Alignments for a candidate for fadA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dechlorosoma suillum PS

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__PS:Dsui_0323
          Length = 645

 Score =  312 bits (799), Expect = 4e-89
 Identities = 214/695 (30%), Positives = 334/695 (48%), Gaps = 64/695 (9%)

Query: 30  TTSSALLSRTHINYGVKGDVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAV 89
           T +S      H+     G +A + ++      N+L+K V +E   V++E+      ++ +
Sbjct: 5   TQTSLTQQHWHLTREADG-LAWLSLDKAGESANSLSKAVMAELSGVLDEL-DRQPPKALI 62

Query: 90  LISSKPGCFVAGADINMLASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGG 149
           + S+K   F+AGADI+      +P+ A  +   G ++F +L   P P +A + G CLGGG
Sbjct: 63  IRSAKSAGFIAGADISEFDQLDSPEAAKAMVARGWELFNRLAAVPYPTLALVRGHCLGGG 122

Query: 150 LELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRA 209
           LELA+AC+  +   +  T LG+PEV+LGI PG GG  RLP+ VG   A D+ML G+ + A
Sbjct: 123 LELALACRTLLVVDEPGTKLGLPEVMLGIFPGWGGMLRLPRRVGPAVALDLMLAGKTVDA 182

Query: 210 DRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLT 269
            +AK++GL D+ V P               +E  A   A     RK      +  +  L 
Sbjct: 183 KKAKRLGLADECVPP-------------RVMESAARQLALNPPSRKPLPLLQRLFLGPLR 229

Query: 270 SYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGE 329
                   V  Q  K V ++ + +    YPAP  IID     L    D   LA  E    
Sbjct: 230 GV------VAGQARKQVAKRARPEH---YPAPYAIID-----LWAKYDGNALAAPEITDR 275

Query: 330 LALTKESKALMGLYNGQVLCKKNKFGAPQKTV-QQLAILGAGLMGAGIAQVSVDKGLKTL 388
           +  +  ++ L+ +++ Q   K   FG     V +++ ++GAG+MG  IA     +GL   
Sbjct: 276 IVRSATARNLVRVFHLQERLKA--FGKDSAFVAKRVHVVGAGVMGGDIAAWCAGRGLTVT 333

Query: 389 LKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAV 448
           L+D  V  +    ++   G   +++ K     +  ++   LI   +  G   AD+VIEA+
Sbjct: 334 LQDQNVERIAPAIKRAHAGFARRIRDK----LQLRAVMDRLIPDPEGHGAAHADVVIEAI 389

Query: 449 FEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQL 508
           FE+L  KH +LK +E+      + A+NTS+L +  I  V QRPE+++G+H+F+PV KM L
Sbjct: 390 FENLEAKHSLLKGLEARMKPDAVLATNTSSLKLEDIRTVLQRPERLVGIHFFNPVAKMPL 449

Query: 509 LEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDP 568
           +E++T      + T  A A      K+ + V+  PGF     L P + E +R + EG+ P
Sbjct: 450 VEVVTAAGGDAEVTRQACAFVRGIDKLPLPVQSAPGFLVNAVLGPYLLEAMRCVDEGIAP 509

Query: 569 KKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMV---SK 625
           + +D     FG P+G   LAD VG+D+A         A G+   G   E  K +V    +
Sbjct: 510 ETVDEAALAFGMPMGPIELADTVGLDIAM--------AAGKALAGNGTEPPKCLVQRFER 561

Query: 626 GFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEA 685
           G LGRKSGKGFY Y +G   K     +         PA         +  R++   +   
Sbjct: 562 GDLGRKSGKGFYAYPAGKIQKGAAGAV---------PA--------GLAERLVQPLLQRT 604

Query: 686 VLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRF 720
              +  G++A  E  D G +FG GF P  GGP  +
Sbjct: 605 QQLVDAGVVADAELADAGVIFGTGFAPFTGGPLNY 639


Lambda     K      H
   0.317    0.135    0.380 

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: 1018
Number of extensions: 53
Number of successful extensions: 4
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: 763
Length of database: 645
Length adjustment: 39
Effective length of query: 724
Effective length of database: 606
Effective search space:   438744
Effective search space used:   438744
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: 54 (25.4 bits)

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

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Protein sequences (fasta format)
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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