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.
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:
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