Alignments for a candidate for fadA in Bacillus alkalinitrilicus DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Bacillus alkalinitrilicus DSM 22532

Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_078428403.1 BK574_RS09250 thiolase family protein

Query= metacyc::G185E-7833-MONOMER
         (386 letters)



>NCBI__GCF_002019605.1:WP_078428403.1
          Length = 383

 Score =  381 bits (978), Expect = e-110
 Identities = 206/393 (52%), Positives = 266/393 (67%), Gaps = 18/393 (4%)

Query: 1   MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60
           M EA V++ VR+ VG+R GAL+   P DL A   + ++ R +I P  ++DVI GCV  +G
Sbjct: 1   MKEAVVVEVVRSPVGRRNGALSNYRPDDLAAEVLKEVVKRANISPKIIEDVIMGCVSQVG 60

Query: 61  GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120
            QA +I R++ L AG+P EVPG T+DRQCGSSQQA+ F AQAIMSG  DV++A GV++MS
Sbjct: 61  EQAADIGRVAALIAGFPIEVPGTTIDRQCGSSQQAVHFAAQAIMSGDMDVVIAAGVESMS 120

Query: 121 QIPISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSL 180
           ++P+ S +   E          S++   +Y  + I+Q   +E IAEKW +S++E++ ++L
Sbjct: 121 RVPMFSNLQGAEL---------SERLTSKY--EMINQGFSAERIAEKWGISKQELDEFAL 169

Query: 181 TSHERAFAAIRAGHFENEIITVETE-----SGPFRVDEGPR-ESSLEKMAGLQP-LVEGG 233
            SH +A AA   G FE EI+ +E             DEGPR E++LEK+A L+P  VE G
Sbjct: 170 QSHHKAIAAQDEGRFEREIMPLEVTLPDGTKATITADEGPRRETNLEKLASLKPSFVENG 229

Query: 234 RLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRYA 293
            +T   ASQISDGA+A+LL S    ++ GL+PR RI   S   +DP  MLTGPIPAT   
Sbjct: 230 TVTPGNASQISDGAAAILLMSREKAEELGLKPRFRIVARSVIGSDPTLMLTGPIPATEKV 289

Query: 294 LDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLFT 353
           L K GL+IDDID  E+NEAFA V + WLKE  ADP K+NPNGGAIALGHPLG +GA+L T
Sbjct: 290 LKKAGLSIDDIDIFEVNEAFASVPLVWLKETGADPNKLNPNGGAIALGHPLGGSGARLMT 349

Query: 354 TMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386
           TM+ ELER GGRYGLQTMCEG G AN TIIERL
Sbjct: 350 TMMYELERTGGRYGLQTMCEGHGMANATIIERL 382


Lambda     K      H
   0.317    0.134    0.389 

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: 395
Number of extensions: 16
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: 386
Length of database: 383
Length adjustment: 30
Effective length of query: 356
Effective length of database: 353
Effective search space:   125668
Effective search space used:   125668
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_078428403.1 BK574_RS09250 (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.5208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-144  467.4   0.2     2e-144  467.2   0.2    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078428403.1  BK574_RS09250 thiolase family pr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078428403.1  BK574_RS09250 thiolase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.2   0.2    2e-144    2e-144       1     385 []       6     380 ..       6     380 .. 0.96

  Alignments for each domain:
  == domain 1  score: 467.2 bits;  conditional E-value: 2e-144
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               +v+ vR+p+g+ +g+l++ +++dL+a+v+ke+++ra+++p+ i++vi+G+v q geq a+i+R aal a
  lcl|NCBI__GCF_002019605.1:WP_078428403.1   6 VVEVVRSPVGRRNGALSNYRPDDLAAEVLKEVVKRANISPKIIEDVIMGCVSQVGEQaADIGRVAALIA 74 
                                               799*******88********************************************************* PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+p +vp++t++r+C+S+ qAv+ aaq+i++G++dvv+a+GvEsmSrvp++++ +    +++l +  ++
  lcl|NCBI__GCF_002019605.1:WP_078428403.1  75 GFPIEVPGTTIDRQCGSSQQAVHFAAQAIMSGDMDVVIAAGVESMSRVPMFSNLQ----GAELSERLTS 139
                                               **************************************************99875....4444333344 PP

                                 TIGR01930 138 dqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kk 203
                                               +       ++ +++g +Ae++a+k+gis++e+De+al+Sh+ka +A++eg+f++ei+p+ev      k 
  lcl|NCBI__GCF_002019605.1:WP_078428403.1 140 K-------YEMINQGFSAERIAEKWGISKQELDEFALQSHHKAIAAQDEGRFEREIMPLEVTLPdgtKA 201
                                               4.......56899***********************************************998899999 PP

                                 TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsa 272
                                               +++ Deg+r++t+lekLa+Lkp f e +g tvt gN+sq++DGAaa+llms+e+a+elgl+p  riv+ 
  lcl|NCBI__GCF_002019605.1:WP_078428403.1 202 TITADEGPRRETNLEKLASLKPSFVE-NG-TVTPGNASQISDGAAAILLMSREKAEELGLKPRFRIVAR 268
                                               ************************96.9*.6************************************** PP

                                 TIGR01930 273 avagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAl 341
                                               +v+g+dp+ m++gp+pA+ek+Lkkaglsi+did++E+nEAFA++ l++ ke+g  d++k+N nGGAiAl
  lcl|NCBI__GCF_002019605.1:WP_078428403.1 269 SVIGSDPTLMLTGPIPATEKVLKKAGLSIDDIDIFEVNEAFASVPLVWLKETG-ADPNKLNPNGGAIAL 336
                                               *****************************************************.88************* PP

                                 TIGR01930 342 GHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               GHPlG sGar+++t+++eL++ g++yGl+t+C g G+++A+i+e
  lcl|NCBI__GCF_002019605.1:WP_078428403.1 337 GHPLGGSGARLMTTMMYELERTGGRYGLQTMCEGHGMANATIIE 380
                                               ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (383 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: 7.56
//
[ok]

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

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

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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