GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfovibrio vulgaris Hildenborough

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate 207735 DVU2250 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>MicrobesOnline__882:207735
          Length = 551

 Score =  360 bits (923), Expect = e-103
 Identities = 212/530 (40%), Positives = 299/530 (56%), Gaps = 20/530 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+  DV  D    E   + A+   D + G     ++  L+  S R+ + L+  G++KG 
Sbjct: 24  FNFAFDVL-DAMANETPDRLAIAHVD-DAGVRRDYTFAWLADASARLANALKARGVRKGH 81

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V L+       W   LA+ + G V +P+   LT  ++ +R    +  A+I D      +
Sbjct: 82  RVMLVLHRRIEFWVSMLALHRLGAVAIPAPAQLTPKDIVFRVERAQVRAVIVDDGITDRI 141

Query: 158 EEALGSLKVEKFLID----GKRETWNSLEDESSNAEPEDTR---------GEDVIINYFT 204
           E A         L+        + W   E   ++A P   R         GED ++ +F+
Sbjct: 142 EAARPDCPTLSVLVQCGGTPLPDGWCDYEALCADASPSFPRPTAPDELACGEDPLLIFFS 201

Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263
           SGTTGMPK V H   +YP+G + T      +R  DLHL ++ TGW K  W  F+   + G
Sbjct: 202 SGTTGMPKMVEHVH-TYPLGHLVTGMYWHDLRPGDLHLTVADTGWGKAVWGKFYGQWMAG 260

Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323
           A V   ++ GK D    L  V   GVT+FCAPPT +R  +  DL ++   +LR   +AGE
Sbjct: 261 AAVFVYDFRGKFDPEALLDVVAKNGVTTFCAPPTVYRFLVRADLSRYDLSKLRHCTTAGE 320

Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383
            LN  V   WK    L+I + YGQTETT  +     ++ KPGS+G+P P + I LLD EG
Sbjct: 321 LLNESVFHGWKAATGLSIYEGYGQTETTLQIATLSCMEAKPGSIGRPMPGWGITLLDHEG 380

Query: 384 KEITKPYEVGHITVKLNPR-PIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYF 441
           KE     E G I ++++   P+GLF GY  D +K      +GYY+TGDKA+ DE+GY +F
Sbjct: 381 KECPTGEE-GEICIRISDGLPVGLFRGYVEDAEKTASVMFDGYYHTGDKAWMDEDGYLWF 439

Query: 442 VGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPS 501
           +GR DD+IK+S YR+GPFEVESAL+ HPAV EAAV GVPD +R Q VKA IVL  GY   
Sbjct: 440 LGRVDDLIKSSGYRIGPFEVESALVAHPAVVEAAVTGVPDPLRGQAVKATIVLAAGYEAG 499

Query: 502 KELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEK 551
           + L +E+++ +K + +PYK PRI+E+V ELPKTISGKI+R E+R+R+ EK
Sbjct: 500 EVLTKELQDHVKKVTAPYKYPRIVEYVAELPKTISGKIKRAEIRQRDSEK 549


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: 724
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: 551
Length adjustment: 36
Effective length of query: 528
Effective length of database: 515
Effective search space:   271920
Effective search space used:   271920
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