GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Novosphingobium fuchskuhlense FNE08-7

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067906016.1 AQZ52_RS00510 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_001519075.1:WP_067906016.1
          Length = 260

 Score =  297 bits (760), Expect = 2e-85
 Identities = 161/261 (61%), Positives = 195/261 (74%), Gaps = 4/261 (1%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59
           M+YE ILVE RG V L+TLNRPK+LNALN  +++EL  A   ++AD +    V+TGS EK
Sbjct: 1   MSYETILVEQRGAVTLITLNRPKSLNALNSQVLEELIVAFGAYEADPSQRCAVLTGSGEK 60

Query: 60  AFAAGADIGMMSTYTYMDVYKGDYITRNWET--VRSIRKPIIAAVAGFALGGGCELAMMC 117
           AFAAGADI  M+     D Y GD+ +R W +  V++ RKP IAAV GFALGGGCELAMM 
Sbjct: 61  AFAAGADIKEMADKAATDFYTGDFFSR-WTSHLVKTTRKPWIAAVNGFALGGGCELAMMA 119

Query: 118 DIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLV 177
           D I A++ AKFGQPEIKLG+ PG GG+QRL RAV KAKAMD+CLT+R MDA EAER+GLV
Sbjct: 120 DFIIASENAKFGQPEIKLGVAPGMGGSQRLTRAVGKAKAMDMCLTSRMMDAVEAERSGLV 179

Query: 178 SRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFAT 237
           SRV+P ASL+DEA+AAA  IA  P  A +  KE VN A+E TL +G+ FERR+F  L AT
Sbjct: 180 SRVVPLASLIDEAVAAAEAIAAMPPVATIANKEMVNAAFEMTLDQGLLFERRVFQILTAT 239

Query: 238 EDQKEGMAAFVEKRKPVFKHR 258
           ED+ EGMAAF+EKR  V+K R
Sbjct: 240 EDKAEGMAAFIEKRPGVWKGR 260


Lambda     K      H
   0.321    0.134    0.380 

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: 216
Number of extensions: 6
Number of successful extensions: 3
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 (21.9 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