GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Bacillus altitudinis 41KF2b

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_008342913.1 BA79_RS08330 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000691145.1:WP_008342913.1
          Length = 272

 Score =  127 bits (318), Expect = 3e-34
 Identities = 87/256 (33%), Positives = 129/256 (50%), Gaps = 31/256 (12%)

Query: 17  ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGAD--------- 66
           IT+NRP   NA   K + EL  A S+A  + ++ VI++ G G KAFC+G D         
Sbjct: 25  ITINRPHVHNAFTPKTVSELIDAFSRARDNSDVGVIVLAGAGGKAFCSGGDQKVRGHGGY 84

Query: 67  -----ITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121
                I + N L             ++   I  + KP IAM+ GYA+GGG  L + CD+ 
Sbjct: 85  VGDDQIPRLNVL-------------DLQRLIRVIPKPVIAMVAGYAIGGGHVLHVVCDLT 131

Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181
           IAA+ A  G     +G +    G+  L R++G  +A E+     +   ++A   GLVN V
Sbjct: 132 IAADNAIFGQTGPKVGSFDAGYGSGYLARIVGHKKAREIWYLCRQYNAQEALDMGLVNTV 191

Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-ALESVGWGVVFSTED 240
           VPL  LE+ET K  E + +KSP +L  +K   N   D   L+G+         + ++T++
Sbjct: 192 VPLEQLEEETVKWCEDMLEKSPTALRFLKAAFNADTDG--LAGIQQFAGDATLLYYTTDE 249

Query: 241 KKEGVSAFLEKREPTF 256
            KEG  +F EKR+P F
Sbjct: 250 AKEGRDSFKEKRKPDF 265


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: 149
Number of extensions: 9
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: 259
Length of database: 272
Length adjustment: 25
Effective length of query: 234
Effective length of database: 247
Effective search space:    57798
Effective search space used:    57798
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 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