GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Cupriavidus basilensis 4G11

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate RR42_RS27120 RR42_RS27120 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>FitnessBrowser__Cup4G11:RR42_RS27120
          Length = 218

 Score =  123 bits (309), Expect = 4e-33
 Identities = 74/207 (35%), Positives = 115/207 (55%), Gaps = 12/207 (5%)

Query: 161 TLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLF 220
           T+V++ V   G   +G+++ L R S     R     FIE ++G PL+  LF++   L LF
Sbjct: 20  TVVLSLVAFAGGAVIGLLVLLMRISRRAPARRAAWAFIEVFQGTPLLMQLFLAFFGLALF 79

Query: 221 LPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVIL 280
              G+     L A + + L+  AY+AE+ RG ++AIPKGQ+EAA  + LG+ + M  VIL
Sbjct: 80  ---GVEIPAWLAAGLALSLWSGAYLAEIWRGCVEAIPKGQWEAAGCLSLGHLQQMRYVIL 136

Query: 281 PQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNS---VKQAAADPKWLGMATEGYVFA 337
           PQAL++ I   V   + + K T+L  IIG  +L  +   +  A   P  +      Y   
Sbjct: 137 PQALRIAIAPTVGFVVQIIKGTALASIIGFVELSKAGTVITNATFSPFTV------YALV 190

Query: 338 ALVFWIFCFGMSRYSMHLERKLDTGHK 364
           AL+++  C+ +SRYS +LERKL+  H+
Sbjct: 191 ALIYFALCWPLSRYSRYLERKLNVAHR 217


Lambda     K      H
   0.330    0.144    0.469 

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: 269
Number of extensions: 13
Number of successful extensions: 3
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: 365
Length of database: 218
Length adjustment: 26
Effective length of query: 339
Effective length of database: 192
Effective search space:    65088
Effective search space used:    65088
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 (21.9 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