Align Oligosaccharide:H+ symporter family protein (characterized, see rationale)
to candidate 14481 b0343 galactoside permease (NCBI)
Query= uniprot:Q4KBP0 (429 letters) >FitnessBrowser__Keio:14481 Length = 417 Score = 294 bits (752), Expect = 4e-84 Identities = 158/407 (38%), Positives = 235/407 (57%), Gaps = 5/407 (1%) Query: 1 MQFAAKREYWLISGLLFFFFFSWSSSYSLFSIWLHRVIGLNGTETGFIFAANAIAALLVQ 60 M + +W+ FF+FF + + F IWLH + ++ ++TG IFAA ++ +LL Q Sbjct: 1 MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQ 60 Query: 61 PFYGALQDRLGLSKKLLVWIGILLCAAAPFAIYVYAGLLAQNVMLGALVGAAFLALAMLA 120 P +G L D+LGL K LL I +L APF I+++ LL N+++G++VG +L A Sbjct: 61 PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA 120 Query: 121 GVGVIESYTERLSRHAGFEFGTTRMWGSLGWASATGVVGVVFNIDPDIAFYMSSLAGIVF 180 G +E++ E++SR + FEFG RM+G +GWA +VG++F I+ F++ S ++ Sbjct: 121 GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL 180 Query: 181 LLILF--RLDLDRLAQPAVQAGAVVHPVRLNDLWKLLALPRFWAFSLYLTGVCGIYMIYE 238 ++LF + D A A GA L +L P+ W SLY+ GV Y +++ Sbjct: 181 AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD 240 Query: 239 QQFPVYFSSFFPTPEEGTRAYGYLNSSQVLVEAVLMLLAPWVVSRTGAKYGLILAGSIMF 298 QQF +F+SFF T E+GTR +GY+ + L+ A +M AP +++R G K L+LAG+IM Sbjct: 241 QQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS 300 Query: 299 VRILGSGLVTQAWAIAACKMLHALEVPILLVSIFKYISLNFDSRLSASIYLVGFQFAQQL 358 VRI+GS T A + K LH EVP LLV FKYI+ F+ R SA+IYLV F F +QL Sbjct: 301 VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL 360 Query: 359 TAMLLSPLVGYGYDHFGFSSVYVLMAGLV--GACLLLSWTLLRKDPV 403 + +S L G Y+ GF Y L+ GLV G L+ +TL P+ Sbjct: 361 AMIFMSVLAGNMYESIGFQGAY-LVLGLVALGFTLISVFTLSGPGPL 406 Lambda K H 0.329 0.142 0.441 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: 461 Number of extensions: 21 Number of successful extensions: 2 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: 429 Length of database: 417 Length adjustment: 32 Effective length of query: 397 Effective length of database: 385 Effective search space: 152845 Effective search space used: 152845 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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