Alignments for a candidate for fadA in Geobacter metallireducens GS-15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Geobacter metallireducens GS-15

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_004513384.1 GMET_RS08650 acetyl-CoA C-acyltransferase

Query= reanno::MR1:200842
         (396 letters)



>NCBI__GCF_000012925.1:WP_004513384.1
          Length = 391

 Score =  395 bits (1016), Expect = e-115
 Identities = 204/388 (52%), Positives = 264/388 (68%)

Query: 8   QEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGL 67
           Q++ +V A RTP GSF G L+ + +  LAAT +K LLA   +APD V+EV++G VL  G 
Sbjct: 2   QDVFVVDALRTPFGSFSGMLADVEAPKLAATVMKELLAKAGLAPDTVNEVIVGQVLSGGC 61

Query: 68  GQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQA 127
           GQAPARQA  GAG+P S  A T+NKVCGSG+K +ML  D I+ G +++VIAGGME+MS A
Sbjct: 62  GQAPARQAMRGAGIPDSAHALTINKVCGSGLKAIMLGADSIRLGESQIVIAGGMENMSLA 121

Query: 128 PYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALS 187
           P+ L KARAG RMGH ++LD +  DGL+D YTG  MG   + +A+  G+TR++ DAFA  
Sbjct: 122 PFFLKKARAGYRMGHSELLDLLIYDGLQDPYTGRHMGEIGEVSAERGGLTRKEQDAFARR 181

Query: 188 SLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTIT 247
           S E A AA+  G F  EIVPV    ++GD TI TDE+P    P K+P+LR AF KDGTIT
Sbjct: 182 SYELAQAAVTGGIFADEIVPVVKKGKKGDETIGTDEEPFKGDPSKLPSLRAAFKKDGTIT 241

Query: 248 AANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSN 307
           A N+S+I+DGAA  +LT     ++  LT  A I    T ++ P  F  AP+GA+ K  + 
Sbjct: 242 AGNASTINDGAALALLTDADGLKKHNLTPKARIVASATESRHPDNFPEAPIGAIEKACAK 301

Query: 308 VGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLI 367
            G +  ++DLFEINEAFA V +LA+  LGL + KVNVNGGACA+GHPIG SG RL  T+I
Sbjct: 302 AGLTVSDIDLFEINEAFASVALLAIKGLGLPLDKVNVNGGACAIGHPIGASGGRLAATVI 361

Query: 368 HALKARGLKRGVASLCIGGGEATAMAIE 395
             L  R  + G+A+LCIGGGEA A+  E
Sbjct: 362 RELHRRQKRYGLATLCIGGGEAVAVIFE 389


Lambda     K      H
   0.316    0.131    0.364 

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: 480
Number of extensions: 16
Number of successful extensions: 1
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: 396
Length of database: 391
Length adjustment: 31
Effective length of query: 365
Effective length of database: 360
Effective search space:   131400
Effective search space used:   131400
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_004513384.1 GMET_RS08650 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.4109.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-131  423.3   0.5   4.7e-131  423.2   0.5    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004513384.1  GMET_RS08650 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004513384.1  GMET_RS08650 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.2   0.5  4.7e-131  4.7e-131       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 423.2 bits;  conditional E-value: 4.7e-131
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               +vda+Rtp+g++ g l++++a +L+a+v+kell++agl p+ ++evi+G+vl+ g+++++aR+a+  ag
  lcl|NCBI__GCF_000012925.1:WP_004513384.1   6 VVDALRTPFGSFSGMLADVEAPKLAATVMKELLAKAGLAPDTVNEVIVGQVLSGGCGQAPARQAMRGAG 74 
                                               79******************************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p+s  alt+n+vC+Sgl+A++l+a++i+ Ge ++v+aGG+E+mS +p++lk++  r+++++g+++l d
  lcl|NCBI__GCF_000012925.1:WP_004513384.1  75 IPDSAHALTINKVCGSGLKAIMLGADSIRLGESQIVIAGGMENMSLAPFFLKKA--RAGYRMGHSELLD 141
                                               ****************************************************98..89*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                                l++d+   ++t+ +mge  e  a++ g++R+eqD++a rS++ a++A+  g f+deivpv+ kgk  +
  lcl|NCBI__GCF_000012925.1:WP_004513384.1 142 LLIYDGlqdPYTGRHMGEIGEVSAERGGLTRKEQDAFARRSYELAQAAVTGGIFADEIVPVVKKGKkgD 210
                                               *********99**************************************************99999999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               +++ +De++  +    kL +L++afk+ +g t+tAgN+s +nDGAa++ll+  + +k+++ltp+ariv+
  lcl|NCBI__GCF_000012925.1:WP_004513384.1 211 ETIGTDEEPF-KGDPSKLPSLRAAFKK-DG-TITAGNASTINDGAALALLTDADGLKKHNLTPKARIVA 276
                                               999***9998.56789*********95.9*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                                a+ + +p++++ +p+ Aieka +kagl++sdidl+EinEAFA+++l+++k lg l l+kvNvnGGA A
  lcl|NCBI__GCF_000012925.1:WP_004513384.1 277 SATESRHPDNFPEAPIGAIEKACAKAGLTVSDIDLFEINEAFASVALLAIKGLG-LPLDKVNVNGGACA 344
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasG+r+ +t+++eL++r+k+yGlatlC+ggG ++Avi+e
  lcl|NCBI__GCF_000012925.1:WP_004513384.1 345 IGHPIGASGGRLAATVIRELHRRQKRYGLATLCIGGGEAVAVIFE 389
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.89
//
[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