GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacI in Pseudomonas putida KT2440

Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate PP_1017 PP_1017 mannose/glucose ABC transporter, permease protein

Query= uniprot:D4GP37
         (309 letters)



>FitnessBrowser__Putida:PP_1017
          Length = 281

 Score =  159 bits (403), Expect = 6e-44
 Identities = 99/293 (33%), Positives = 167/293 (56%), Gaps = 26/293 (8%)

Query: 19  VNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVAR-SLPFAPPVGEGFTLGNIQFA 77
           ++L R+A +A+++  +  +LVPL   ++T+ KT E +   +L   P V  G  +G ++ A
Sbjct: 10  LSLSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWPAVITG--IGWVK-A 66

Query: 78  LEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFVPYQAVL 137
              +SG F+NS+++++PA + S   G++  Y L+M  +R       L + G F+P+Q VL
Sbjct: 67  WGAVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVL 126

Query: 138 VPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFRSYYQSL 197
           +P +      F L ++            G  +    LV+ H+ YG+   T+ FR++Y S+
Sbjct: 127 LPAS------FTLGKL------------GLASTTGGLVLVHVVYGLAFTTLFFRNFYVSI 168

Query: 198 PNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVTGSDAPA 257
           P++LV+A ++DGA    I+RRIILP+S P+  V  I+QFTQI+N+FLF    V  S   +
Sbjct: 169 PDALVKAARLDGAGFFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFG---VVFSSGDS 225

Query: 258 APVTLVL-PAIGASTSGINFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309
            P+T+ L   +  ST    + + M+AA +A +PTL++YV   + F +GL   A
Sbjct: 226 QPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGA 278


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: 246
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: 281
Length adjustment: 26
Effective length of query: 283
Effective length of database: 255
Effective search space:    72165
Effective search space used:    72165
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 17 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