GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kce in Pseudomonas simiae WCS417

Align 3-keto-5-aminohexanoate cleavage enzyme; EC 2.3.1.247 (characterized)
to candidate GFF1426 PS417_07250 hypothetical protein

Query= SwissProt::B0VHH0
         (276 letters)



>FitnessBrowser__WCS417:GFF1426
          Length = 310

 Score =  167 bits (424), Expect = 2e-46
 Identities = 105/299 (35%), Positives = 162/299 (54%), Gaps = 29/299 (9%)

Query: 3   PLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIRE-DDGRPSQRLD 61
           P+I+T A+TGA  T +  P+LPIT +E A  A    EAGA ++HLH R+ +DGRPSQ   
Sbjct: 6   PVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQDPA 65

Query: 62  RFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAP-LALKPEMATLNAGTLNFG----- 115
            F E +  I+    +++I I+TGGA     ++RL P +  KPE+A+LN G++NFG     
Sbjct: 66  LFAEFLPQIK-AASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGLYEML 124

Query: 116 -------------------DDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARL 156
                              D IF N   DI  +  A  +     E+E Y+ G +   A  
Sbjct: 125 NRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYTAAHF 184

Query: 157 IKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTA-TWAVAGIGRWHIPTS 215
           +++G++ + PL IQ V G+ GG+ G P++L +M         +   W++ G GR  IP +
Sbjct: 185 LERGLL-KPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLFGSDYVWSILGAGRGQIPLA 243

Query: 216 LIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILAL 274
            + +  G + R G ED+++   G +A SNA  V R+  + + +G  +ATP++AREIL L
Sbjct: 244 TMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREILGL 302


Lambda     K      H
   0.320    0.137    0.396 

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: 224
Number of extensions: 11
Number of successful extensions: 4
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: 276
Length of database: 310
Length adjustment: 26
Effective length of query: 250
Effective length of database: 284
Effective search space:    71000
Effective search space used:    71000
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 (21.8 bits)
S2: 48 (23.1 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