +  l+gl+e+i ++ea+i   e++  ke+ k+  +dh++a++++l +++
  lcl|FitnessBrowser__psRCH2:GFF3154   2 SARNILVINCGSSSIKFALVNEAQ-ATFPLQGLAECIGSPEAVIH-FESAAGKESVKVPNADHQAALAQILPRVE 74 
                                         5678******************96.55669************666.6777788999999**************** PP

                           TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvav 151
                                         +         +++ iGHRvvhGgekf  s +++de+l++i+  ++lAPlHnpa+l+gi+a+   +  ++ ++v v
  lcl|FitnessBrowser__psRCH2:GFF3154  75 E-----AAGGHLDGIGHRVVHGGEKFFASSLLNDETLAGIEANIQLAPLHNPANLSGIHAAI--NLFPELPQVGV 142
                                         5.....67899***************************************************..6667788**** PP

                           TIGR00016 152 FDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknG 226
                                         FDtafHqt+pe+ay Ya+P  lyke+gvRrYGfHGtsh++v++raa++ + p++++  +v+HlGnG s +av nG
  lcl|FitnessBrowser__psRCH2:GFF3154 143 FDTAFHQTMPEHAYRYAVPDVLYKEHGVRRYGFHGTSHRFVSKRAAEMAGVPVENSSWLVAHLGNGCSTCAVVNG 217
                                         *************************************************************************** PP

                           TIGR00016 227 ksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegne 301
                                         +s dtsmGltPLeGlvmGtRsGd+Dp++ ++l++tlg  l++i ++lnk+sGl g+sgls+D+R++ d+ ++g+ 
  lcl|FitnessBrowser__psRCH2:GFF3154 218 ESRDTSMGLTPLEGLVMGTRSGDVDPSLHNFLNKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLADARNAGHP 292
                                         *************************************************************************** PP

                           TIGR00016 302 eaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvi 376
                                          a lA++v+++R+ak ++++  +l + lD++vFtgGiGen++ vre++le+l+++G+kld e n ++++g  + i
  lcl|FitnessBrowser__psRCH2:GFF3154 293 GAVLAFDVFCYRLAKSLAAMSCALPQ-LDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEANARCTRGVAGEI 366
                                         ************************66.************************************************ PP

                           TIGR00016 377 steeskvkvlviptneelviaeDalrl 403
                                             s  +++v+ptnee  ia D+l l
  lcl|FitnessBrowser__psRCH2:GFF3154 367 QAAGS-PRIMVVPTNEERQIALDTLAL 392
                                         96655.689**************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: 00:00:00.02
# Mc/sec: 7.61
//
[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