Alignments for a candidate for acs in Methanoculleus horonobensis T10

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanoculleus horonobensis T10

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_067073433.1 MCUHO_RS03545 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_001602375.1:WP_067073433.1
          Length = 567

 Score =  431 bits (1107), Expect = e-125
 Identities = 237/526 (45%), Positives = 326/526 (61%), Gaps = 19/526 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           +N+  DV +    K+R +K A+IW D   G E K ++ +L  +SN+ ++   K+G+KKGD
Sbjct: 26  YNFGFDVIDAWAKKDR-NKLAMIWVD-QKGNEKKYTFFDLMRLSNQAVNICLKYGIKKGD 83

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V LM    P  W   +A+IK G V  P+ T LT  ++KYR        II+ +  A  +
Sbjct: 84  RVMLMLPRTPEWWIFTIALIKLGAVYCPATTMLTPKDLKYRIQAADIRMIITMAEHADKV 143

Query: 158 EEALGSLKV--EKFLIDGKRETWNSLEDESSNAEP-----------EDTRGEDVIINYFT 204
           EE          + + DG R+ W S   E     P             T+  D ++ +FT
Sbjct: 144 EEIREECPTLAVRLMTDGVRDGWVSYPVELDYPAPCSHKLVNLPGMHRTKATDPLLIFFT 203

Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263
           SGTTG PK V+H A SYP+G + TA +   +  +DLHL +S TGW K AW   F   +VG
Sbjct: 204 SGTTGEPKMVVH-AHSYPLGHLVTAQLWHDLHPNDLHLTISDTGWGKSAWGKLFGQWIVG 262

Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323
           A +   +  G+      L  +E  GVT+FC PPT +R  I  DLD+F    +R   SAGE
Sbjct: 263 ACIFVYDIRGRFHATEILPLLEKYGVTTFCCPPTIYRMLILADLDKFDLADMRHCCSAGE 322

Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383
            LNPEVI+ W++    TI + YGQTET   +G  P +K KPGSMG+P P + I LLDD+G
Sbjct: 323 ALNPEVIRAWEEGTGRTIYEGYGQTETVLCIGTLPGMKTKPGSMGRPMPGWQIELLDDDG 382

Query: 384 KEITKPYEVGHITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFV 442
             +    E G I ++++PRP+GLF GY ++  +N + F  G+Y+TGDKAY DE+GYF+F+
Sbjct: 383 NPVGVGEE-GRIAIRVDPRPVGLFSGYLNNGDENHKVFSNGFYFTGDKAYVDEDGYFWFI 441

Query: 443 GRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSK 502
           GR DDVIK+S YR+GPFEVESAL+EHPAV EAAVVG PD +R  +VKA+IVLK GY P++
Sbjct: 442 GRDDDVIKSSGYRIGPFEVESALMEHPAVQEAAVVGSPDVLRGLVVKAFIVLKPGYRPTE 501

Query: 503 ELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKRE 548
            L +EI++++K + +PYK PR+IEFV+ LPKTISGKI+R ELR+ E
Sbjct: 502 SLVKEIQKQVKRVTAPYKYPRLIEFVESLPKTISGKIKRHELRELE 547


Lambda     K      H
   0.318    0.137    0.402 

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: 829
Number of extensions: 34
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: 564
Length of database: 567
Length adjustment: 36
Effective length of query: 528
Effective length of database: 531
Effective search space:   280368
Effective search space used:   280368
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 (21.7 bits)
S2: 53 (25.0 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)
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