Alignments for a candidate for fadA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhodomicrobium vannielii ATCC 17100

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_013417721.1 RVAN_RS00115 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-13585
         (391 letters)



>NCBI__GCF_000166055.1:WP_013417721.1
          Length = 396

 Score =  550 bits (1416), Expect = e-161
 Identities = 278/389 (71%), Positives = 324/389 (83%), Gaps = 1/389 (0%)

Query: 3   NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62
           ++VI SAART VGSFNG+ A+ PAH+LG  VI   + RA +D  +VSE ILGQVLTAGQG
Sbjct: 7   DIVIASAARTPVGSFNGSLATLPAHELGRIVITEALKRANVDAGEVSEVILGQVLTAGQG 66

Query: 63  QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122
           QNPARQA I A LP E+ A S+N VCGSGLR VA+AAQ ++ GD+ IVVAGGQENMSLSP
Sbjct: 67  QNPARQASIAASLPIETTAMSVNFVCGSGLRTVAMAAQAIRNGDSDIVVAGGQENMSLSP 126

Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182
           HVA+LR GQ+MG+L  ID+MIKDGLWDAFNGYHMG TAENVA +WQI+R+ QD  A+ SQ
Sbjct: 127 HVAYLRNGQRMGNLEMIDTMIKDGLWDAFNGYHMGITAENVARQWQITREDQDALALGSQ 186

Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAF-IKDGTVT 241
           +KA  A+K GRF DEIVP  IKTRKG+V   ADE+IR  AT++ +AKLRPAF  K+GTVT
Sbjct: 187 HKAAVAKKDGRFNDEIVPVTIKTRKGEVVFAADEFIRENATVEDLAKLRPAFNPKEGTVT 246

Query: 242 AANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEK 301
           A NASGINDGAAA++VM   +AEKRGL PLARI S+ATAG+DPSIMG GPI AS++ALEK
Sbjct: 247 AGNASGINDGAAALVVMKRSDAEKRGLEPLARIVSFATAGVDPSIMGTGPIPASKRALEK 306

Query: 302 AGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLL 361
           AGW   DLDL+EANEAFAAQA AVNK +GWD   VNVNGGAIAIGHPIGASGAR+L TLL
Sbjct: 307 AGWSKDDLDLIEANEAFAAQAAAVNKALGWDIEKVNVNGGAIAIGHPIGASGARILTTLL 366

Query: 362 FEMQRRNAKKGLATLCIGGGMGVAMCLER 390
           +E++RR+AKKGLATLCIGGGMG+AMC+ER
Sbjct: 367 YELKRRDAKKGLATLCIGGGMGIAMCVER 395


Lambda     K      H
   0.317    0.130    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: 486
Number of extensions: 13
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: 391
Length of database: 396
Length adjustment: 31
Effective length of query: 360
Effective length of database: 365
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_013417721.1 RVAN_RS00115 (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.685280.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-150  486.8   7.4   2.6e-150  486.6   7.4    1.0  1  NCBI__GCF_000166055.1:WP_013417721.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_013417721.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.6   7.4  2.6e-150  2.6e-150       1     385 []      10     394 ..      10     394 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.6 bits;  conditional E-value: 2.6e-150
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i +a+Rtp+g+++gsl++l+a++L++ vi e+l+ra++d+ ++ evilG+vl+ag+++n+aR+a +aa lp +
  NCBI__GCF_000166055.1:WP_013417721.1  10 IASAARTPVGSFNGSLATLPAHELGRIVITEALKRANVDAGEVSEVILGQVLTAGQGQNPARQASIAASLPIE 82 
                                           789********************************************************************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           + a++vn vC+Sgl++va+aaq+i+ G+ d+vvaGG E+mS +p++      r++ ++g+ ++ d+++kd+  
  NCBI__GCF_000166055.1:WP_013417721.1  83 TTAMSVNFVCGSGLRTVAMAAQAIRNGDSDIVVAGGQENMSLSPHVAYL---RNGQRMGNLEMIDTMIKDGlw 152
                                           ********************************************98776...699****************** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            + ++++mg+tAen+a++++i+Re+qD++al S++kaa A ++g+f+deivpv++k++  ++v++ De ir+n
  NCBI__GCF_000166055.1:WP_013417721.1 153 dAFNGYHMGITAENVARQWQITREDQDALALGSQHKAAVAKKDGRFNDEIVPVTIKTRkgEVVFAADEFIREN 225
                                           *99*****************************************************9999************* PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            t+e+LakL+paf++k+g tvtAgN+s++nDGAaal++m+++ a++ gl+plarivs+a+agvdp++mg+gp+
  NCBI__GCF_000166055.1:WP_013417721.1 226 ATVEDLAKLRPAFNPKEG-TVTAGNASGINDGAAALVVMKRSDAEKRGLEPLARIVSFATAGVDPSIMGTGPI 297
                                           ******************.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA+++aL+kag+s +d+dl+E nEAFAaq+ av+k+lg  d ekvNvnGGAiA+GHP+GasGari++tll+eL
  NCBI__GCF_000166055.1:WP_013417721.1 298 PASKRALEKAGWSKDDLDLIEANEAFAAQAAAVNKALG-WDIEKVNVNGGAIAIGHPIGASGARILTTLLYEL 369
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           k+r++k GlatlC+ggG+G+A+ +e
  NCBI__GCF_000166055.1:WP_013417721.1 370 KRRDAKKGLATLCIGGGMGIAMCVE 394
                                           **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (396 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: 00:00:00.01
# Mc/sec: 15.02
//
[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