GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacI in Paraburkholderia bryophila 376MFSha3.1

Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate H281DRAFT_00168 H281DRAFT_00168 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= uniprot:D4GP37
         (309 letters)



>FitnessBrowser__Burk376:H281DRAFT_00168
          Length = 285

 Score =  153 bits (387), Expect = 4e-42
 Identities = 93/299 (31%), Positives = 153/299 (51%), Gaps = 29/299 (9%)

Query: 19  VNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVG-------EGFTL 71
           + + R   YA +V F  +FL PL   + T+ K  + +       PP         + ++ 
Sbjct: 5   MTISRAVIYAALVLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPSHWTVEPWIKAWSG 64

Query: 72  GNIQFALEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFV 131
                  + +   F NS+ M IPA + S + G+   Y LT   +R    +  + +VG F+
Sbjct: 65  ACTGVRCDGMQPFFMNSVRMVIPAVLLSSIIGAFNGYVLTHWRFRGADPIFTMLLVGCFI 124

Query: 132 PYQAVLVPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFR 191
           P+QA+L+P+ARF                    F G       LV+ H+ YGI   T+ FR
Sbjct: 125 PFQAILLPMARFEG------------------FLGLSNTTTGLVVVHVIYGIAFTTMFFR 166

Query: 192 SYYQSLPNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVT 251
           ++Y S+P  LV+A +IDGA    I+ +I+LP+S P+F V  I+QFTQI+N+FLF    + 
Sbjct: 167 NFYVSIPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFG---IV 223

Query: 252 GSDAPAAPVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309
            S   + P+T+ L  +  +++G+  + + M+ A +AA+PTL++Y+     F +GL   A
Sbjct: 224 FSGVDSMPITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIVAGRYFVRGLTAGA 282


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: 256
Number of extensions: 14
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: 285
Length adjustment: 26
Effective length of query: 283
Effective length of database: 259
Effective search space:    73297
Effective search space used:    73297
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