GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Marinobacter adhaerens HP15

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Marino:GFF929
          Length = 259

 Score =  162 bits (411), Expect = 5e-45
 Identities = 100/260 (38%), Positives = 151/260 (58%), Gaps = 6/260 (2%)

Query: 1   MSELI-VSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RF 58
           MS+LI + ++  + +LT+N P A N      L+ L N ++    D  I   V+TG   +F
Sbjct: 1   MSDLIQLEKRGHIAVLTINNPPA-NTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKF 59

Query: 59  FAAGADLNEMAEKDLAAT--LNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDV 116
           ++AGADL   A+ D A    +     + ++ LQ F    IAAVNGYA+G G E A+ CD+
Sbjct: 60  YSAGADLKTFADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDI 119

Query: 117 VVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSD 176
            +A E+A+  LPE  +G++P AGGTQ L   VG+  A +M+L GE + A  A + GLV +
Sbjct: 120 RIAEEHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEE 179

Query: 177 VFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQE-VALQAGLAQERQLFTLLAATE 235
           V PS   L+ AL+LA    + SP +    K  +  +++  +   G   ER+LF  L +TE
Sbjct: 180 VVPSGQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFVELFSTE 239

Query: 236 DRHEGISAFLQKRTPDFKGR 255
           D+ EG++AFL+KR P++K R
Sbjct: 240 DQKEGVNAFLEKRKPEWKNR 259


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: 125
Number of extensions: 10
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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