GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF1647 PGA1_c16700 binding
           protein-dependent transport system, inner membrane
           component
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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