GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate H281DRAFT_01203 H281DRAFT_01203 acetyl-CoA synthetase

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__Burk376:H281DRAFT_01203
          Length = 567

 Score =  360 bits (923), Expect = e-103
 Identities = 215/537 (40%), Positives = 306/537 (56%), Gaps = 20/537 (3%)

Query: 35  LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94
           L +FNW  D F+ I        TAL   D    E  +LSY ++S  S R+ + LR  G+K
Sbjct: 33  LEQFNWALDYFDVI--ARDNDNTALWIVDDPASEGLRLSYAQMSERSARMANFLRSVGVK 90

Query: 95  KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154
           +GD V LM       W V LA +K G +++P+ T L+  +++ R      + ++ DS   
Sbjct: 91  RGDRVLLMLPNRVELWDVMLAAMKLGAIVLPATTQLSADDVRDRVQIGGANFVVVDSAEL 150

Query: 155 SVMEEALGSLKVEKFLIDGKRETWNSLE---DESSNAEPED-TRGEDVIINYFTSGTTGM 210
           S  +     + + +  +   R  W  L    D S    P+  TR  D ++ YFTSGTT  
Sbjct: 151 SKFDSL--DVPLTRLSVGTPRAGWTDLAAAYDASPQFTPDGVTRAADPLLLYFTSGTTSK 208

Query: 211 PKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270
           PK V HT  SYPVG ++T   +G++  D+H N+S+ GWAK AWS FF+P    A V   N
Sbjct: 209 PKLVEHTHQSYPVGHLSTMYWIGLQPGDIHWNISSPGWAKHAWSCFFAPWNAQACVFVFN 268

Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVI 330
           +  +   +  L  +    VT+ CAPPT WR  +   L  +   +LR +V AGEPLNPE+I
Sbjct: 269 F-ARFVPKDTLDVLVRFNVTTVCAPPTVWRMLVQEHLTDYPV-KLREIVGAGEPLNPEII 326

Query: 331 KIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPY 390
           +  K  + +TIRD +GQTETT  +GN P   V  GSMG+P P Y I LLD + + +T+  
Sbjct: 327 ERVKHAWGITIRDGFGQTETTCQIGNSPGQPVVAGSMGRPLPGYRIELLDADDQPVTE-- 384

Query: 391 EVGHITVKLNP----RPIGLFLGYSD-EKKNMESFREGYYYTGDKAYFDEEGYFYFVGRG 445
             G I + + P    RP+GL  GY++ E+   ++ R G+Y T D A   E+GY+ +VGR 
Sbjct: 385 --GEIALPIGPDGKQRPLGLMTGYANSEQATAQAMRNGFYRTSDVALRREDGYYVYVGRA 442

Query: 446 DDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELA 505
           DDV K+SDYR+ PFE+ES L+EH A+ EAAVV   D +R  + KA++ ++ GY    ELA
Sbjct: 443 DDVFKSSDYRLSPFELESVLIEHEAIGEAAVVPSADALRLSVPKAFVTVRHGYQAGPELA 502

Query: 506 EEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVGQNEY 562
             +    +  L+PYK  R ++F  ELPKTISGKIRRVELR+RE E++ +     +EY
Sbjct: 503 RAVFAFSREKLAPYKRIRRLQF-SELPKTISGKIRRVELRRREMERQAEPARLPDEY 558


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: 758
Number of extensions: 38
Number of successful extensions: 7
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 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