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.4161943.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.44
//
[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:

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:

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:

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:

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