Alignments for a candidate for fadA in Sulfuritalea hydrogenivorans sk43H DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_041096687.1 SUTH_RS01990 acetyl-CoA C-acyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000828635.1:WP_041096687.1
          Length = 394

 Score =  395 bits (1014), Expect = e-114
 Identities = 203/389 (52%), Positives = 268/389 (68%)

Query: 2   KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGL 61
           +EVV+ + VRTAIG+Y  SLKDV A  LGA AI+E +K+A + P+ V  +++GNV+QAG+
Sbjct: 4   REVVLCNPVRTAIGTYNGSLKDVAAPMLGAAAIRETLKRANLSPDKVEALVMGNVIQAGV 63

Query: 62  GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRA 121
             NPARQA    GLPVE+PA+T+N+VCGSG + V  AA  I +G  D  I GGMENM RA
Sbjct: 64  KMNPARQAGIAGGLPVEVPALTVNRVCGSGAQGVVSAALEIWSGMIDCAIGGGMENMDRA 123

Query: 122 PYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALA 181
           PYL    RWG RMG+    D M+ DGL DAF+D H G   E++  +  ISR +QD +AL 
Sbjct: 124 PYLMPQVRWGARMGDVTVYDAMLFDGLNDAFSDKHSGWHTEDLVTKNGISRADQDAWALR 183

Query: 182 SQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTV 241
           SQ+    A  +G+F  EIV V + GRKG T+ D DEH R  +T E LAKLKPAF+K+GT+
Sbjct: 184 SQQNFSAAQAAGKFAAEIVAVEVPGRKGPTLFDKDEHNRPETTAESLAKLKPAFRKEGTI 243

Query: 242 TAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIE 301
           TAGNA GLN  AA +V+     A++ G+KP+AK+V+YG   V+P   G GP  A + A+ 
Sbjct: 244 TAGNAPGLNTGAAAMVVAERNWAEKNGLKPMAKLVAYGIGAVEPGFFGLGPVPAVRQALA 303

Query: 302 KAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTL 361
           +AGW+V ++  +E NEAFAA +LA  ++L F  + VNV GGAIA GHPIGASGA +   L
Sbjct: 304 RAGWSVADVQRVEINEAFAAIALACQRELGFAPDIVNVEGGAIAHGHPIGASGAVLATRL 363

Query: 362 VHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           +H+MQ+   K+G+ TLCIGGGQG A+ +E
Sbjct: 364 MHSMQRDGLKRGIVTLCIGGGQGIALAIE 392


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: 466
Number of extensions: 17
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: 392
Length of database: 394
Length adjustment: 31
Effective length of query: 361
Effective length of database: 363
Effective search space:   131043
Effective search space used:   131043
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_041096687.1 SUTH_RS01990 (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.444598.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-132  427.2   2.3   3.1e-132  427.0   2.3    1.0  1  NCBI__GCF_000828635.1:WP_041096687.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041096687.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.0   2.3  3.1e-132  3.1e-132       5     385 .]      12     392 ..       8     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 427.0 bits;  conditional E-value: 3.1e-132
                             TIGR01930   5 vRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 
                                           vRt+ig+++gslk++ a  L+aa+i+e l+ra+l+p+k++ +++Gnv+qag ++n+aR+a +a glp +vpal
  NCBI__GCF_000828635.1:WP_041096687.1  12 VRTAIGTYNGSLKDVAAPMLGAAAIRETLKRANLSPDKVEALVMGNVIQAGVKMNPARQAGIAGGLPVEVPAL 84 
                                           8*****99***************************************************************** PP

                             TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147
                                           tvnrvC+Sg q v +aa +i +G++d+++ GG+E+m r+p+l+++   r+++++g+ +++d++l d+   + +
  NCBI__GCF_000828635.1:WP_041096687.1  85 TVNRVCGSGAQGVVSAALEIWSGMIDCAIGGGMENMDRAPYLMPQV--RWGARMGDVTVYDAMLFDGlndAFS 155
                                           ******************************************9996..9***************999999888 PP

                             TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttle 218
                                           + + g ++e l +k gisR +qD++alrS+q+ ++A+++gkf++eiv vev+g+  ++ ++kDe+ rp+tt+e
  NCBI__GCF_000828635.1:WP_041096687.1 156 DKHSGWHTEDLVTKNGISRADQDAWALRSQQNFSAAQAAGKFAAEIVAVEVPGRkgPTLFDKDEHNRPETTAE 228
                                           999***************************************************9****************** PP

                             TIGR01930 219 kLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAie 291
                                           +LakLkpaf++ +g t+tAgN+ +ln GAaa++++++++a++ gl+p+a++v++++ +v+p  +glgpvpA++
  NCBI__GCF_000828635.1:WP_041096687.1 229 SLAKLKPAFRK-EG-TITAGNAPGLNTGAAAMVVAERNWAEKNGLKPMAKLVAYGIGAVEPGFFGLGPVPAVR 299
                                           *********95.8*.6********************************************************* PP

                             TIGR01930 292 kaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkerg 364
                                           +aL++ag+s+ d++ vEinEAFAa +la+++elg  +++ vNv GGAiA GHP+GasGa + ++l+++++++g
  NCBI__GCF_000828635.1:WP_041096687.1 300 QALARAGWSVADVQRVEINEAFAAIALACQRELG-FAPDIVNVEGGAIAHGHPIGASGAVLATRLMHSMQRDG 371
                                           **********************************.66************************************ PP

                             TIGR01930 365 kkyGlatlCvggGqGaAvile 385
                                            k+G++tlC+ggGqG+A+ +e
  NCBI__GCF_000828635.1:WP_041096687.1 372 LKRGIVTLCIGGGQGIALAIE 392
                                           *****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 23.67
//
[ok]

This GapMind analysis is from Apr 09 2024. 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