GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate 8499218 DvMF_0003 AMP-dependent synthetase and ligase (RefSeq)

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__Miya:8499218
          Length = 557

 Score =  341 bits (875), Expect = 4e-98
 Identities = 205/534 (38%), Positives = 292/534 (54%), Gaps = 20/534 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+  DV + I   + G     I    + G     ++  ++  S ++ + LR  G++KGD
Sbjct: 27  FNFAFDVLDPIAAADPGR--LCIAHVDDAGVRRDYTFAWMAEASAKLANALRLRGIRKGD 84

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V L+       W   LA+ + G V +P+   LT  ++ +R    K   +I D      +
Sbjct: 85  RVMLVLYRRIEFWVSMLALHRLGAVAIPAPAQLTPKDIVFRVERAKTRCVIVDHSITERV 144

Query: 158 EEALGSLKVEKFLI----DGKRETWNSLEDESSNAEPEDTR---------GEDVIINYFT 204
           E A          +    D     W   +   + AE    R         GED ++ +F+
Sbjct: 145 EAARPDCPGLAVCVQVGGDALPRGWVDYDTIFTPAEARFPRPESPLEFAGGEDPLLIFFS 204

Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263
           SGTTGMPK V H   +YP+G + T      +   DLHL L+ TGW K  W  F+   + G
Sbjct: 205 SGTTGMPKMVEHVH-TYPLGHLLTGMYWHDLVPGDLHLTLADTGWGKAVWGKFYGQWMAG 263

Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323
           A+V   ++ GK +    L  +    VT+FCAPPT +R  +  DL  +   +LR   +AGE
Sbjct: 264 ASVFVYDFRGKFEPAALLDVLAAHAVTTFCAPPTVYRFLVRQDLSAYDLSKLRHCTTAGE 323

Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383
            LN  V   WK    L I + YGQTETT  +   P +  K GS+G+P P +D+ L D  G
Sbjct: 324 LLNDSVFHDWKAATGLEIHEGYGQTETTLQIATLPCMTPKAGSIGRPMPGWDVVLQDAAG 383

Query: 384 KEITKPYEVGHITVKL-NPRPIGLFLGYSDEKKNMESFR-EGYYYTGDKAYFDEEGYFYF 441
             I  P E G I V++    P+GLF GY +E +   S    GYY+TGDKA+ DE+GY++F
Sbjct: 384 N-ICPPGEEGEICVRVAEGLPVGLFRGYLEEPEKTASVMFGGYYHTGDKAWMDEDGYYWF 442

Query: 442 VGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPS 501
           +GR DD+IK+S YR+GPFEVESAL+ HPAV EAAV GVPD +R Q VKA +VL  GY  S
Sbjct: 443 LGRVDDLIKSSGYRIGPFEVESALVAHPAVVEAAVTGVPDPLRGQAVKATVVLAAGYTAS 502

Query: 502 KELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKG 555
             L +E+++ +K + +PYK PRII++V ELPKTISGKI+R E+R+R+++    G
Sbjct: 503 DALTKELQDHVKKVTAPYKYPRIIDYVAELPKTISGKIKRAEIRERDQQASGPG 556


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: 733
Number of extensions: 38
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: 557
Length adjustment: 36
Effective length of query: 528
Effective length of database: 521
Effective search space:   275088
Effective search space used:   275088
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 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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