GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Paraburkholderia bryophila 376MFSha3.1

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_01187 H281DRAFT_01187 short chain enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_01187
          Length = 265

 Score =  159 bits (403), Expect = 4e-44
 Identities = 92/249 (36%), Positives = 139/249 (55%), Gaps = 10/249 (4%)

Query: 12  VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEK 71
           V L+TLNRP  +NAL+ A+  +L+   +  +    I   V+TG    F +GADL +  + 
Sbjct: 22  VALVTLNRPEVKNALSRAMRRRLIAIFDEISARNDIRCAVLTGAGDTFCSGADLRDRPDP 81

Query: 72  DLAATLNDTRPQLWAR-----LQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFG 126
           D+     D     W R     ++   KP+IAAVNG ALGAG  L   CD++ A +NA F 
Sbjct: 82  DVPGDFLDHNR--WTRETGNAIKECVKPVIAAVNGAALGAGLGLMAACDIMYASDNAVFA 139

Query: 127 LPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEY 186
           +PEI +G+   AGG   L    G+S   +M  +G+ +TAQ   +  ++ DV P+D  + Y
Sbjct: 140 MPEINVGL---AGGASMLRTLFGRSTVRRMFFTGDKLTAQDLLRRNVLEDVLPADTLMPY 196

Query: 187 ALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQ 246
            ++LA ++AR SP+AL  AK+A   + ++  +     E+ +  +L+ TED  E   AFL+
Sbjct: 197 VMELARRIARKSPIALIEAKKAANFTDQMPQREAYRHEQDITMMLSRTEDAKEARMAFLE 256

Query: 247 KRTPDFKGR 255
           KR P FKGR
Sbjct: 257 KREPVFKGR 265


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: 119
Number of extensions: 7
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: 265
Length adjustment: 24
Effective length of query: 231
Effective length of database: 241
Effective search space:    55671
Effective search space used:    55671
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.

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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