Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS16065 BPHYT_RS16065 LacI family transcriptional regulator
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__BFirm:BPHYT_RS16065 Length = 317 Score = 145 bits (365), Expect = 2e-39 Identities = 100/295 (33%), Positives = 164/295 (55%), Gaps = 11/295 (3%) Query: 6 LATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ 65 LATL ++ A +A A A I + LNNP+FV+++ A +G +VV D+ Sbjct: 21 LATLAFGLSFIAAPAAQA-APLKIGMTFQELNNPYFVTMQKALNDAAASIGATVVVTDAH 79 Query: 66 NNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSH 125 ++ +K++++V+D+ + ILL+NPTDS + +AV A +A + V+ +D A G V S Sbjct: 80 HDVSKQVSDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANA-NGPVDSF 138 Query: 126 IASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVA-AHKFNVLAS 184 + S N G++A +Y+AK G +V L GI ER G + A+A A ++ + Sbjct: 139 VGSKNYDAGEMACEYLAKSIGGSGEVAILDGIP-VVPILERVRGCKAALAKAPGVKLVDT 197 Query: 185 QPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPD 244 Q +R L+V +N++ AHP+++ VF+ ND ++GAL A++++GK D+ + DG P+ Sbjct: 198 QNGKQERATALSVTENMIQAHPNLKGVFSVNDGGSMGALSAIESSGK-DIKLTSVDGAPE 256 Query: 245 GEKAVN--DGKLAATIAQLP-DQIG-AKGVETADKVLKGEKVQAKYPVDLKLVVK 295 A+ + K T AQ P DQ+ A G+ A K G V PVD+K++ K Sbjct: 257 AIAAIQKPNSKFVETSAQFPADQVRIALGIALAKK--WGANVPKTIPVDVKMIDK 309 Lambda K H 0.313 0.129 0.344 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: 217 Number of extensions: 11 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: 296 Length of database: 317 Length adjustment: 27 Effective length of query: 269 Effective length of database: 290 Effective search space: 78010 Effective search space used: 78010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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