GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Sphingopyxis indica DS15

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_089217560.1 CHB69_RS19545 sugar MFS transporter

Query= SwissProt::P11551
         (438 letters)



>NCBI__GCF_900188185.1:WP_089217560.1
          Length = 417

 Score =  221 bits (563), Expect = 3e-62
 Identities = 139/415 (33%), Positives = 217/415 (52%), Gaps = 14/415 (3%)

Query: 27  PFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMK 86
           P ALL SLFF+W     +N+ LLP  +  F L   Q  LI+S ++  Y +  +P+  L++
Sbjct: 4   PLALLASLFFMWGFITVINNTLLPHLRSVFELDYTQTTLIESVWFIAYAVASMPSAFLIE 63

Query: 87  KLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLG 146
           ++ YK  II GL + A GA    PAA I +Y + L+ LF+IA G+  L+ AANP+V V+G
Sbjct: 64  RVGYKRAIIIGLLIMAAGALGMVPAARIPSYEITLLALFVIACGIALLQVAANPYVAVIG 123

Query: 147 PESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKH-SLV 205
           P  S   RL L Q FNS G   A  FG  LILS          + +   QL+A +  +  
Sbjct: 124 PPESSESRLTLVQAFNSMGTFFAPYFGGYLILSRTTGG-----NSLEGAQLTAAERLADA 178

Query: 206 LSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSR-----LARIRHW 260
            + Q PY+++ A+++++AL+    K PAL +           +  L +     + + R+ 
Sbjct: 179 QATQLPYVMVAAVLVIIALVFWRAKLPALGAATRRAHASERTTVPLWKVWAHPIYKHRNL 238

Query: 261 RWAVLAQFCYVGAQTACWSYLIRYAV-EEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLI 319
            + + A F Y+ A+    +  I +A+  EI G+T   AANYL        +GRF G +++
Sbjct: 239 AFGIPAIFIYLIAEIGVANLFINFAILPEIAGITPAKAANYLVLLWGGMMVGRFAGAFIM 298

Query: 320 SRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQD 379
             F  +KVLA YA  A  + + +A   G V +  L L     SI +P IF++GIK LG  
Sbjct: 299 RAFPANKVLAVYASAAFLVMIGAATLHGPVAMWCLILVGLCHSIMFPAIFAMGIKGLGPL 358

Query: 380 TKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFRSQ 434
           T+ GS  ++M I GG +V  V G+++D  G +  +  +   C   +  +A + S+
Sbjct: 359 TEEGSGLLIMAIAGGALVV-VQGWLADTVG-LQNSFWLTVACELYVLFYALWGSK 411


Lambda     K      H
   0.329    0.140    0.425 

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: 436
Number of extensions: 30
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: 438
Length of database: 417
Length adjustment: 32
Effective length of query: 406
Effective length of database: 385
Effective search space:   156310
Effective search space used:   156310
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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