GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate AO356_12905 AO356_12905 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_12905
          Length = 245

 Score =  256 bits (654), Expect = 3e-73
 Identities = 139/247 (56%), Positives = 177/247 (71%), Gaps = 10/247 (4%)

Query: 12  PLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIM 71
           PLL I  L K YG   VLKG+DL+++ G VV +IG SGSGK+TLLR +N LE    G I 
Sbjct: 2   PLLRITALHKYYGDHHVLKGIDLTVEEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVIE 61

Query: 72  LDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLP 131
           +DGE +     D + +R  +KV        GM FQQFNLFPHLT  +NV L    V+K+P
Sbjct: 62  VDGEYLDAARADLRSLR--QKV--------GMVFQQFNLFPHLTVGENVMLAPQVVQKVP 111

Query: 132 KDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 191
           K +A  LA + LERVGL E+ D FP +LSGGQQQRVAIARA+AM+P ++L DE+TSALDP
Sbjct: 112 KAKAAELARQMLERVGLGEKFDAFPDRLSGGQQQRVAIARALAMSPKVLLCDEITSALDP 171

Query: 192 ELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 251
           ELV EVL+V++ LA++GMT+++VTHEMRFA EV DK+VFM+QG++ E G PK LF  PQ+
Sbjct: 172 ELVNEVLSVVRQLAKEGMTLIMVTHEMRFAREVGDKLVFMHQGKVHEVGDPKVLFADPQT 231

Query: 252 PRLAEFL 258
             LA F+
Sbjct: 232 AELANFI 238


Lambda     K      H
   0.320    0.138    0.392 

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: 188
Number of extensions: 7
Number of successful extensions: 2
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: 263
Length of database: 245
Length adjustment: 24
Effective length of query: 239
Effective length of database: 221
Effective search space:    52819
Effective search space used:    52819
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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