Alignments for a candidate for fadA in Desulfarculus baarsii DSM 2075

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfarculus baarsii DSM 2075

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_013258114.1 DEBA_RS06450 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000143965.1:WP_013258114.1
          Length = 392

 Score =  493 bits (1268), Expect = e-144
 Identities = 249/392 (63%), Positives = 308/392 (78%), Gaps = 1/392 (0%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           MKEVVIA A RTA+G +G    D+ AV LG TA KEA+ +AG+    V+E+I GNVL AG
Sbjct: 1   MKEVVIAGAARTAVGRFGGMYSDISAVQLGVTAAKEALARAGVGVAMVDELIFGNVLGAG 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
           LGQN ARQ    AG+PV+  A T+NKVC SGL++V LAAQ +   DA++++AGG ENMS+
Sbjct: 61  LGQNVARQVQIGAGVPVDKNAFTVNKVCASGLKSVMLAAQAVMCDDAEIVVAGGTENMSQ 120

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           APYL    R+GYRMGN   +D MI DGLWD FN YHMGITAEN+AE++ ++R+ QD+ A 
Sbjct: 121 APYLMPKGRFGYRMGNGSLIDSMINDGLWDIFNGYHMGITAENVAEKYGLTRQAQDQLAC 180

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGE-TVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239
           ASQ +A+ AI +G+FKDEIVPV+   RKGE   +DTDE PRF +TI+ LAKLKPAFKKDG
Sbjct: 181 ASQNRAQAAITAGRFKDEIVPVMAPQRKGEPKALDTDEFPRFDTTIDDLAKLKPAFKKDG 240

Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299
           TVTAGNASG+ND AA +V+ S EKA  LG+  LAKI SYG  GVDP++MG GP  A+K+A
Sbjct: 241 TVTAGNASGINDGAAAVVVTSREKANALGLPILAKIKSYGWGGVDPSVMGLGPIEASKSA 300

Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359
           + KAG TV++LDLIE+NEAFAAQ+LAV  +LKF+ + VNVNGGAIALGHPIGASGARILV
Sbjct: 301 LTKAGLTVEDLDLIEANEAFAAQALAVIGELKFNTDIVNVNGGAIALGHPIGASGARILV 360

Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           +L++ M +RDAK GLATLCIGGGQG A++LE+
Sbjct: 361 SLIYEMLRRDAKLGLATLCIGGGQGAAMILER 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: 535
Number of extensions: 20
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: 392
Length of database: 392
Length adjustment: 31
Effective length of query: 361
Effective length of database: 361
Effective search space:   130321
Effective search space used:   130321
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_013258114.1 DEBA_RS06450 (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.31223.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-145  468.6   7.1   8.6e-145  468.4   7.1    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013258114.1  DEBA_RS06450 acetyl-CoA C-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013258114.1  DEBA_RS06450 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.4   7.1  8.6e-145  8.6e-145       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.4 bits;  conditional E-value: 8.6e-145
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a+Rt++g++gg ++++sa++L++++ ke+l+rag+  + +de+i+Gnvl ag ++n+aR++ + ag
  lcl|NCBI__GCF_000143965.1:WP_013258114.1   6 IAGAARTAVGRFGGMYSDISAVQLGVTAAKEALARAGVGVAMVDELIFGNVLGAGLGQNVARQVQIGAG 74 
                                               7899***************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p + +a+tvn+vCaSgl++v+laaq++++ +a++vvaGG E+mS++p+l+++   r ++++g+ +l d
  lcl|NCBI__GCF_000143965.1:WP_013258114.1  75 VPVDKNAFTVNKVCASGLKSVMLAAQAVMCDDAEIVVAGGTENMSQAPYLMPKG--RFGYRMGNGSLID 141
                                               ****************************************************97..89*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                               ++++d+     ++++mg+tAen+a+kyg++R+ qD++a +S+++a++Ai +g+fkdeivpv  +++   
  lcl|NCBI__GCF_000143965.1:WP_013258114.1 142 SMINDGlwdIFNGYHMGITAENVAEKYGLTRQAQDQLACASQNRAQAAITAGRFKDEIVPVMAPQRkge 210
                                               *********99***************************************************9999999 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               +k +++De +r +tt+++LakLkpafk+ +g tvtAgN+s++nDGAaa++++s+e+a++lgl +la+i 
  lcl|NCBI__GCF_000143965.1:WP_013258114.1 211 PKALDTDEFPRFDTTIDDLAKLKPAFKK-DG-TVTAGNASGINDGAAAVVVTSREKANALGLPILAKIK 277
                                               9*************************95.9*.6************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               s+++ gvdp++mglgp++A++ aL kagl+++d+dl+E nEAFAaq+lav+ el+  +++ vNvnGGAi
  lcl|NCBI__GCF_000143965.1:WP_013258114.1 278 SYGWGGVDPSVMGLGPIEASKSALTKAGLTVEDLDLIEANEAFAAQALAVIGELK-FNTDIVNVNGGAI 345
                                               *******************************************************.669********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasGari+++l++e+ +r++k+GlatlC+ggGqGaA+ile
  lcl|NCBI__GCF_000143965.1:WP_013258114.1 346 ALGHPIGASGARILVSLIYEMLRRDAKLGLATLCIGGGQGAAMILE 391
                                               ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.38
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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