Align Inner-membrane translocator (characterized, see rationale)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__BFirm:BPHYT_RS01810 Length = 319 Score = 168 bits (426), Expect = 1e-46 Identities = 106/302 (35%), Positives = 163/302 (53%), Gaps = 17/302 (5%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L + + G +++ F S +T+ R N+ + ++GM VII+GGIDLSVG V AL+ V Sbjct: 11 LAALVVFGLVRYEHFGSAYNITSFWRYNSMFALISVGMAFVIITGGIDLSVGTVAALASV 70 Query: 76 VTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTL 135 V +L W +LA G G L G II K+ PFIVTLA A G+A L Sbjct: 71 VAALTSVYGGWVAVLAGC---GAGLAVGVLNGLIITRLKILPFIVTLATSLGAHGVALLL 127 Query: 136 SEESIAIDHPFYDAVAEMSIALPGNG---ALDLSSLIFILFFVIIAVVMHYTRFGTNVYA 192 + AE + G G L + ++ ++ V + + TRFG + A Sbjct: 128 GKNDAV------SIAAESNFGNFGQGDLFGLPIPGIVAVVAAVAGWLALRSTRFGRHSLA 181 Query: 193 IGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAV 252 IGG++ +A LMG+++ +T + YA+S LA +AG++ +G +G EL AI+AV Sbjct: 182 IGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGVGWELFAISAV 241 Query: 253 VIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDG-----SLSSWWTKIVIGLLLFFFIL 307 V+GGTLLTGG G + T+ GV+L+G++ + F+ SLS++W ++ G+ L I+ Sbjct: 242 VLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVIRGVFLLLVIV 301 Query: 308 LQ 309 LQ Sbjct: 302 LQ 303 Lambda K H 0.330 0.145 0.424 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: 335 Number of extensions: 32 Number of successful extensions: 4 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: 320 Length of database: 319 Length adjustment: 28 Effective length of query: 292 Effective length of database: 291 Effective search space: 84972 Effective search space used: 84972 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: 48 (23.1 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