GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Phaeobacter inhibens BS107

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate GFF3367 PGA1_c34200 carnitinyl-CoA dehydratase CaiD

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Phaeo:GFF3367
          Length = 261

 Score =  136 bits (343), Expect = 4e-37
 Identities = 91/261 (34%), Positives = 137/261 (52%), Gaps = 12/261 (4%)

Query: 6   IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64
           I T++ G +  ITL+RP K NA++ K    +         DPE+RV I+TG G K FC G
Sbjct: 6   IRTRRNGPILEITLDRP-KANAIDLKTSVAMGEVFRDFRDDPELRVAILTGGGEKFFCPG 64

Query: 65  ADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA 124
            D+         +   +   G   + ++  ++KP IA +NG A GGGLELAL+ D+ +AA
Sbjct: 65  WDLKAAADGDAVDG-NYGVGGFGGLQELRDMNKPVIAAVNGIACGGGLELALSADMIVAA 123

Query: 125 EEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPL 184
           + A   LPEI  G       + +L + I    A+E+++TG     ++A ++GLVN +V  
Sbjct: 124 DHATFALPEIRSGTVAD-AASIKLPKRIPYHIAMELLLTGRWFDAEEAHRWGLVNEIVTA 182

Query: 185 ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL------ALESVGWGVVFST 238
             L     +LA  +A   P+  A IKE+V    DS     +       L SV   V++ +
Sbjct: 183 DQLLDRAWELARLLASGPPLVYAAIKEIVRDAEDSKFQDAMNRITKRQLRSV--DVLYDS 240

Query: 239 EDKKEGVSAFLEKREPTFKGK 259
           ED+ EG  AF EKR+P +KG+
Sbjct: 241 EDQMEGARAFAEKRDPVWKGR 261


Lambda     K      H
   0.315    0.135    0.382 

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: 145
Number of extensions: 7
Number of successful extensions: 5
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: 259
Length of database: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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: 42 (22.0 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