Alignments for a candidate for fadA in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Brevibacterium jeotgali SJ5-8

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_101588980.1 BJEO58_RS08110 acetyl-CoA C-acetyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_900169175.1:WP_101588980.1
          Length = 413

 Score =  345 bits (886), Expect = 1e-99
 Identities = 188/403 (46%), Positives = 255/403 (63%), Gaps = 13/403 (3%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           ++V+   +R+ +G FGG  KD+AP ELG  VV   + ++ +  + +  V+FG        
Sbjct: 10  DIVICEPLRSPVGAFGGQFKDIAPEELGRQVVTALIEKSGIRPEAIDDVIFGQCYPHMEA 69

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
              +GRV A++ G+ +  P   V+R CGSGLQA++     I  G   V + GGAESMSRA
Sbjct: 70  PA-IGRVVALDSGLPVTVPGRQVDRRCGSGLQAVLDGMGAIATGGAQVVVAGGAESMSRA 128

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIH-----MGVTAENVAKEYDISRAQQDE 178
           P+     RWG R G+  L D ++        + H     M  TAEN+ +EY I R +QD 
Sbjct: 129 PFFNEDIRWGIRGGNVELKDGLVRGRLTAGGKNHPVPGGMIETAENLREEYSIGREEQDR 188

Query: 179 AALESHRRASAAIKAGYFKDQIVPVV--SKGRKGDVTFDTDEHVRHDATIDDMTKLRPVF 236
            A+ESHRRA+AA  +G F ++I P+   +  ++ +     DEH+R  A+++ + KL+ + 
Sbjct: 189 LAVESHRRATAATDSGVFAEEIAPITLPATRKQPEQQITLDEHIRPSASLESLGKLKAMR 248

Query: 237 VK--ENGTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGP 294
            K  EN TVTAGNASG ND AAA ++  RA+A+  GLKPL R+VS+G AGV P+ MGIGP
Sbjct: 249 AKLDENSTVTAGNASGQNDGAAATIVTTRAKADELGLKPLVRIVSWGVAGVPPRTMGIGP 308

Query: 295 VPATKIALERAGLQVSDLDVIEANEAFAAQACAVTKALGL---DPAKVNPNGSGISLGHP 351
           VPATK+ALERAGL++ DLD+IE NEAFAAQA AVT+  G    D  + N +GSGISLGHP
Sbjct: 309 VPATKVALERAGLEIKDLDLIELNEAFAAQALAVTREWGFGESDFERTNVHGSGISLGHP 368

Query: 352 IGATGALITVKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           +GATG  I      E++R   RY L TMCIGGGQG+AAIFER+
Sbjct: 369 VGATGVRILTTLAREMDRRGARYGLETMCIGGGQGLAAIFERV 411


Lambda     K      H
   0.318    0.134    0.381 

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: 479
Number of extensions: 19
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: 394
Length of database: 413
Length adjustment: 31
Effective length of query: 363
Effective length of database: 382
Effective search space:   138666
Effective search space used:   138666
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_101588980.1 BJEO58_RS08110 (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.4127919.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-134  434.4   0.0     2e-134  434.2   0.0    1.0  1  NCBI__GCF_900169175.1:WP_101588980.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900169175.1:WP_101588980.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.2   0.0    2e-134    2e-134       2     385 .]      14     409 ..      13     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 434.2 bits;  conditional E-value: 2e-134
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesv 74 
                                            + +R+p+g++gg++k++ +e+L+++v+ +l+e++g+ pe+id+vi+G+  ++ e  +i+R +al +glp +v
  NCBI__GCF_900169175.1:WP_101588980.1  14 CEPLRSPVGAFGGQFKDIAPEELGRQVVTALIEKSGIRPEAIDDVIFGQCYPHMEAPAIGRVVALDSGLPVTV 86 
                                           6679********************************************************************* PP

                             TIGR01930  75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl... 144
                                           p+ +v+r C+SglqAv +++ +i++G a+vvvaGG+EsmSr+p+++++   r++++ g+ +l+d l++     
  NCBI__GCF_900169175.1:WP_101588980.1  87 PGRQVDRRCGSGLQAVLDGMGAIATGGAQVVVAGGAESMSRAPFFNEDI--RWGIRGGNVELKDGLVRGRlta 157
                                           *******************************************999985..8************888866899 PP

                             TIGR01930 145 ....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk....kkvvskDe 209
                                                     m+etAenl ++y+i ReeqD++a++Sh++a++A+++g f++ei p++++ +    +++++ De
  NCBI__GCF_900169175.1:WP_101588980.1 158 ggknHPVPGGMIETAENLREEYSIGREEQDRLAVESHRRATAATDSGVFAEEIAPITLPATrkqpEQQITLDE 230
                                           9976334568************************************************98899999999**** PP

                             TIGR01930 210 girpnttlekLakLkpafke..kkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpe 280
                                           +irp  +le+L+kLk++ ++  ++  tvtAgN+s+ nDGAaa++++++++a+elgl+pl rivs++vagv+p+
  NCBI__GCF_900169175.1:WP_101588980.1 231 HIRPSASLESLGKLKAMRAKldENS-TVTAGNASGQNDGAAATIVTTRAKADELGLKPLVRIVSWGVAGVPPR 302
                                           ****************999874444.8********************************************** PP

                             TIGR01930 281 emglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld..lekvNvnGGAiAlGHPlGasGar 351
                                           +mg+gpvpA++ aL++agl+i+d+dl+E+nEAFAaq+lav++e+g ++   e+ Nv+G+ i+lGHP+Ga+G r
  NCBI__GCF_900169175.1:WP_101588980.1 303 TMGIGPVPATKVALERAGLEIKDLDLIELNEAFAAQALAVTREWGFGEsdFERTNVHGSGISLGHPVGATGVR 375
                                           *********************************************955559********************** PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           i++tl++e+ +rg++yGl t+C+ggGqG A+i+e
  NCBI__GCF_900169175.1:WP_101588980.1 376 ILTTLAREMDRRGARYGLETMCIGGGQGLAAIFE 409
                                           ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (413 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.72
//
[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 2024 update 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