GapMind for catabolism of small carbon sources

 

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

Align Histidine transport system permease protein HisQ (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease

Query= SwissProt::P0A2I9
         (228 letters)



>NCBI__GCF_001294205.1:WP_053937456.1
          Length = 221

 Score =  105 bits (263), Expect = 5e-28
 Identities = 69/210 (32%), Positives = 113/210 (53%), Gaps = 11/210 (5%)

Query: 9   ILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLVLMLLI 68
           +L+G   TL  A+ ++V  +L+G + A  +LS  +        Y + +RG P LV + +I
Sbjct: 14  LLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPLLVQIFII 73

Query: 69  FYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAAT 128
           +YGL         ++GI     +P+ AGI+ L    GAY +ET RGA   V +G  EAA 
Sbjct: 74  YYGLP--------AIGIQ---FEPITAGILALSLNTGAYVSETMRGAINGVDRGQWEAAF 122

Query: 129 AFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQLAGKSTW 188
           + G    QT   I++P  +R A+P + N+   ++K T+LVS++ + +++ AT+    +T+
Sbjct: 123 SQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLATKEVISTTF 182

Query: 189 EPFYFAVVCGLIYLVFTTVSNGVLLLLERR 218
           +PF   V    IY   + +   V  LLERR
Sbjct: 183 QPFPLYVAAAAIYWCLSLIFEQVQRLLERR 212


Lambda     K      H
   0.328    0.144    0.422 

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: 121
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: 228
Length of database: 221
Length adjustment: 22
Effective length of query: 206
Effective length of database: 199
Effective search space:    40994
Effective search space used:    40994
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 (21.7 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