Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Stenotrophomonas chelatiphaga DSM 21508

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_057506694.1 ABB28_RS00230 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_001431535.1:WP_057506694.1
          Length = 402

 Score =  374 bits (960), Expect = e-108
 Identities = 207/397 (52%), Positives = 271/397 (68%), Gaps = 9/397 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+  RTPVGKA KG     RPDD+ A  ++  + +A G + N IDD IIGCA P
Sbjct: 5   IQDAYIVAATRTPVGKAPKGVFRNTRPDDMLAHVLRSVVAQAPGIDVNRIDDAIIGCAMP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQG+N+AR    LAGLP T+ A TVNR+CSSGLQ++A AA++I LG  D  +AGG ES
Sbjct: 65  EAEQGMNVARIGVLLAGLPDTIAAQTVNRFCSSGLQAVAMAADQIRLGNADLMLAGGTES 124

Query: 120 MSQVPMMGH--VTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           MS VPMMG+     P++   +     Y  MG TAE+VA+++ VSRE+QDAFA+ SHQ A 
Sbjct: 125 MSMVPMMGNKIAMAPSVFDNDHVAIAY-GMGITAEKVAEEWKVSREEQDAFALASHQKAI 183

Query: 178 KALAEGKFKDEIVPVEVTVTE--IGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAF- 234
            A+  G+FKDEI P +V   +  + +  + + +  +   DEG R  ++A+ L+ LRP F 
Sbjct: 184 AAIQNGEFKDEISPYDVRTRQPDLADGRRIITRDKIVDTDEGPRLDSSAEGLAKLRPVFR 243

Query: 235 --SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPV 292
                GTVTAGNSSQ SDGA AV+L   +     GL PL +F SF+V GV PEVMGIGP+
Sbjct: 244 NGQFGGTVTAGNSSQMSDGAGAVLLASEQAVKDYGLKPLARFVSFSVAGVRPEVMGIGPI 303

Query: 293 EAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCT 352
            AIP+ALK AGL    +   ELNEAFA+Q++ VIR+ G+D  KVN  GGAIALGHPLG T
Sbjct: 304 AAIPKALKQAGLTQDQLDWIELNEAFAAQSLAVIRDCGLDPSKVNPLGGAIALGHPLGAT 363

Query: 353 GTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           G   T +L+H ++RR +++G+VTMCIG GMGAAG+FE
Sbjct: 364 GAIRTATLLHGLRRRQQKYGMVTMCIGTGMGAAGIFE 400


Lambda     K      H
   0.316    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: 441
Number of extensions: 20
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: 391
Length of database: 402
Length adjustment: 31
Effective length of query: 360
Effective length of database: 371
Effective search space:   133560
Effective search space used:   133560
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_057506694.1 ABB28_RS00230 (acetyl-CoA 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.24116.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-146  472.5   2.5   5.7e-146  472.3   2.5    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506694.1  ABB28_RS00230 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506694.1  ABB28_RS00230 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.3   2.5  5.7e-146  5.7e-146       1     385 []      10     400 ..      10     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.3 bits;  conditional E-value: 5.7e-146
                                 TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 
                                               iv+a+Rtp+g + +g++++++++d+la+v+++++++a g+d ++id++i+G++++++eq +n+aR  +l
  lcl|NCBI__GCF_001431535.1:WP_057506694.1  10 IVAATRTPVGkAPKGVFRNTRPDDMLAHVLRSVVAQApGIDVNRIDDAIIGCAMPEAEQgMNVARIGVL 78 
                                               8*********988******************************************************** PP

                                 TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135
                                                aglp++++a tvnr+C+SglqAva+aa++i+ G+ad+++aGG EsmS vp++ ++      + +  ++
  lcl|NCBI__GCF_001431535.1:WP_057506694.1  79 LAGLPDTIAAQTVNRFCSSGLQAVAMAADQIRLGNADLMLAGGTESMSMVPMMGNK----IAMAPSVFD 143
                                               ***************************************************97766....467777777 PP

                                 TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                               +++      v  ++ mg+tAe++a+++++sReeqD++al+Shqka +Ai++g+fkdei p++v+++   
  lcl|NCBI__GCF_001431535.1:WP_057506694.1 144 NDH------VAIAYGMGITAEKVAEEWKVSREEQDAFALASHQKAIAAIQNGEFKDEISPYDVRTRqpd 206
                                               777......5678***************************************************999** PP

                                 TIGR01930 202 ..........kkvvskDegirpnttlekLakLkpafke.kkgstvtAgNssqlnDGAaalllmseevak 259
                                                         +k+v++Deg+r ++++e LakL+p+f++ + g tvtAgNssq++DGA+a+ll+se+++k
  lcl|NCBI__GCF_001431535.1:WP_057506694.1 207 ladgrriitrDKIVDTDEGPRLDSSAEGLAKLRPVFRNgQFGGTVTAGNSSQMSDGAGAVLLASEQAVK 275
                                               **********9*************************97522339************************* PP

                                 TIGR01930 260 elgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld 328
                                               ++gl+plar+vs++vagv pe+mg+gp+ Ai+kaLk+agl+ +++d++E+nEAFAaq lav+++ g ld
  lcl|NCBI__GCF_001431535.1:WP_057506694.1 276 DYGLKPLARFVSFSVAGVRPEVMGIGPIAAIPKALKQAGLTQDQLDWIELNEAFAAQSLAVIRDCG-LD 343
                                               ******************************************************************.99 PP

                                 TIGR01930 329 lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               ++kvN  GGAiAlGHPlGa+Ga+ ++tll+ L++r++kyG++t+C+g+G+GaA i+e
  lcl|NCBI__GCF_001431535.1:WP_057506694.1 344 PSKVNPLGGAIALGHPLGATGAIRTATLLHGLRRRQQKYGMVTMCIGTGMGAAGIFE 400
                                               ******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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: 00:00:00.02
# Mc/sec: 7.26
//
[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