GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglG in Pseudomonas simiae WCS417

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate GFF4503 PS417_23050 trehalose permease IIC protein

Query= TCDB::P08722
         (625 letters)



>FitnessBrowser__WCS417:GFF4503
          Length = 480

 Score =  220 bits (560), Expect = 1e-61
 Identities = 141/465 (30%), Positives = 241/465 (51%), Gaps = 29/465 (6%)

Query: 4   LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63
           +AR+I+  +GG+DN+    HC TRLR  LKD S   +  L +   +     +GG FQVVI
Sbjct: 8   IAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTGGLFQVVI 67

Query: 64  G-NHVADVFLAVNSVAGLDEK--AQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI 120
           G   V  V+ A+    GL     A    +  DK N + R V V S +F P++  +   G+
Sbjct: 68  GPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILPALIIAGL 127

Query: 121 LKG----MLALALTFQWTT------EQSGTYLILFSASDALFWFFPIILGYTAGKRFGGN 170
           L G    M A  +  +  T         G + ++   ++  F F P ++G++A KRFGG+
Sbjct: 128 LMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSAAKRFGGS 187

Query: 171 PFTAMVIGGALVHPLILTAFENGQKADALGLDFLGIP---------VTLLNYSSSVIPII 221
               +V+G  LVHP +L A+  G+     GLD   +P         +  + Y   ++PI+
Sbjct: 188 EILGIVLGLMLVHPDLLNAWNYGKAV--AGLDGQSLPYFDIFGWFKIEKVGYQGQILPIL 245

Query: 222 FSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWL 281
            +A++ S++E+ L A +P+AI+    P+  ++V   +   ++GP++  +  LI  G + L
Sbjct: 246 MAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITEGVVTL 305

Query: 282 YQAVPAFAGAVMGGFWQIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAAL 341
           +   P   GA+ G  +   V+ G+H   + + +   +  G   + P+++ + +AQ  AAL
Sbjct: 306 FDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQGSAAL 365

Query: 342 GVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQ 401
            VF   R+A+ K +A ++A+++ FGITEPA++GVNL  K+PF  A +  ALG+  +   +
Sbjct: 366 AVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSIFLALNK 425

Query: 402 TKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAFVGT 446
            +  + G+  +  F+  +P      ++   VIG VIA+   FV T
Sbjct: 426 VQASAIGVGGLPGFISIVPQ-----SIAVFVIGMVIAMVVPFVLT 465


Lambda     K      H
   0.324    0.141    0.427 

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: 855
Number of extensions: 47
Number of successful extensions: 5
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: 625
Length of database: 480
Length adjustment: 36
Effective length of query: 589
Effective length of database: 444
Effective search space:   261516
Effective search space used:   261516
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 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