GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Cupriavidus basilensis 4G11

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate RR42_RS00195 RR42_RS00195 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__Cup4G11:RR42_RS00195
          Length = 309

 Score =  184 bits (467), Expect = 2e-51
 Identities = 101/305 (33%), Positives = 175/305 (57%), Gaps = 10/305 (3%)

Query: 6   QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV 65
           Q + NGL LG IY ++A+G+T+ +G++ +I F+HG+  M+GAF  L     +  L I   
Sbjct: 6   QYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLMLDIQSP 65

Query: 66  PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQIL--QG 123
            + LL +++ ++  T + G  + +    PLR +  L  L++ + +   ++  V++    G
Sbjct: 66  WIRLLAVVLCAICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRESVRLFYPDG 125

Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183
           +  KP   +LP   ++  G++S+    L  +   IA++ G   LITRT  G A RA  QD
Sbjct: 126 SNPKPFPALLP-TASIELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGMAIRAVAQD 184

Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243
            + A L+G+N + V+ LTF +G+ +AA+AG+M  L Y  I+F +G L GV  F AA+LGG
Sbjct: 185 GETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIGFAAAILGG 244

Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYM-------GSEWKDVATFTILVLVLIFRPTGLLGRP 296
           +G++ GA+LGG +   ++   S  +        S +KDV  F ++++++ ++PTGL+   
Sbjct: 245 LGNIYGAILGGFLFAALQVLGSATLPALIPDIPSAYKDVFAFAVVIVLMAWKPTGLIAEK 304

Query: 297 EIEKV 301
             E+V
Sbjct: 305 SSERV 309


Lambda     K      H
   0.329    0.144    0.425 

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: 297
Number of extensions: 17
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: 301
Length of database: 309
Length adjustment: 27
Effective length of query: 274
Effective length of database: 282
Effective search space:    77268
Effective search space used:    77268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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