Alignments for a candidate for fadA in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Streptacidiphilus oryzae TH49

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_037573406.1 BS73_RS16990 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000744815.1:WP_037573406.1
          Length = 406

 Score =  300 bits (767), Expect = 6e-86
 Identities = 183/411 (44%), Positives = 255/411 (62%), Gaps = 27/411 (6%)

Query: 1   MKEVVIASAVRTAIG-SYGKSLKDVPAVDLGATAIKEAVKKAG-IKPEDVNEVILGNVLQ 58
           M E VI SA R+ IG ++  SLKDV   DL A  IK A+ K   + P  +++++LG  L 
Sbjct: 1   MPEAVIVSAARSPIGRAFKGSLKDVRPDDLSAQIIKAALDKVPELDPTQIDDLMLGCGLP 60

Query: 59  AG-LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMEN 117
            G  G N AR  + + G+   +P  TI + C S L+T  +A   IKAG+ DV I+ G+E 
Sbjct: 61  GGEQGHNLARVIAVQMGMD-HLPGATITRYCSSSLQTSRMALHAIKAGEGDVFISAGVEC 119

Query: 118 MSRAPYLANNARWGYRMGNAKFVDEMI------TDGLWDAFNDYH-----------MGIT 160
           +SR    +++   G    N  F D          +G  DA++D             MG T
Sbjct: 120 VSRQVNGSSDGMPGTH--NPVFADAEARTQARSAEGA-DAWHDPRQDGQVPDVYIAMGQT 176

Query: 161 AENIAERWNISREEQDEFALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPR 220
           AEN+A+   I+R+E DEF + SQ  AE+AI  G +  EI PV +      TVV  D+ PR
Sbjct: 177 AENLAQLKGITRQEMDEFGVRSQNLAEKAIADGFWAREITPVTLPDG---TVVGKDDGPR 233

Query: 221 FGSTIEGLAKLKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGS 280
            G T+EG++ LKP F+ DGTVTAGN   LND AA LVIMS  KA+ELG+ PLA+IVS G 
Sbjct: 234 AGVTLEGVSGLKPVFRPDGTVTAGNCCPLNDGAAALVIMSDTKARELGLTPLARIVSTGV 293

Query: 281 AGVDPAIMGYGPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVN 340
            G+ P IMGYGP  A+K A+++AG ++ ++DL+E NEAFAAQ +   +DL  D++++NVN
Sbjct: 294 TGLSPEIMGYGPVEASKQALKRAGLSIGDIDLVEINEAFAAQVIPSYRDLGIDLDRLNVN 353

Query: 341 GGAIALGHPIGASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           GGAIA+GHP G +GARI  TL++++Q  D + GL T+C+GGGQG A+++E+
Sbjct: 354 GGAIAVGHPFGMTGARITTTLINSLQWHDKQFGLETMCVGGGQGMAMVIER 404


Lambda     K      H
   0.315    0.132    0.375 

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: 422
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: 392
Length of database: 406
Length adjustment: 31
Effective length of query: 361
Effective length of database: 375
Effective search space:   135375
Effective search space used:   135375
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_037573406.1 BS73_RS16990 (acetyl-CoA C-acetyltransferase)
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.1407559.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-145  469.2   0.0   5.6e-145  469.0   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037573406.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037573406.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.0   0.0  5.6e-145  5.6e-145       1     385 []       6     403 ..       6     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 469.0 bits;  conditional E-value: 5.6e-145
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           iv+a+R+pig +++gslk+++++dL+a++ik++l+++ +ldp +id+++lG+ l+ geq  n+aR +a+++g+
  NCBI__GCF_000744815.1:WP_037573406.1   6 IVSAARSPIGrAFKGSLKDVRPDDLSAQIIKAALDKVpELDPTQIDDLMLGCGLPGGEQgHNLARVIAVQMGM 78 
                                           8**********9************************************************************* PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                           ++ +p+ t++r+C+S+lq+ ++a ++ikaGe dv++++GvE++Sr+  ++++   + ++++ +a+ e++++  
  NCBI__GCF_000744815.1:WP_037573406.1  79 DH-LPGATITRYCSSSLQTSRMALHAIKAGEGDVFISAGVECVSRQVNGSSDG-MPGTHNPVFADAEARTQAR 149
                                           97.**********************************************9998.5777777777777655554 PP

                             TIGR01930 144 l................vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkg 200
                                                            ++  ++mg+tAenla+ +gi+R+e+De+ +rS++ a+kAi++g++++ei+pv++++
  NCBI__GCF_000744815.1:WP_037573406.1 150 SaegadawhdprqdgqvPDVYIAMGQTAENLAQLKGITRQEMDEFGVRSQNLAEKAIADGFWAREITPVTLPD 222
                                           46789************999***************************************************98 PP

                             TIGR01930 201 kkkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaa 273
                                             +vv kD+g+r+++tle +++Lkp+f+ ++g tvtAgN+++lnDGAaal++ms+++a+elgltplarivs++
  NCBI__GCF_000744815.1:WP_037573406.1 223 -GTVVGKDDGPRAGVTLEGVSGLKPVFR-PDG-TVTAGNCCPLNDGAAALVIMSDTKARELGLTPLARIVSTG 292
                                           .7999**********************9.69*.6*************************************** PP

                             TIGR01930 274 vagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlG 346
                                           v+g++pe+mg+gpv+A+++aLk+aglsi didlvEinEAFAaqv+ + ++lg +dl+++NvnGGAiA+GHP+G
  NCBI__GCF_000744815.1:WP_037573406.1 293 VTGLSPEIMGYGPVEASKQALKRAGLSIGDIDLVEINEAFAAQVIPSYRDLG-IDLDRLNVNGGAIAVGHPFG 364
                                           ****************************************************.88****************** PP

                             TIGR01930 347 asGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           ++Gari++tl+++L+ ++k++Gl t+CvggGqG+A+++e
  NCBI__GCF_000744815.1:WP_037573406.1 365 MTGARITTTLINSLQWHDKQFGLETMCVGGGQGMAMVIE 403
                                           *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (406 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 17.35
//
[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 2024 update 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