GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Bacillus altitudinis 41KF2b

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_008343095.1 BA79_RS07740 acyl--CoA ligase

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_000691145.1:WP_008343095.1
          Length = 526

 Score =  326 bits (835), Expect = 2e-93
 Identities = 200/520 (38%), Positives = 289/520 (55%), Gaps = 18/520 (3%)

Query: 37  RFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKG 96
           ++N V ++    H +E   K AL W+D N G EA ++Y  L   +N++   L   G KKG
Sbjct: 11  QYNLVSEIEAFSHDQE---KIALHWQDGN-GHEAHVTYAALVEEANKIGHVLLNAGFKKG 66

Query: 97  DVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASV 156
           D + +M       ++++LA++K G V++P +  L   ++ YR    +    I  +     
Sbjct: 67  DKIIVMVPRMLEAYSIYLAILKTGMVVIPCSEMLRAKDIDYRIEHAEAKGAIVYASFIQS 126

Query: 157 MEEALGSLKVEKFLIDGKRETWNSL----EDESSNAEPEDTRGEDVIINYFTSGTTGMPK 212
            E        + F I      W ++    E++SS  +  DT   D+    +TSGTTG PK
Sbjct: 127 FEGTNQPKDFKTFSIGENDHGWTNIVAQKEEQSSELKLADTTRTDMAFLSYTSGTTGNPK 186

Query: 213 RVIHTAVSYPVGSITTASI--VGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270
            V+HT   +    + TA+   + + E D     +  GW K+ WS   S L  GA   G  
Sbjct: 187 GVVHTH-GWAYAHLRTAAKAWLSINEGDKVWATAGPGWQKWVWSPLLSVLGSGAE--GFV 243

Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEV 329
           Y GK +   YL  ++   +   C  PT +R    +D L Q+   +L S VSAGEPLN EV
Sbjct: 244 YGGKFNPDTYLELLQKNEINVLCCTPTEYRFMAKVDDLSQYELPKLHSAVSAGEPLNREV 303

Query: 330 IKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKP 389
           I  +K  F++ +RD YGQTE+T +VG    + +KPGSMGKP P  ++ ++D+ G +I  P
Sbjct: 304 IDTFKKHFDIEVRDGYGQTESTLLVGVLKGMDIKPGSMGKPTPGNEVEIIDENG-QICAP 362

Query: 390 YEVGHITVKLNPRPIGLFLGYSDEKKNMESFREG-YYYTGDKAYFDEEGYFYFVGRGDDV 448
            E+G I V L      LF  Y  + +  ++ R G Y+ TGD+A  DE+GYF+F  R DD+
Sbjct: 363 GEIGDIAVHLETP--ALFKEYYKDAERTKAQRRGDYFITGDRAKKDEDGYFWFESRRDDI 420

Query: 449 IKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEI 508
           I +S Y +GPFEVE AL++HPAV E AVV  PD +R  +VKAY+VL+     S EL +E+
Sbjct: 421 IVSSGYTIGPFEVEDALIKHPAVKECAVVASPDEIRGSIVKAYVVLRDASTQSDELIKEL 480

Query: 509 REKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKRE 548
           +  +K   +PYK PR IEF+DELPKT S KIRRVELR+RE
Sbjct: 481 QTHVKNTTAPYKYPREIEFIDELPKTPSAKIRRVELRERE 520


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: 678
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: 526
Length adjustment: 35
Effective length of query: 529
Effective length of database: 491
Effective search space:   259739
Effective search space used:   259739
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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