GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Cupriavidus basilensis 4G11

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_05500
         (242 letters)



>FitnessBrowser__Cup4G11:RR42_RS04400
          Length = 219

 Score =  139 bits (350), Expect = 5e-38
 Identities = 78/218 (35%), Positives = 130/218 (59%), Gaps = 11/218 (5%)

Query: 21  PLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGVPDLVLML 80
           P+L+QG  +TIK + LS++  ++LG + A   +S   + +  A+ Y +++RG P LV + 
Sbjct: 12  PVLLQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPLLVQIF 71

Query: 81  LIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAVPRGQVEA 140
           +++Y L               I ++P  AGV+TL    GAY +E+ RGAIL +PRGQ  A
Sbjct: 72  VVYYGLPGI-----------GIALEPTPAGVLTLSLNVGAYLSESMRGAILGIPRGQWLA 120

Query: 141 ATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKS 200
           A + GL +GQ  R+V+ PQ +R A+P + N+ + ++K T+LVS+I + +L++ AQ+   +
Sbjct: 121 AYSLGLTQGQALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAA 180

Query: 201 TYQLFYFLVLAALIYLLITSASNFILRWLERRYAAGAR 238
           TYQ     +  A IY ++++A   + R LERR +   R
Sbjct: 181 TYQPLPLYLAVAAIYWMLSTALAHMQRLLERRLSLPGR 218


Lambda     K      H
   0.329    0.142    0.423 

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: 151
Number of extensions: 5
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: 242
Length of database: 219
Length adjustment: 23
Effective length of query: 219
Effective length of database: 196
Effective search space:    42924
Effective search space used:    42924
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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