GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Amantichitinum ursilacus IGB-41

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>NCBI__GCF_001294205.1:WP_053937456.1
          Length = 221

 Score =  135 bits (340), Expect = 7e-37
 Identities = 79/217 (36%), Positives = 125/217 (57%), Gaps = 11/217 (5%)

Query: 16  LQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPD 75
           LQ   P L++GT  T+  +  +++  +L+G L A  +LS +K L+ PA LY + +RG P 
Sbjct: 7   LQSAWPYLLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPL 66

Query: 76  LVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPR 135
           LV + +I+Y L               I+ +P  AG++ L    GAY +ET RGAI  V R
Sbjct: 67  LVQIFIIYYGLPAI-----------GIQFEPITAGILALSLNTGAYVSETMRGAINGVDR 115

Query: 136 GQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQ 195
           GQ EAA + G+ R Q   ++V+PQ +R A+P + N+ + ++K T+LVS+I + +L+ A +
Sbjct: 116 GQWEAAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLATK 175

Query: 196 DAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERR 232
           +   +T+Q F   V AA IY  ++     + R LERR
Sbjct: 176 EVISTTFQPFPLYVAAAAIYWCLSLIFEQVQRLLERR 212


Lambda     K      H
   0.329    0.142    0.418 

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: 139
Number of extensions: 6
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: 221
Length adjustment: 23
Effective length of query: 219
Effective length of database: 198
Effective search space:    43362
Effective search space used:    43362
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 24 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