GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02872 in Phaeobacter inhibens BS107

Align N-Acetyl-D-glucosamine ABC transport system, permease component 1 (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component

Query= reanno::Phaeo:GFF2751
         (308 letters)



>FitnessBrowser__Phaeo:GFF1647
          Length = 316

 Score =  115 bits (289), Expect = 1e-30
 Identities = 93/295 (31%), Positives = 149/295 (50%), Gaps = 23/295 (7%)

Query: 16  VFLAPAVLVYTAIMIFPLFNTLRLALYSESDQIRQF----VGLANFETLFGNPNWSEQ-F 70
           ++L+P +L+  ++M+ PL   +  +  S  + +  F    VG  N+E L     WS++ F
Sbjct: 35  LYLSPMILLIGSVMLIPLIVGISYSFQS-IELLNPFATGWVGFENYEKL-----WSDRKF 88

Query: 71  WNALGNNFWFFFVHMLVQNPIGVALAAILSHPRLRFAALYRTAIFVPTILSFVIVGFAWK 130
           W AL N F++ F  +  Q  +G+ LA +L+  +     L++  +F+P  +   +    W 
Sbjct: 89  WIALENTFFWTFWSIFFQFFLGLGLAMLLN-TQFFGKKLFQALVFLPWAVPTFLSALTWA 147

Query: 131 LILSPIWGITPDLLDAIGLKWLFAPW--LGKEDYALTTLALISVWQFVGIPMMLIYAALL 188
            + +P+ G  P  L A+G+  L  P+  LG  D A+      ++W  V    + + AAL 
Sbjct: 148 WLFNPVIGPIPHWLAALGV--LSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQ 205

Query: 189 SIPEEVIEAGEVDGITGMSAFWKIKLPLILPSIGIISILTFVGNFNAFDLIYTTQGALAG 248
           SIP E+ EA E+DG T   +F KI LP + P I I  +L  +   N  DLI+   G   G
Sbjct: 206 SIPGELYEAAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTG--GG 263

Query: 249 PDFSTDILGTFMYRTFFGFQLQLGDPHMGSAIATAMFAIILIGVCIYLFGIQTRL 303
           P  ST IL T+++ T F  +L  G     S IA A+  IIL+   + L  ++ RL
Sbjct: 264 PANSTQILSTYIFTTAFR-KLDFG---YASTIAVALL-IILLAYAVILLWMRKRL 313


Lambda     K      H
   0.331    0.145    0.468 

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: 358
Number of extensions: 34
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: 308
Length of database: 316
Length adjustment: 27
Effective length of query: 281
Effective length of database: 289
Effective search space:    81209
Effective search space used:    81209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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