GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Chryseobacterium arthrosphaerae CC-VM-7

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate WP_065397633.1 BBI00_RS04415 acetyl-CoA C-acyltransferase

Query= SwissProt::P41338
         (398 letters)



>NCBI__GCF_001684965.1:WP_065397633.1
          Length = 391

 Score =  347 bits (889), Expect = e-100
 Identities = 183/396 (46%), Positives = 271/396 (68%), Gaps = 7/396 (1%)

Query: 3   QNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKVPELDASKDFDEIIFGNVLSA 62
           + V+I++  RTP+G F GSLS  TA +LGA A++ A   V    A +  D +  GNVLSA
Sbjct: 2   KEVFIIAAKRTPVGGFMGSLSGLTAPQLGAAAIQNAYESVQL--APEYIDSVYMGNVLSA 59

Query: 63  NLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGGCESMT 122
            LGQ+PARQ A+ A +     A+T+NKVCAS MKA +LGAQ I+ G   +V+ GG ESM+
Sbjct: 60  GLGQSPARQAAVFAEIPVDKDAATINKVCASGMKATMLGAQQIQLGLEKIVMTGGMESMS 119

Query: 123 NAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQQDNFA 182
           N P+Y    R G K G +VL DG+ +DGL D Y+   MG  AE   + + +TR+Q D++A
Sbjct: 120 NVPHYADV-RQGKKLGDSVLTDGLIKDGLWDVYNDFHMGSAAELGVKKYGLTRQQLDDYA 178

Query: 183 IESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSARTVFQKE 242
           + SYQ++Q++  + KF NE++ ++++G +G   + +++DE+  +L  EK+   +  F+ +
Sbjct: 179 LLSYQRAQEATSKNKFSNELISISVEGRKGT--SVISRDEDIDKLIPEKIALLKPAFEND 236

Query: 243 NGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAPSLAVP 302
            G +TAAN+S +NDGAAA++L S + +++  L PLA I  + +AA  P  FT +PS+A+ 
Sbjct: 237 -GALTAANSSNLNDGAAAILLGSSEAVQQHELVPLARIIAYADAAQSPEWFTTSPSIAIN 295

Query: 303 KALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLGCSGAR 362
           K LK AG+  +  +DY E NEA+S V L N +IL  D ++VNVYGGAVALGHP+G SGAR
Sbjct: 296 KVLKQAGLS-LADIDYLEINEAYSSVILSNQQILGYDLNRVNVYGGAVALGHPIGASGAR 354

Query: 363 VVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEKI 398
           ++ TL+++L+QE G+ G+AAICNGGGGAS+++IE +
Sbjct: 355 IIATLINVLRQEKGRYGIAAICNGGGGASAVLIENM 390


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: 398
Number of extensions: 12
Number of successful extensions: 6
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: 391
Length adjustment: 31
Effective length of query: 367
Effective length of database: 360
Effective search space:   132120
Effective search space used:   132120
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 WP_065397633.1 BBI00_RS04415 (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.1789370.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-127  412.2   2.7   1.1e-127  412.1   2.7    1.0  1  NCBI__GCF_001684965.1:WP_065397633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001684965.1:WP_065397633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.1   2.7  1.1e-127  1.1e-127       1     385 []       6     388 ..       6     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 412.1 bits;  conditional E-value: 1.1e-127
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i++a Rtp+g + gsl+ l+a +L+aa+i+++ e ++l pe id v++Gnvl+ag ++++aR+aa+ a++p +
  NCBI__GCF_001684965.1:WP_065397633.1   6 IIAAKRTPVGGFMGSLSGLTAPQLGAAAIQNAYESVQLAPEYIDSVYMGNVLSAGLGQSPARQAAVFAEIPVD 78 
                                           89********99************************************************************* PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                            +a t+n+vCaSg++A +l+aq+i+ G +++v++GG+EsmS+vp++ + +   ++ klg++ l d l+kd+  
  NCBI__GCF_001684965.1:WP_065397633.1  79 KDAATINKVCASGMKATMLGAQQIQLGLEKIVMTGGMESMSNVPHYADVR---QGKKLGDSVLTDGLIKDGlw 148
                                           ********************************************999985...89999*************** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            v+++++mg  Ae   kkyg++R+++D+yal S+q+a++A++++kf++e++ ++v+g+  + v+s+De i  +
  NCBI__GCF_001684965.1:WP_065397633.1 149 dVYNDFHMGSAAELGVKKYGLTRQQLDDYALLSYQRAQEATSKNKFSNELISISVEGRkgTSVISRDEDID-K 220
                                           *99******************************************************9999999******8.8 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           +  ek+a Lkpaf+ ++g   tA+Nss+lnDGAaa+ll s+e++++++l plari+++a a+ +pe ++++p 
  NCBI__GCF_001684965.1:WP_065397633.1 221 LIPEKIALLKPAFE-NDGA-LTAANSSNLNDGAAAILLGSSEAVQQHELVPLARIIAYADAAQSPEWFTTSPS 291
                                           99***********9.59*6.***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            Ai+k+Lk+agls+ did+ EinEA+++++l +++ lg  dl++vNv+GGA+AlGHP+GasGari++tl++ L
  NCBI__GCF_001684965.1:WP_065397633.1 292 IAINKVLKQAGLSLADIDYLEINEAYSSVILSNQQILG-YDLNRVNVYGGAVALGHPIGASGARIIATLINVL 363
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++++++yG+a++C+ggG ++Av++e
  NCBI__GCF_001684965.1:WP_065397633.1 364 RQEKGRYGIAAICNGGGGASAVLIE 388
                                           **********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 14.17
//
[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:

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:

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