GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases

Query= SwissProt::P41338
         (398 letters)



>lcl|FitnessBrowser__Cola:Echvi_3705 Echvi_3705 acetyl-CoA
           acetyltransferases
          Length = 393

 Score =  409 bits (1052), Expect = e-119
 Identities = 214/396 (54%), Positives = 288/396 (72%), Gaps = 5/396 (1%)

Query: 3   QNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKVPELDASKDFDEIIFGNVLSA 62
           + VYI+S  RTP+GSF G LS  TAVELGA A+KGAL +       +  DE+I GNVLSA
Sbjct: 2   KEVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQV--TPEQVDEVIMGNVLSA 59

Query: 63  NLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGGCESMT 122
           NLGQAPARQ A+ AG+  H+  +TVNKVCAS MK+++  AQSI  G +D++VAGG ESM+
Sbjct: 60  NLGQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMS 119

Query: 123 NAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQQDNFA 182
           N PYY+P AR G KFG    VDG+ +DGL++ Y    MG  A+  A++ +I+RE QD +A
Sbjct: 120 NVPYYIPKARFGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTAKEKNISREAQDEYA 179

Query: 183 IESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSARTVFQKE 242
           I+SY+++ ++ K   F +E++PVT K  +G+  T V +DEE   +  EK+ S R VF KE
Sbjct: 180 IQSYRRAAEAWKAQAFQDEVIPVTFKSRKGESIT-VDEDEEYQNVLFEKIPSLRPVFDKE 238

Query: 243 NGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAPSLAVP 302
            GTVTAANAS +NDGAAA++L+S++  +   L+P+A I G+ +AA  P  FT AP+LA+P
Sbjct: 239 -GTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAIP 297

Query: 303 KALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLGCSGAR 362
           KALK+AGI+   +VDY+E NEAFS V L N + L +   ++NV+GGAV+LGHPLG SGAR
Sbjct: 298 KALKNAGIQ-AEAVDYYEINEAFSAVALANQQELNIPNDRLNVFGGAVSLGHPLGASGAR 356

Query: 363 VVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEKI 398
           ++ TL S+L+Q+GGKIGVA ICNGGGGAS++VIE +
Sbjct: 357 IMATLHSVLRQKGGKIGVAGICNGGGGASAMVIENL 392


Lambda     K      H
   0.315    0.131    0.372 

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: 414
Number of extensions: 17
Number of successful extensions: 5
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: 398
Length of database: 393
Length adjustment: 31
Effective length of query: 367
Effective length of database: 362
Effective search space:   132854
Effective search space used:   132854
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate Echvi_3705 Echvi_3705 (acetyl-CoA acetyltransferases)
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.26523.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   8.3e-144  465.2   4.6   9.3e-144  465.0   4.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3705  Echvi_3705 acetyl-CoA acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3705  Echvi_3705 acetyl-CoA acetyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.0   4.6  9.3e-144  9.3e-144       1     385 []       6     390 ..       6     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 465.0 bits;  conditional E-value: 9.3e-144
                            TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesv 74 
                                          i++avRtp g++gg l+ l+a++L+a++ik++l ra+++pe++devi+Gnvl+a+ ++++aR+aa+ ag++++v
  lcl|FitnessBrowser__Cola:Echvi_3705   6 IISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQVTPEQVDEVIMGNVLSANLGQAPARQAAIGAGIGYHV 79 
                                          89************************************************************************ PP

                            TIGR01930  75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...v 145
                                          p +tvn+vCaSg+++v+ aaq+i++G+ d++vaGG+EsmS+vp++++++  r ++k+g+ +  d l+kd+   v
  lcl|FitnessBrowser__Cola:Echvi_3705  80 PCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMSNVPYYIPKA--RFGYKFGNGEFVDGLAKDGlheV 151
                                          ***********************************************98..89********************9 PP

                            TIGR01930 146 ktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpntt 216
                                          + +++mg++A+n+ak+++isRe qDeya++S+++aa+A+++  f+de++pv++k +   + +v++ ++ ++n+ 
  lcl|FitnessBrowser__Cola:Echvi_3705 152 YYNFPMGNCADNTAKEKNISREAQDEYAIQSYRRAAEAWKAQAFQDEVIPVTFKSRkgeSITVDE-DEEYQNVL 224
                                          99****************************************************99995555555.55567*** PP

                            TIGR01930 217 lekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAi 290
                                           ek+ +L+p+f++ +g tvtA+N+s +nDGAaal+lms+e+a++lgl+p+a+i ++a a+ dp  ++++p+ Ai
  lcl|FitnessBrowser__Cola:Echvi_3705 225 FEKIPSLRPVFDK-EG-TVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAI 296
                                          ***********95.8*.6******************************************************** PP

                            TIGR01930 291 ekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkerg 364
                                          +kaLk ag++++ +d++EinEAF+a++la+++el+ + ++++Nv GGA++lGHPlGasGari++tl + L+++g
  lcl|FitnessBrowser__Cola:Echvi_3705 297 PKALKNAGIQAEAVDYYEINEAFSAVALANQQELN-IPNDRLNVFGGAVSLGHPLGASGARIMATLHSVLRQKG 369
                                          ***********************************.88************************************ PP

                            TIGR01930 365 kkyGlatlCvggGqGaAvile 385
                                          +k+G+a +C+ggG ++A+++e
  lcl|FitnessBrowser__Cola:Echvi_3705 370 GKIGVAGICNGGGGASAMVIE 390
                                          *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.50
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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, or view the source code.

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