GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21105 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= reanno::Smeli:SM_b21105
         (288 letters)



>FitnessBrowser__Burk376:H281DRAFT_05890
          Length = 317

 Score =  164 bits (415), Expect = 2e-45
 Identities = 93/289 (32%), Positives = 155/289 (53%), Gaps = 30/289 (10%)

Query: 27  LVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQ------------- 73
           L+  LP LWI L+S +   + +A PPV + +  S++ Y  +F+   +             
Sbjct: 30  LIAILPILWICLTSFKTQEDAIAYPPVVLFQP-SMEGYVNLFTIRSRQTPEFIASLPPAQ 88

Query: 74  ---------------GGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAI 118
                          G   V   F NSL++   ST +A+ +G    YAF+R++      +
Sbjct: 89  TWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDL 148

Query: 119 FLGFMLTRAVPGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPK 178
               + TR +P IA+++P++++Y   G+ D++  +I+ Y A+NV   +WL+ GF  ++P+
Sbjct: 149 LFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDEIPR 208

Query: 179 DLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLP 238
           +  EAA +DG T  QAF +V  P A  GIA+  IF  + +WNEYA AS +T S +++T+P
Sbjct: 209 EYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLT-SGDAQTMP 267

Query: 239 VGLLDYTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVK 287
             +     E   DW  + A   + +VP L  T +++KHL+ G+TFGAV+
Sbjct: 268 PFIPFIIGEGGQDWPAVAAATTLFVVPILIFTVVLRKHLLRGITFGAVR 316


Lambda     K      H
   0.328    0.141    0.442 

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: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 288
Length of database: 317
Length adjustment: 27
Effective length of query: 261
Effective length of database: 290
Effective search space:    75690
Effective search space used:    75690
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 (21.8 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