Alignments for a candidate for fadB in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Lacinutrix algicola AKS293

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_055437599.1 ASC41_RS15630 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_001418085.1:WP_055437599.1
          Length = 802

 Score =  708 bits (1827), Expect = 0.0
 Identities = 374/800 (46%), Positives = 519/800 (64%), Gaps = 14/800 (1%)

Query: 3   KHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLS 62
           + I+K A++GSG+MGSGIA H ANIG+ VLLLDIVP +LT +E+ KGLT +   VR+RL 
Sbjct: 4   RRIKKVAIIGSGIMGSGIACHFANIGVDVLLLDIVPRELTDKEKAKGLTLEDKVVRNRLV 63

Query: 63  RQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALV 122
             A+   +K KPAPL      + IT GNL+DD  K+K+ DWI+EVVVE L++K+++F  +
Sbjct: 64  NDALTASIKSKPAPLYDISFKNRITTGNLDDDIAKVKDVDWIMEVVVERLDIKQQVFEKL 123

Query: 123 DEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPD 182
           +++R  G++++SNTSGI ++ M EGRS+DF+ HF GTHFFNPARYLKL EIIP  +TD  
Sbjct: 124 EKYRTPGTLITSNTSGIPIKFMNEGRSEDFQKHFCGTHFFNPARYLKLFEIIPGPKTDAS 183

Query: 183 ILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPL 242
           +L+F+  +GE  LGK  V AKDTP FI NR+G + +      + +    V EVD ++GP+
Sbjct: 184 VLEFLNEYGEKFLGKTSVIAKDTPAFIGNRVGIFSIQSLFHAVKELDLTVEEVDKLSGPV 243

Query: 243 IGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDEK-EVFRIPSFMNDMLEKGWIGSKAG 301
           IGRPKSATFRT+DVVGLDT  HVA  + +    DE+ E+F +P F+N M+E  W+GSK G
Sbjct: 244 IGRPKSATFRTVDVVGLDTLVHVANGIRENCPKDERLELFELPDFINTMMENKWLGSKTG 303

Query: 302 QGFYKKE-----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRA 356
           QGFYKK+      K I  LD  TL Y    + K   LE  K       + K L+   D+A
Sbjct: 304 QGFYKKQVSADGKKEILSLDLNTLEYRSAKRAKFATLELTKSIDRVADRFKVLVKGKDKA 363

Query: 357 GRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLE 416
           G       S    Y +  + EI D+++ ID AMK GFGWE GPF++WDAIG+++  E ++
Sbjct: 364 GEFYRKSFSALFAYVSNRIPEITDELYKIDDAMKAGFGWEHGPFQIWDAIGVEKGIEMMQ 423

Query: 417 QLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETKGV 474
             G     W+ +M+  G+++FY  ++G  + YD  +     +      I L  +++T  V
Sbjct: 424 AEGLKPADWVHDMVASGSDSFYSIQDGATYSYDIPKKIQEKIPGQDSFIILDNVRKTTEV 483

Query: 475 IAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFC 534
             KNSG S+ DLGD +  +EF SK N IG D++  ++K ++  E+++ GLV+GNQG NF 
Sbjct: 484 F-KNSGVSVQDLGDGILNVEFQSKMNTIGGDVLAGLNKAIDMAEKDFAGLVVGNQGPNFS 542

Query: 535 VGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPA 594
           VGAN+ MI M   +  + E++  I+ FQ+TMM+++YS+ P ++AP GM LGGG E  L A
Sbjct: 543 VGANIGMIFMMAAEQEYDELNAAIKYFQDTMMRMRYSSIPTISAPHGMALGGGCEISLHA 602

Query: 595 ARIQAASEAYMGLVESGVGLIPGGGGNKELYI---NHLRRGHDPMNAAMKTFETIAMAKV 651
            +I AA+E YMGLVE GVG+IPGGGG+KE+ +   +  R+G   +N   + F TI MAKV
Sbjct: 603 DKIVAAAETYMGLVEFGVGVIPGGGGSKEMALRASDTFRKGDVQLNTLQEYFLTIGMAKV 662

Query: 652 SASAQEAREMNIL-KETDQISVNQDHLLYDAKQLAASLYDTGWRPPVK-EKVKVPGETGY 709
           S SA EA ++ ++ K  D + VN+D  +  AK  A  + D G+  PVK + V V G+   
Sbjct: 663 STSAYEAFDLGLMQKGKDIVVVNKDRQIATAKAHAKLMADAGYTQPVKRDDVLVLGKQAL 722

Query: 710 AALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSG 769
              ++G   MK S YISEHD KIA KLAYV+AGG +   T+V E+YLL++EREAFLSL  
Sbjct: 723 GMFMVGTNSMKDSNYISEHDMKIANKLAYVMAGGDLSEPTKVTEQYLLDLEREAFLSLCT 782

Query: 770 EAKSQARMQHMLVKGKPLRN 789
           E K+  R+QHML KGKPLRN
Sbjct: 783 ERKTLERIQHMLTKGKPLRN 802


Lambda     K      H
   0.316    0.134    0.382 

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: 1505
Number of extensions: 77
Number of successful extensions: 8
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: 789
Length of database: 802
Length adjustment: 41
Effective length of query: 748
Effective length of database: 761
Effective search space:   569228
Effective search space used:   569228
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: 55 (25.8 bits)

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)
Organisms (tab-delimited)
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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