Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3009
          Length = 427

 Score =  284 bits (726), Expect = 4e-81
 Identities = 162/426 (38%), Positives = 242/426 (56%), Gaps = 11/426 (2%)

Query: 14  RIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQMPEA 73
           R+ ++ G+R PF R  TA+  +    +   V+G L+ R  +  E + ++  G V++    
Sbjct: 7   RVGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERFRLHGEELGEVAMGAVIKHSSE 66

Query: 74  PNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLP 133
            N+ARE VL +G+   T   + +RAC TS      +A  + AG I AGIAGG+D++S +P
Sbjct: 67  WNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDVP 126

Query: 134 IGVSKKLARVLVDVNKARTMSQRLKLFSR-LRLRDLMPVPPAVAEYSTGLRMGDTAEQMA 192
           I + ++  + L+ +N+A+    ++  F+R   L++L P  P VAE  TG+ MGD  E+MA
Sbjct: 127 IVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHCERMA 186

Query: 193 KTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSLAD 252
           K + I RE QD LA  SHQ+ A A+  G  ++ V+     P++  L  D  +R +SS+  
Sbjct: 187 KEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVV-----PFRG-LKRDGFLRADSSMEK 240

Query: 253 YAKLRPAFDR--KHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
              L+PAFD+   HGT+TA NST L+DGAAAV+L ++  A   GL    Y       A+D
Sbjct: 241 LGTLKPAFDKISGHGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVAAVD 300

Query: 311 V--WQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALG 368
               + +L+ P  + P  L R GLT+ D    ++HEAFAAQ L  ++   SE + R  LG
Sbjct: 301 FVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCRNRLG 360

Query: 369 RAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLG 428
                G +D +K NV G S+A GHPFAATGAR++      L  +G G GL++ C AGG+G
Sbjct: 361 LEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISICTAGGMG 420

Query: 429 AAMVLE 434
              +LE
Sbjct: 421 VTAILE 426


Lambda     K      H
   0.319    0.133    0.377 

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: 426
Number of extensions: 24
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: 436
Length of database: 427
Length adjustment: 32
Effective length of query: 404
Effective length of database: 395
Effective search space:   159580
Effective search space used:   159580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate N515DRAFT_3009 N515DRAFT_3009 (acetyl-CoA C-acetyltransferase)
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.13657.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.9e-117  378.4   0.1   2.1e-117  378.2   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009  N515DRAFT_3009 acetyl-CoA C-acet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3009  N515DRAFT_3009 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.2   0.1  2.1e-117  2.1e-117       1     385 []      10     426 ..      10     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 378.2 bits;  conditional E-value: 2.1e-117
                                    TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaal 66 
                                                  +++++R+p+++ +++++++ +  ++++v+ +l+er+ l+ e++ ev++G+v++++++ n+aRea+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009  10 VIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERFRLHGEELGEVAMGAVIKHSSEWNLAREAVL 75 
                                                  789*******88****************************************************** PP

                                    TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklg 132
                                                  ++gl  ++p++t  r+C+++l+  ++ a+ki+aG++++ +aGG +++S+vpi+l ++ r++ l ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009  76 SSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDVPIVLGERFRKRLLAIN 141
                                                  ****************************************************************99 PP

                                    TIGR01930 133 kakledqllkdl..................vktklsmgetAenlakkygisReeqDeyalrShqka 180
                                                  +ak  + ++  +                  ++t++smg + e++ak+++i Re qD++al+Shqk 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009 142 RAKGWQDKMAAFtrgfslkelkpsfpgvaePRTGMSMGDHCERMAKEWHIGREAQDRLALESHQKL 207
                                                  999888777766899***************9*********************************** PP

                                    TIGR01930 181 akAieegkfkdeivpvevkgkkkvvskDegirpnttlekLakLkpafke..kkgstvtAgNssqln 244
                                                  a+A+e+g+f+d +vp++       +++D  +r+++++ekL++Lkpaf++   +g t tAgNs++l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009 208 AAAYEAGFFEDLVVPFRG------LKRDGFLRADSSMEKLGTLKPAFDKisGHG-TLTAGNSTGLS 266
                                                  ***************655......679*********************977777.7********** PP

                                    TIGR01930 245 DGAaalllmseevakelgltplarivsaavagvdp...eemglgpvpAiekaLkkaglsisdidlv 307
                                                  DGAaa+ll s+e+a++ gl++ a++ +a+va+vd    e ++++p+ A++++L+++gl+++d+d++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009 267 DGAAAVLLGSDEWAARRGLKVQAYFLDAEVAAVDFvhgEGLLMAPTVAVPRMLARHGLTLQDFDFY 332
                                                  **********************************9999**************************** PP

                                    TIGR01930 308 EinEAFAaqvlavekelgs................ldlekvNvnGGAiAlGHPlGasGarivltll 357
                                                  Ei+EAFAaqvl   ++++s                +d++k+Nv+G+++A+GHP++a+Gariv+tl+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009 333 EIHEAFAAQVLCTLRAWESetycrnrlgleqplgsIDPAKLNVHGSSLAAGHPFAATGARIVATLA 398
                                                  *********************************8777***************************** PP

                                    TIGR01930 358 keLkergkkyGlatlCvggGqGaAvile 385
                                                  k+L+e+g  +Gl+++C +gG+G+++ile
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3009 399 KMLEEKGSGRGLISICTAGGMGVTAILE 426
                                                  *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (427 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: 10.82
//
[ok]

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

Downloads

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

Related tools

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