Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_041098262.1 SUTH_RS07375 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000828635.1:WP_041098262.1
          Length = 795

 Score = 1085 bits (2805), Expect = 0.0
 Identities = 557/808 (68%), Positives = 644/808 (79%), Gaps = 14/808 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MSNFIV+KVAVLGAGVMGAQIAAH +NA+VPVVLFDLPAKEG KNGI LRAIE LKKLSP
Sbjct: 1   MSNFIVRKVAVLGAGVMGAQIAAHCVNAKVPVVLFDLPAKEGAKNGIVLRAIEGLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APLG K++A  I+ ANY+D++ LLK CDL+IEAIAERMDWKHDLYKKVAP +A +AIFA+
Sbjct: 61  APLGNKDDAACIEVANYDDNLELLKGCDLIIEAIAERMDWKHDLYKKVAPFIAPNAIFAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSITALS+GF  +LK+RFCGVHFFNPPRYMHLVELIPTATT+P+ILDQLE FL TT
Sbjct: 121 NTSGLSITALSEGFSDELKARFCGVHFFNPPRYMHLVELIPTATTRPEILDQLEGFLVTT 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRAKDTPNFIANRVG+FS++A   EAEKFG+  DVVDDLTGSKLGRAKS TFRTA
Sbjct: 181 LGKGVVRAKDTPNFIANRVGVFSMMATIHEAEKFGLSCDVVDDLTGSKLGRAKSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTM HVIKTMQDTL DDPFA +YKTP VL  LV AGALGQKTGAGFYKK G+ ++
Sbjct: 241 DVVGLDTMGHVIKTMQDTLPDDPFAAIYKTPEVLTKLVAAGALGQKTGAGFYKKVGREVQ 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
            LD  TGQYV  G KAD++V R+LK KD A+R+K L +STNPQAQFLWA+FRD FHYIAV
Sbjct: 301 RLDFATGQYVAGGGKADDLVARILKEKDPAKRMKALHDSTNPQAQFLWAIFRDAFHYIAV 360

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419
           +LE +A +A DID A+RWGFG   GPFE WQ+AGW QVA WVKED++AGKAL + PLPAW
Sbjct: 361 HLEAVADNARDIDFAMRWGFGQKLGPFETWQAAGWHQVANWVKEDIDAGKALCSVPLPAW 420

Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479
           VF+G      GVH A GSWSPA ++ VARS LPVY RQ FRA + G A  D   AG TV 
Sbjct: 421 VFDG----RNGVHGADGSWSPARKANVARSTLPVYLRQRFRAPVLGEAGVDGTTAGITVF 476

Query: 480 ENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQL 539
           E+D+VRIW  +  D VL++S K+KM+ IG  VI GL++AI  AE  YKGLV+W   +   
Sbjct: 477 EDDSVRIWHED--DGVLILSLKTKMHVIGAGVIAGLSKAIAEAEQHYKGLVIWSADA--- 531

Query: 540 GAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGG 599
            A GG FSAGA+L++ +P FM GG K IEP V + Q     +KYA+VPVV+A +G+ALGG
Sbjct: 532 -AEGGAFSAGADLQSMLPLFMSGGVKAIEPEVAKLQQAFQAMKYANVPVVAAVAGLALGG 590

Query: 600 GCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTS 659
           GCEL LH+A RVA +E+YIGLVEVGVGL+PAGGGLKEAA+   R A  A   ++LQFL +
Sbjct: 591 GCELALHAAKRVALIESYIGLVEVGVGLIPAGGGLKEAAV---RTAAEAKGNDLLQFLKN 647

Query: 660 RFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTLV 719
            F + A A VS SALEARQMG+L+P D IVFN +ELL+VA+ E RA+  AGYR PL  L+
Sbjct: 648 NFMNPATAAVSKSALEARQMGFLKPDDVIVFNPYELLHVAKVEARAMHDAGYRPPLQRLI 707

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PVAGR  I TI   LVNMRDGGFIS HDF +   IA  V GGDV+ GSLVSE WLL LER
Sbjct: 708 PVAGRYAIGTIMMQLVNMRDGGFISAHDFKLGQMIATVVSGGDVDQGSLVSEQWLLDLER 767

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           KAF++LL   KTQERIMGM+QTGKPVRN
Sbjct: 768 KAFMELLNHPKTQERIMGMMQTGKPVRN 795


Lambda     K      H
   0.319    0.134    0.391 

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: 1743
Number of extensions: 80
Number of successful extensions: 6
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: 807
Length of database: 795
Length adjustment: 41
Effective length of query: 766
Effective length of database: 754
Effective search space:   577564
Effective search space used:   577564
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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)
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