Alignments for a candidate for fadA in Sphingopyxis indica DS15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingopyxis indica DS15

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_089214379.1 CHB69_RS02585 acetyl-CoA C-acyltransferase

Query= reanno::acidovorax_3H11:Ac3H11_2994
         (397 letters)



>NCBI__GCF_900188185.1:WP_089214379.1
          Length = 395

 Score =  488 bits (1256), Expect = e-142
 Identities = 245/394 (62%), Positives = 300/394 (76%)

Query: 4   TIQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLM 63
           T  DP+V +  ARTPMG +QG  S  +A DLG  A+KAA+ERAGV  + V  +  G  L 
Sbjct: 2   TATDPVVFLSYARTPMGGMQGVLSDASATDLGATAVKAAVERAGVKGEDVERIYMGCVLP 61

Query: 64  AGQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESM 123
           AG GQAPARQAA K GLPK   A T++K+CGSGM+  +M  + L AGS D+ VAGGMESM
Sbjct: 62  AGLGQAPARQAAIKAGLPKSVQATTVNKVCGSGMQTVIMGAEALAAGSIDLAVAGGMESM 121

Query: 124 TNAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDA 183
           TNAPYLL+K R G R+GHD  +DHM LDGLEDAY+AGR+MGTF +D A  Y  +R+ QD 
Sbjct: 122 TNAPYLLKKHRSGARIGHDTAYDHMFLDGLEDAYDAGRAMGTFAQDTADAYQLSRQAQDD 181

Query: 184 FATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKD 243
           +A  S++RA+AA   GAFAAEI PVT+ TR GE VV  DE PGK   +KI TL+PAF KD
Sbjct: 182 YAIESLRRAQAAIADGAFAAEITPVTLTTRKGEVVVDTDEQPGKGNPDKIPTLRPAFAKD 241

Query: 244 GTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQK 303
           GTITAA+SSSI+DGAAA+V+ R+S A+K GAKP+A++V+HA HAQEP+ F  AP+GA  K
Sbjct: 242 GTITAATSSSISDGAAAVVLTRQSVAEKKGAKPVAKLVAHAAHAQEPKDFTVAPIGAINK 301

Query: 304 ALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIM 363
            LAKAGW +GDV L+E+NEAFA V M  M +L +PHD++NVNGGA ALGHPIGASG RI+
Sbjct: 302 VLAKAGWSIGDVDLFEVNEAFACVAMFAMHDLGIPHDRINVNGGATALGHPIGASGTRII 361

Query: 364 VTLIHALKARGLTKGLATLCIGGGEATAVALELV 397
            TLI AL+ RG  +G+A+LCIGGGEATAVA+ELV
Sbjct: 362 ATLIAALQNRGKKRGIASLCIGGGEATAVAIELV 395


Lambda     K      H
   0.317    0.131    0.376 

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: 531
Number of extensions: 22
Number of successful extensions: 1
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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_089214379.1 CHB69_RS02585 (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.368515.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-129  417.6  11.8   2.7e-129  417.4  11.8    1.0  1  NCBI__GCF_900188185.1:WP_089214379.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188185.1:WP_089214379.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.4  11.8  2.7e-129  2.7e-129       2     385 .]      10     393 ..       9     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 417.4 bits;  conditional E-value: 2.7e-129
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesv 74 
                                           ++++Rtp+g ++g+l+++sa dL+a+++k+++erag++ e+++ +++G+vl+ag ++++aR+aa++aglp+sv
  NCBI__GCF_900188185.1:WP_089214379.1  10 LSYARTPMGGMQGVLSDASATDLGATAVKAAVERAGVKGEDVERIYMGCVLPAGLGQAPARQAAIKAGLPKSV 82 
                                           5789*****99************************************************************** PP

                             TIGR01930  75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl... 144
                                           +a+tvn+vC+Sg+q+v+++a++++aG +d++vaGG+Esm+++p+llk++  r+++++g+ + +d++  d+   
  NCBI__GCF_900188185.1:WP_089214379.1  83 QATTVNKVCGSGMQTVIMGAEALAAGSIDLAVAGGMESMTNAPYLLKKH--RSGARIGHDTAYDHMFLDGled 153
                                           ***********************************************97..8999999******999888999 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                             +++ +mg+ A+ +a+ y++sR+ qD+ya++S ++a++Ai++g f++ei+pv++ ++  ++vv++De++  +
  NCBI__GCF_900188185.1:WP_089214379.1 154 aYDAGRAMGTFAQDTADAYQLSRQAQDDYAIESLRRAQAAIADGAFAAEITPVTLTTRkgEVVVDTDEQPG-K 225
                                           88899**************************************************9999888889998887.7 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            + +k+ +L+paf++ +g t+tA+ ss+++DGAaa++l+ ++va+++g +p+a++v++a  + +p++++++p+
  NCBI__GCF_900188185.1:WP_089214379.1 226 GNPDKIPTLRPAFAK-DG-TITAATSSSISDGAAAVVLTRQSVAEKKGAKPVAKLVAHAAHAQEPKDFTVAPI 296
                                           799**********95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            Ai+k+L+kag+si d+dl+E+nEAFA ++++++++lg + ++++NvnGGA AlGHP+GasG+ri++tl+ +L
  NCBI__GCF_900188185.1:WP_089214379.1 297 GAINKVLAKAGWSIGDVDLFEVNEAFACVAMFAMHDLG-IPHDRINVNGGATALGHPIGASGTRIIATLIAAL 368
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++rgkk+G+a+lC+ggG ++Av +e
  NCBI__GCF_900188185.1:WP_089214379.1 369 QNRGKKRGIASLCIGGGEATAVAIE 393
                                           **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (395 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.04
# Mc/sec: 3.73
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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