Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate GFF2185 PS417_11145 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__WCS417:GFF2185 Length = 542 Score = 159 bits (401), Expect = 2e-43 Identities = 93/244 (38%), Positives = 148/244 (60%), Gaps = 14/244 (5%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP----PTSGEIYFEGKDIWKDIKD 80 AV ++SF + EIV+LVGESGSGKT A+ + LLP G + F+G+D+ Sbjct: 24 AVDDLSFSIAPGEIVALVGESGSGKTMAARAAIGLLPLPMQVCGGRLDFQGRDLAS--VS 81 Query: 81 RESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLEN--KPSNKKEALELIKESL 137 E+L R + VFQ+P S NP + + + +A+ L + P ++ L +++ Sbjct: 82 TEALRAIRGASIGMVFQEPMVSLNPALKIGQQMSEALKLHTDLDPPQIRERCLTMLR--- 138 Query: 138 FRVGIDPKD-VLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKL 196 R+GI + L YPHQ SGG +QRIM+A +LRP L++ADEPT+ +D ++ +I+L Sbjct: 139 -RIGIKAAERCLESYPHQFSGGMRQRIMLASVMLLRPALLIADEPTTALDCLAQLDVIEL 197 Query: 197 LEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVG 256 + EL EQGT+I+FI+HDL L + + VM++G+ VE+G + ++L P EYT+ L+ Sbjct: 198 MLELTREQGTAILFISHDLSLVARYAHKVVVMRHGKAVEQGSIEDILLAPKAEYTRQLLE 257 Query: 257 SIPK 260 ++P+ Sbjct: 258 ALPR 261 Score = 140 bits (354), Expect = 4e-38 Identities = 83/247 (33%), Positives = 137/247 (55%), Gaps = 11/247 (4%) Query: 17 FFSKRR-IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIW 75 F+ KR+ V + S + E ++LVG SGSGKTT + ++ L+ P +G I F+G DI Sbjct: 291 FWGKRQHTRVVHSASLVIAPGETLALVGGSGSGKTTLGRSLVGLIKPCAGSIRFKGVDIL 350 Query: 76 KDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPS-NKKEALELIK 134 K L + +FQDP++S NP + L + L ++P N E E + Sbjct: 351 KAANRTHRL-----QCQMIFQDPYSSLNPRMKIGEILAEP---LRHEPGLNAAERRERVT 402 Query: 135 ESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 ++L +G+ + V ++PHQ+SGGQ+QR+ I R + P L++ADEP S +D + + I+ Sbjct: 403 QTLKDIGLGEQFV-ERFPHQLSGGQRQRVAIGRALVRHPQLVIADEPISALDMTIQKQIL 461 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +L E L+ + G + +FI+HDL ++ + VM G +VE G +++ P H YT+ L Sbjct: 462 ELFERLQAQYGFACLFISHDLAAVERIAHRVAVMHQGNVVEVGAREQIFDHPQHPYTRQL 521 Query: 255 VGSIPKL 261 + + L Sbjct: 522 LAAASPL 528 Lambda K H 0.319 0.139 0.397 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: 341 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 268 Length of database: 542 Length adjustment: 30 Effective length of query: 238 Effective length of database: 512 Effective search space: 121856 Effective search space used: 121856 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 (21.7 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