GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacI in Halococcus hamelinensis 100A6

Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate WP_007695789.1 C447_RS16065 carbohydrate ABC transporter permease

Query= uniprot:D4GP37
         (309 letters)



>NCBI__GCF_000336675.1:WP_007695789.1
          Length = 305

 Score =  355 bits (910), Expect = e-102
 Identities = 168/288 (58%), Positives = 223/288 (77%), Gaps = 2/288 (0%)

Query: 20  NLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVGEGFTLGNIQFALE 79
           +L R   Y L++FF+ FFLVPLETG+MTA KT + V  +LPF PP+GE FT      A +
Sbjct: 18  DLSRALLYLLILFFVAFFLVPLETGLMTAFKTTQGVTNTLPFFPPLGEAFTFQKWVDAFD 77

Query: 80  QLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFVPYQAVLVP 139
            L     NS+++++PAT+  +LFGS AAYGLT++NWR Q+ +L+LF++G+F+PYQAVLVP
Sbjct: 78  MLGRGLVNSMVLTVPATLLCLLFGSTAAYGLTLINWRGQIFVLVLFLIGIFIPYQAVLVP 137

Query: 140 LARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSLPN 199
           L+RFW+ + PL   + P+   + F Q  HA+LV L+IT  AYGIPICT+LFR YY SLP 
Sbjct: 138 LSRFWSMV-PLEEWLSPLYV-LSFVQPEHAQLVELIITDAAYGIPICTLLFRGYYLSLPG 195

Query: 200 SLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPAAP 259
            L+EA K+DGAS+T IYRRI+LP+S PM GVVFIYQFTQI+NEFLF  T+V  +D+PAAP
Sbjct: 196 DLIEAAKLDGASVTSIYRRIVLPLSTPMIGVVFIYQFTQIWNEFLFTLTIVGSADSPAAP 255

Query: 260 VTLVLPAIGASTSGINFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRT 307
           VTL+L  +G+S SG++FG+RM+ AF+AA+PTL++YV FAEQFA+GL T
Sbjct: 256 VTLILSGLGSSLSGVDFGMRMAGAFIAALPTLVIYVLFAEQFAEGLET 303


Lambda     K      H
   0.328    0.141    0.413 

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: 344
Number of extensions: 14
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: 309
Length of database: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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: 48 (23.1 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