GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacI in Phyllobacterium brassicacearum STM 196

Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate WP_106712916.1 CU102_RS20280 carbohydrate ABC transporter permease

Query= uniprot:D4GP37
         (309 letters)



>NCBI__GCF_003010955.1:WP_106712916.1
          Length = 316

 Score =  130 bits (327), Expect = 4e-35
 Identities = 88/293 (30%), Positives = 144/293 (49%), Gaps = 33/293 (11%)

Query: 27  YALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVGEGF----TLGNIQFA---LE 79
           Y+++     ++L+PL   +MT++K    +     F+PPV   F    T  N        E
Sbjct: 44  YSVLFVAAIYYLIPLYVMVMTSLKGMPEIRIGNIFSPPVEVTFQPWATAWNSACTGLYCE 103

Query: 80  QLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLML--FVVGVFVPYQAVL 137
            +   FFNS+ + +P+ I S++  S+  Y L+  NWR +   L     + G F+PYQ +L
Sbjct: 104 GIKVGFFNSMKILVPSVILSIIIASVNGYALS--NWRFKGSELFFTALIFGAFIPYQVML 161

Query: 138 VPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSL 197
            PL      +                  G    L  +++ H  +G+PI T+LFR+Y+ SL
Sbjct: 162 YPLVIITRQL------------------GIFGTLTGVIVIHTIFGMPILTLLFRNYFVSL 203

Query: 198 PNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPA 257
           P  L +A ++DGA   +I+ +I+LP+S P+F V  I Q T I+N+FLF    V  +    
Sbjct: 204 PPELFKAARVDGAGFWRIFLQIMLPMSLPIFVVAVILQVTGIWNDFLFG---VIFAGTKN 260

Query: 258 APVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309
            P+T+ L  I  ST G+  + + M+A  L     L++Y    + F +G+   A
Sbjct: 261 FPMTVQLNNIVNSTQGVKEYNVNMAATILTGAVPLLVYFFSGKYFVRGIAAGA 313


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: 260
Number of extensions: 17
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: 309
Length of database: 316
Length adjustment: 27
Effective length of query: 282
Effective length of database: 289
Effective search space:    81498
Effective search space used:    81498
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