Alignments for a candidate for fadB in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Sedimenticola selenatireducens DSM 17993

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_029133066.1 A3GO_RS0108695 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000428045.1:WP_029133066.1
          Length = 774

 Score =  531 bits (1367), Expect = e-155
 Identities = 305/795 (38%), Positives = 468/795 (58%), Gaps = 33/795 (4%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I+K AV+G+GVMG+GIAAH++N GIPV+LLDIVP         KG+       R+ ++  
Sbjct: 3   IKKVAVIGAGVMGAGIAAHISNAGIPVVLLDIVP---------KGVDN-----RNAIAEG 48

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
           A++K+LK +PAP    +N   +T GN+ED  E L E DWIIE V+E L++K+ ++  +D 
Sbjct: 49  AVQKMLKVQPAPFMHKRNARLVTTGNIEDHMELLAECDWIIEAVIERLDIKQDLYRKIDS 108

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
            RK GS+VSSNTS I ++++   ++D F   F+ THFFNP RY++LLEI   ++T  D +
Sbjct: 109 VRKPGSVVSSNTSTIPLRDLVAEQTDAFVGDFMITHFFNPPRYMRLLEITAGEKTRADAV 168

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
             +  F +  LGKGVV   DTP FIANRIG + + V + E +  G  V E D++ G  +G
Sbjct: 169 MGIRDFCDRSLGKGVVDCNDTPGFIANRIGIFWIQVAILEAMALGLSVEEADAVMGRPLG 228

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDEKEVFR--IPSFMNDMLEKGWIGSKAGQ 302
            PK+  F   D+VG+D   H+  ++      D+  + +  IP  ++ M+  G+ G K   
Sbjct: 229 IPKTGVFGLSDLVGIDLMPHLMESMQRTLSKDDPFLAKSTIPELVSRMIADGYTGRKGKG 288

Query: 303 GFYK----KEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGR 358
           GFY+      GK    +D V+  Y    K +  +L+A++Q       +KAL+   D+ G+
Sbjct: 289 GFYRINRTAGGKVKESIDLVSGEYNPSRKAQLDSLQASRQ-----GGLKALVNHPDKGGQ 343

Query: 359 LLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQL 418
               + +Q L Y+A L+ EIA++I A+D+AMK G+ W+ GPFE+ D +G     + LE  
Sbjct: 344 YARRVLAQVLGYAASLIPEIAENILAVDEAMKLGYAWKYGPFELIDRLGGSLFGQLLESE 403

Query: 419 GADMPGWIKEMLDKGNETFYIKENGTVFYYD-RGEYRAVKENKKRIHLQALKETKGVIAK 477
           G  +P  I+   +   ++FY  ++G + Y D  G Y+ V   +  + L  +K     +AK
Sbjct: 404 GLSLPPLIQLAAE---QSFYRVQDGQLQYLDTSGIYQDVVRPEGVLLLSDIKRRSEPLAK 460

Query: 478 NSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGA 537
           N  A+L D+GD V  LE+ SK NA+  DI+ ++ + +    + YK LV+ N+G+N+ VGA
Sbjct: 461 NGSAALWDIGDGVVCLEYTSKMNAMDPDILALMREAIGIVSKEYKALVLHNEGENYSVGA 520

Query: 538 NLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARI 597
           NL ++L       + +++ ++   Q+T   +KY+  PV+ AP GM LGGG E  L    +
Sbjct: 521 NLGLLLFAANIGTWDQIEEMVEGGQQTYKALKYAPFPVIGAPAGMALGGGCETLLHCDAV 580

Query: 598 QAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKVSAS 654
           QA +E Y+GLVE GVGLIPG GG KE+   ++ + RR   PM A +K FETI+ A V+ S
Sbjct: 581 QAHAETYIGLVEVGVGLIPGWGGCKEMLQRWMINKRRPGGPMPAVIKCFETISTATVAKS 640

Query: 655 AQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLL 714
           A EA++    +  D +++N+D LL DAK  A +L D G++PP   ++ +PG T  AA+ +
Sbjct: 641 AAEAKDYLFFRPDDGVTMNRDRLLADAKSRALALAD-GYQPPQPIEISLPGPTAKAAMEM 699

Query: 715 GAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQ 774
             +   L+G  ++HD  +A  LA +++GG       + E+ LL +ERE F+SL     + 
Sbjct: 700 AVKGFHLAGKATDHDVVVAMALAEMLSGGDTDITESLTEDDLLGLEREVFMSLIRHPDTL 759

Query: 775 ARMQHMLVKGKPLRN 789
            RM+HML  GKPLRN
Sbjct: 760 DRMEHMLETGKPLRN 774


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: 1396
Number of extensions: 70
Number of successful extensions: 7
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: 774
Length adjustment: 41
Effective length of query: 748
Effective length of database: 733
Effective search space:   548284
Effective search space used:   548284
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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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