Alignments for a candidate for fadA in Rubrivirga marina SAORIC-28

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rubrivirga marina SAORIC-28

Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_095511582.1 BSZ37_RS16360 thiolase family protein

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



>NCBI__GCF_002283365.1:WP_095511582.1
          Length = 390

 Score =  414 bits (1064), Expect = e-120
 Identities = 210/385 (54%), Positives = 277/385 (71%)

Query: 11  VIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQA 70
           VI++A RTP+GSF GSLS +++  L ATAI+  L    V    VDEV+MG V+ AG GQA
Sbjct: 4   VILSAARTPVGSFGGSLSSVSAPDLGATAIRGALTWADVGEGDVDEVIMGNVVTAGEGQA 63

Query: 71  PARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPYL 130
           PARQA LGAGLP SV   T+NKVCGSGMK VMLA   I+AG A+VV+AGGME+MSQAP+ 
Sbjct: 64  PARQAALGAGLPQSVHCMTINKVCGSGMKAVMLADQAIRAGDAQVVVAGGMENMSQAPFY 123

Query: 131 LDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALSSLE 190
           L KAR G   G+G+++D +F DGL DAY G AMG  A +  +  G+ R++ DAF++ S  
Sbjct: 124 LPKARYGYGYGNGELIDGLFHDGLRDAYDGVAMGVAADQCGETCGVPRDRQDAFSIESYR 183

Query: 191 KANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTITAAN 250
           +A A+  +GAF  EIVPVTV  R+GD  +DTDE+P     +KIP LRP F+K+GT+TAAN
Sbjct: 184 RAQASTENGAFAEEIVPVTVPGRKGDTVVDTDEEPARTNFDKIPQLRPVFSKEGTVTAAN 243

Query: 251 SSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNVGW 310
           +S+I+DGAAAL++ +   AE  G T +A I   + H+Q P  FTTAP+ A+ K+L   G 
Sbjct: 244 ASTINDGAAALVVASAEWAEASGKTPMARIVATSQHSQAPMEFTTAPIEAVNKVLDKAGL 303

Query: 311 SKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLIHAL 370
           + D++DLFE+NEAFA+V + A   LG+   K+NV GG+ A+GHPIG SGAR+L TL+HA+
Sbjct: 304 TLDDIDLFEVNEAFAVVALAAQDALGIPSEKLNVRGGSVAVGHPIGASGARILTTLLHAM 363

Query: 371 KARGLKRGVASLCIGGGEATAMAIE 395
             R  KRG+A++CIGGGEATA+ +E
Sbjct: 364 AERDAKRGLAAICIGGGEATAIIVE 388


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: 475
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: 396
Length of database: 390
Length adjustment: 31
Effective length of query: 365
Effective length of database: 359
Effective search space:   131035
Effective search space used:   131035
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_095511582.1 BSZ37_RS16360 (thiolase family protein)
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.1260922.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-137  445.1   6.2   1.2e-137  444.9   6.2    1.0  1  NCBI__GCF_002283365.1:WP_095511582.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002283365.1:WP_095511582.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.9   6.2  1.2e-137  1.2e-137       1     385 []       5     388 ..       5     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.9 bits;  conditional E-value: 1.2e-137
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i++a+Rtp+g++ggsl+++sa dL+a++i+++l  a++ + ++devi+Gnv++age++++aR+aal aglp+s
  NCBI__GCF_002283365.1:WP_095511582.1   5 ILSAARTPVGSFGGSLSSVSAPDLGATAIRGALTWADVGEGDVDEVIMGNVVTAGEGQAPARQAALGAGLPQS 77 
                                           899********************************************************************** PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           v  +t+n+vC+Sg++Av+la q+i+aG+a+vvvaGG+E+mS++p++l+++  r ++ +g+ +l d l +d+  
  NCBI__GCF_002283365.1:WP_095511582.1  78 VHCMTINKVCGSGMKAVMLADQAIRAGDAQVVVAGGMENMSQAPFYLPKA--RYGYGYGNGELIDGLFHDGlr 148
                                           ************************************************98..89******************* PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            ++++++mg+ A+++ ++ g+ R++qD+++++S+++a++++e+g f++eivpv+v+g+  ++vv++De++  +
  NCBI__GCF_002283365.1:WP_095511582.1 149 dAYDGVAMGVAADQCGETCGVPRDRQDAFSIESYRRAQASTENGAFAEEIVPVTVPGRkgDTVVDTDEEPA-R 220
                                           *99*******************************************************9888888888876.9 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           t+ +k+ +L+p+f + +g tvtA+N+s +nDGAaal+++s e+a++ g tp+ariv++++ +  p e++++p+
  NCBI__GCF_002283365.1:WP_095511582.1 221 TNFDKIPQLRPVFSK-EG-TVTAANASTINDGAAALVVASAEWAEASGKTPMARIVATSQHSQAPMEFTTAPI 291
                                           *************95.8*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           +A++k+L+kagl+++didl+E+nEAFA+++la++++lg +  ek+Nv GG++A+GHP+GasGari++tll+++
  NCBI__GCF_002283365.1:WP_095511582.1 292 EAVNKVLDKAGLTLDDIDLFEVNEAFAVVALAAQDALG-IPSEKLNVRGGSVAVGHPIGASGARILTTLLHAM 363
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           +er++k+Gla++C+ggG ++A+i+e
  NCBI__GCF_002283365.1:WP_095511582.1 364 AERDAKRGLAAICIGGGEATAIIVE 388
                                           ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (390 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: 19.97
//
[ok]

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

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