GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Bacillus altitudinis 41KF2b

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>NCBI__GCF_000691145.1:WP_035704417.1
          Length = 260

 Score =  184 bits (467), Expect = 2e-51
 Identities = 101/246 (41%), Positives = 155/246 (63%), Gaps = 5/246 (2%)

Query: 14  LLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITG-NARFFAAGADLNE---MA 69
           ++TLNRPA  NAL+ A+L ++   ++    D +I   ++TG  A+ F AGADL E   M 
Sbjct: 16  IMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLKERRLMT 75

Query: 70  EKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129
           E++    +  T  Q +  +++   P+IA +NG+ALG G ELAL CD+ +A   A  GLPE
Sbjct: 76  EQEAKEAVL-TIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAALGLPE 134

Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQ 189
             L I+PGAGGTQRL R +G   A +M+ +G S+ A++A Q GL+  +  +D  +  A+ 
Sbjct: 135 TGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLMNDAIT 194

Query: 190 LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRT 249
           LA ++ ++ P+AL+ AKQA++ S +  LQ GL +E + +  L  TEDR EG+ AF +KRT
Sbjct: 195 LAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKAFQEKRT 254

Query: 250 PDFKGR 255
           P ++G+
Sbjct: 255 PHYRGK 260


Lambda     K      H
   0.318    0.130    0.356 

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: 101
Number of extensions: 2
Number of successful extensions: 1
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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