Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 160 bits (406), Expect = 4e-44 Identities = 98/301 (32%), Positives = 166/301 (55%), Gaps = 9/301 (2%) Query: 65 PLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGID 124 PL L ++ L +FF +S + ++L + + V +L++GMS VI TGGID Sbjct: 32 PLAGLVVVSLLMGLASDNFFTLS--------NWFNVLRQVSIVGILAVGMSFVILTGGID 83 Query: 125 LSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLL 184 LSVGA MA+AG + A L++ + + G+ + G +NG LV++ + I+ TL Sbjct: 84 LSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLA 143 Query: 185 LMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTALG 244 M RGV + + G I+ + GVG+ +P+PV +++ + + LLL++TA G Sbjct: 144 TMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFG 203 Query: 245 LFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWLEL 304 + A+G N A+R G+ IKL Y I+G + LA +I T + S NAG+ EL Sbjct: 204 RHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLM-SGQPNAGVGFEL 262 Query: 305 DAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTVLL 364 DA+ AVV+GG A+ GGR ++ +++GA+++ L + + G+ +I+ ++IL + Sbjct: 263 DAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIY 322 Query: 365 L 365 + Sbjct: 323 I 323 Lambda K H 0.323 0.136 0.379 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: 373 Number of extensions: 24 Number of successful extensions: 1 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: 405 Length of database: 328 Length adjustment: 29 Effective length of query: 376 Effective length of database: 299 Effective search space: 112424 Effective search space used: 112424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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