GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bglF in Pseudomonas fluorescens FW300-N2E3

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate AO353_15980 AO353_15980 trehalose permease IIC protein

Query= TCDB::P08722
         (625 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15980 AO353_15980 trehalose
           permease IIC protein
          Length = 480

 Score =  214 bits (546), Expect = 5e-60
 Identities = 139/465 (29%), Positives = 236/465 (50%), Gaps = 29/465 (6%)

Query: 4   LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63
           +A +++  +GGADN+    HC TRLR  LKD  +  +  L +   +     +GG FQVVI
Sbjct: 8   IASELLHSLGGADNLEQAAHCVTRLRLALKDPQRVDSATLNQIDLVKGSFFTGGLFQVVI 67

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

Query: 121 L---------KGMLALALTF-QWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGN 170
           L         KGM     T  +      G + ++   ++  F F P ++G++A KRFGG+
Sbjct: 128 LMGVNNLIGAKGMFIAGKTLLEAYPTLDGVWSLINLMANTSFVFLPALVGWSAAKRFGGS 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 MAAYVMSVIEKWLRARVPNAIQLLVVPITTIVVTGVLALAVIGPVTRHLGILITEGVVTL 305

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

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

Query: 402 TKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAFVGT 446
            +  + G+  +  F+  IP       +   ++G VIA+   FV T
Sbjct: 426 VQASAIGVGGLPGFISIIPQ-----FIPMFIVGMVIAMVVPFVLT 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: 881
Number of extensions: 53
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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