GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|MicrobesOnline__882:207735 DVU2250 AMP-binding protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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