Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate H281DRAFT_03379 H281DRAFT_03379 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Burk376:H281DRAFT_03379 Length = 343 Score = 207 bits (528), Expect = 2e-58 Identities = 132/321 (41%), Positives = 177/321 (55%), Gaps = 20/321 (6%) Query: 28 ERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDL 87 ++ ALG L VL+ + FS+ + F NL +A Q + L T VI+TGGIDL Sbjct: 25 QKFAALGSLVVLI---VAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGIDL 81 Query: 88 SVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTL 147 SVGS+L+++ V A L+ +++ +L G G VNG V M LPPFI TLG + Sbjct: 82 SVGSVLALAGVAAALLVKAGVPVPVAMAGGMLVGAACGWVNGICVTRMGLPPFIATLGMM 141 Query: 148 TAVRGLARLVGNDSTIYNPDIGFAFIGNGEVL----------------GVPWLVIIAFAV 191 RGLA + + F +GNG + G+P+ V+I + Sbjct: 142 LVARGLALQITGARPVSGLGDAFGELGNGALFKVSHIGADGFPDTVFPGIPYPVVIMVIL 201 Query: 192 VAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARL 251 +L RT LG IYAVG NAEAARLSG+ V V LF Y +SGLLAG G + +RL Sbjct: 202 FVAVSVLLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRL 261 Query: 252 YAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIW 311 A + G YELDAIA+ ++GGTS +GG G+I GT +GA +I VL NGL + GVS Sbjct: 262 VTAQPNE-GVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFI 320 Query: 312 QYIIKGLVIIGAVALDSYRRK 332 Q II G+VI+G V +D R + Sbjct: 321 QQIIIGVVILGTVWIDQLRNR 341 Lambda K H 0.325 0.141 0.409 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: 394 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 343 Length adjustment: 28 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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