Alignments for a candidate for fadA in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Thauera aminoaromatica S2

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_004312070.1 C665_RS12455 acetyl-CoA C-acyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982
         (397 letters)



>NCBI__GCF_000310185.1:WP_004312070.1
          Length = 402

 Score =  549 bits (1414), Expect = e-161
 Identities = 276/393 (70%), Positives = 329/393 (83%), Gaps = 3/393 (0%)

Query: 5   NDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAG 64
           +DP+VIVS  RTP+GGFQG+L SLT PQLG+ AIKAAVERAGVA   V EV+ GCVLPAG
Sbjct: 2   SDPVVIVSVARTPLGGFQGDLSSLTTPQLGSIAIKAAVERAGVAPAQVQEVIMGCVLPAG 61

Query: 65  LGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSN 124
           LGQAPARQAALGAGL  S  CTT+NK+CGSGM+A +LAHD++LAGS +V+VAGGMESMSN
Sbjct: 62  LGQAPARQAALGAGLPLSAGCTTINKVCGSGMKATMLAHDLILAGSNEVMVAGGMESMSN 121

Query: 125 APYLLDRARAGYRMGHGRVQDSMFLDGLEDAY---DKGRLMGTFAEDCAETNGFSREAQD 181
           APYLL +ARAGYR+GHG++ D MFLDGLED+Y   +KGRLMGTFAEDCA    F+R+AQD
Sbjct: 122 APYLLPKARAGYRLGHGQMFDHMFLDGLEDSYSKENKGRLMGTFAEDCAGHFNFTRQAQD 181

Query: 182 AFAIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFRE 241
            FAIASTTRAQ AI +G F  E+VP+TV   K  VV+  DEQP KA++DKI SLKPAF++
Sbjct: 182 EFAIASTTRAQAAINNGDFSWEVVPVTVASRKGDVVVDKDEQPLKAQIDKIPSLKPAFKK 241

Query: 242 GGTVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIK 301
            GTVT ANSSSISDGAAALVLMR+S A+K G+KP+A I GHA  A  P LF  AP+GA++
Sbjct: 242 DGTVTPANSSSISDGAAALVLMRKSTAEKLGVKPVATIIGHATHAQEPALFTTAPVGAMQ 301

Query: 302 KLMKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARI 361
           K++ K GWS   VDL E+NEAFAVV MAAM  +++PH+K+NV+GGACALGHPIGASGARI
Sbjct: 302 KVLAKAGWSTEQVDLWEINEAFAVVTMAAMHEMKLPHDKVNVNGGACALGHPIGASGARI 361

Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           LV+L+ ALR++GLKRGVA++CIGGGEATAMA+E
Sbjct: 362 LVSLIGALRKRGLKRGVASLCIGGGEATAMAIE 394


Lambda     K      H
   0.318    0.132    0.376 

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: 580
Number of extensions: 17
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: 397
Length of database: 402
Length adjustment: 31
Effective length of query: 366
Effective length of database: 371
Effective search space:   135786
Effective search space used:   135786
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_004312070.1 C665_RS12455 (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.5008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-130  421.1   5.8   2.3e-130  420.9   5.8    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004312070.1  C665_RS12455 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004312070.1  C665_RS12455 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.9   5.8  2.3e-130  2.3e-130       1     385 []       7     394 ..       7     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 420.9 bits;  conditional E-value: 2.3e-130
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+ +Rtp g ++g l++l+  +L++ +ik+++erag+ p+++ evi+G+vl+ag ++++aR+aal ag
  lcl|NCBI__GCF_000310185.1:WP_004312070.1   7 IVSVARTPLGGFQGDLSSLTTPQLGSIAIKAAVERAGVAPAQVQEVIMGCVLPAGLGQAPARQAALGAG 75 
                                               89********99********************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp s   +t+n+vC+Sg++A +la + i aG ++v+vaGG+EsmS++p+ll+++  r++++lg+ ++ d
  lcl|NCBI__GCF_000310185.1:WP_004312070.1  76 LPLSAGCTTINKVCGSGMKATMLAHDLILAGSNEVMVAGGMESMSNAPYLLPKA--RAGYRLGHGQMFD 142
                                               ****************************************************98..89*********** PP

                                 TIGR01930 139 qllkdl.......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkg 200
                                               ++  d+       ++++  mg+ Ae +a +++++R+ qDe+a++S ++a++Ai++g f+ e+vpv+v  
  lcl|NCBI__GCF_000310185.1:WP_004312070.1 143 HMFLDGledsyskENKGRLMGTFAEDCAGHFNFTRQAQDEFAIASTTRAQAAINNGDFSWEVVPVTVAS 211
                                               9999999*****999999*************************************************99 PP

                                 TIGR01930 201 k..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpla 267
                                               +  ++vv+kDe++  + +++k+ +Lkpafk+ +g tvt +Nss+++DGAaal+lm +++a++lg++p+a
  lcl|NCBI__GCF_000310185.1:WP_004312070.1 212 RkgDVVVDKDEQPL-KAQIDKIPSLKPAFKK-DG-TVTPANSSSISDGAAALVLMRKSTAEKLGVKPVA 277
                                               99888899999887.899***********95.9*.6********************************* PP

                                 TIGR01930 268 rivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnG 336
                                               +i+++a+ + +p+ ++++pv A++k+L+kag+s++++dl+EinEAFA++++a+++e++ l ++kvNvnG
  lcl|NCBI__GCF_000310185.1:WP_004312070.1 278 TIIGHATHAQEPALFTTAPVGAMQKVLAKAGWSTEQVDLWEINEAFAVVTMAAMHEMK-LPHDKVNVNG 345
                                               **********************************************************.88******** PP

                                 TIGR01930 337 GAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               GA AlGHP+GasGari+++l+ +L++rg k+G+a+lC+ggG ++A+ +e
  lcl|NCBI__GCF_000310185.1:WP_004312070.1 346 GACALGHPIGASGARILVSLIGALRKRGLKRGVASLCIGGGEATAMAIE 394
                                               **********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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: 9.35
//
[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