Alignments for a candidate for fadA in Flavobacterium glycines Gm-149

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Flavobacterium glycines Gm-149

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate WP_066329932.1 BLR17_RS08645 acetyl-CoA C-acyltransferase

Query= SwissProt::P41338
         (398 letters)



>NCBI__GCF_900100165.1:WP_066329932.1
          Length = 392

 Score =  434 bits (1117), Expect = e-126
 Identities = 233/398 (58%), Positives = 299/398 (75%), Gaps = 6/398 (1%)

Query: 1   MSQNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKVPELDASKDFDEIIFGNVL 60
           MS+ V IV+  RTPIGSF G L++ +A +LGA A+KGAL K+  LD +   DE++ GNV+
Sbjct: 1   MSKKVVIVAAVRTPIGSFMGGLANVSAPQLGAAAIKGALDKI-NLDPNL-VDEVLMGNVI 58

Query: 61  SANLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGGCES 120
            A +GQAPARQ AL AGL N I  +T+NKVCAS MKA+++ AQ+I+ G+A++VVAGG E+
Sbjct: 59  QAGVGQAPARQAALFAGLKNTIPCTTINKVCASGMKAVMMAAQAIQTGDAEIVVAGGMEN 118

Query: 121 MTNAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQQDN 180
           M+  P+Y    R+G KFG   L DG++RDGL DAYD  AMGV+A+ CA  ++I+RE+QDN
Sbjct: 119 MSLIPHYTHL-RSGTKFGPATLTDGMQRDGLVDAYDNQAMGVYADLCANQYNISREEQDN 177

Query: 181 FAIESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSARTVFQ 240
           FAIESY++S ++   GKFD E+VPV +   RG+P   + KDEE   + ++K+ S   VF 
Sbjct: 178 FAIESYRRSAQAWDTGKFDAEVVPVAVPQRRGEPIV-IAKDEEYTNVKLDKIPSLNAVFT 236

Query: 241 KENGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAPSLA 300
           K+ GTVTAANAS INDGAAA+IL+SE+   E  LKPLA IK + +AA +P  FT +P+ A
Sbjct: 237 KD-GTVTAANASTINDGAAALILMSEEKAAELQLKPLAYIKSYADAAQEPKWFTTSPAKA 295

Query: 301 VPKALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLGCSG 360
           +PKAL  AGI  IN VD+FEFNEAFSVVGL N KIL LD +KVNV GGAV+LGHPLGCSG
Sbjct: 296 LPKALDKAGIT-INDVDFFEFNEAFSVVGLANIKILGLDSAKVNVNGGAVSLGHPLGCSG 354

Query: 361 ARVVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEKI 398
           AR++V+LL IL+Q   K G AAICNGGGGAS+IVIE+I
Sbjct: 355 ARILVSLLHILEQNNAKTGAAAICNGGGGASAIVIERI 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: 433
Number of extensions: 16
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: 392
Length adjustment: 31
Effective length of query: 367
Effective length of database: 361
Effective search space:   132487
Effective search space used:   132487
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_066329932.1 BLR17_RS08645 (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.3638905.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-143  462.2   6.1   7.2e-143  462.1   6.1    1.0  1  NCBI__GCF_900100165.1:WP_066329932.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066329932.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.1   6.1  7.2e-143  7.2e-143       1     385 []       7     390 ..       7     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 462.1 bits;  conditional E-value: 7.2e-143
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+avRtpig++ g l+++sa +L+aa+ik++l++ +ldp+ +dev +Gnv+qag ++++aR+aal agl+++
  NCBI__GCF_900100165.1:WP_066329932.1   7 IVAAVRTPIGSFMGGLANVSAPQLGAAAIKGALDKINLDPNLVDEVLMGNVIQAGVGQAPARQAALFAGLKNT 79 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           +p +t+n+vCaSg++Av++aaq+i++G+a++vvaGG+E+mS +p++++    r++ k+g a+l d +++d+  
  NCBI__GCF_900100165.1:WP_066329932.1  80 IPCTTINKVCASGMKAVMMAAQAIQTGDAEIVVAGGMENMSLIPHYTHL---RSGTKFGPATLTDGMQRDGlv 149
                                           ********************************************98887...58999999************* PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirp 213
                                            ++++ +mg+ A+ +a++y+isReeqD++a++S++++a+A++ gkf++e+vpv v+++   + v++kDe+ + 
  NCBI__GCF_900100165.1:WP_066329932.1 150 dAYDNQAMGVYADLCANQYNISREEQDNFAIESYRRSAQAWDTGKFDAEVVPVAVPQRrgePIVIAKDEE-YT 221
                                           *999****************************************************99**6666666666.66 PP

                             TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                           n++l+k+ +L+++f++ +g tvtA+N+s +nDGAaal+lmsee+a+el+l+pla+i s+a a+ +p+ ++++p
  NCBI__GCF_900100165.1:WP_066329932.1 222 NVKLDKIPSLNAVFTK-DG-TVTAANASTINDGAAALILMSEEKAAELQLKPLAYIKSYADAAQEPKWFTTSP 292
                                           **************95.9*.6**************************************************** PP

                             TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359
                                           ++A +kaL+kag++i+d+d++E+nEAF+++ la++k lg ld +kvNvnGGA++lGHPlG+sGari+++ll+ 
  NCBI__GCF_900100165.1:WP_066329932.1 293 AKALPKALDKAGITINDVDFFEFNEAFSVVGLANIKILG-LDSAKVNVNGGAVSLGHPLGCSGARILVSLLHI 364
                                           ***************************************.89******************************* PP

                             TIGR01930 360 LkergkkyGlatlCvggGqGaAvile 385
                                           L+++++k G a++C+ggG ++A+++e
  NCBI__GCF_900100165.1:WP_066329932.1 365 LEQNNAKTGAAAICNGGGGASAIVIE 390
                                           ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 13.54
//
[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