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 AO353_25870 AO353_25870 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25870 Length = 549 Score = 167 bits (423), Expect = 5e-46 Identities = 97/242 (40%), Positives = 148/242 (61%), Gaps = 10/242 (4%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP----PTSGEIYFEGKDIWKDIKD 80 AV ++SF V EIV+LVGESGSGKT A+ + LLP G I FEG+D+ + Sbjct: 24 AVNDLSFTVAPGEIVALVGESGSGKTMAARAAIGLLPLPMEVCGGAIRFEGQDLHQ--LS 81 Query: 81 RESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 L + R ++ VFQ+P S NP + + + + L + NK + + + L R Sbjct: 82 CAQLRDIRGARIGMVFQEPMVSLNPAIRIGEQMAEGLRL--HTDLNKAQIRQRCIDMLTR 139 Query: 140 VGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198 +GI DP+ L YPH+ SGG +QRIM+A +LRP L++ADEPT+ +D ++ +I+L+ Sbjct: 140 IGITDPERCLSAYPHEFSGGMRQRIMLASVMLLRPALLIADEPTTALDCLAQLDVIELML 199 Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258 EL EQGT+I+FI+HDL L + + VM++G+ VE+G + ++L P H YT+ L+ ++ Sbjct: 200 ELTREQGTAILFISHDLSLVARYAHKVVVMRHGQAVEQGSINHILLAPQHAYTRQLLEAL 259 Query: 259 PK 260 PK Sbjct: 260 PK 261 Score = 140 bits (353), Expect = 6e-38 Identities = 80/237 (33%), Positives = 132/237 (55%), Gaps = 8/237 (3%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESL 84 AV + + + E ++LVG SGSGKTT + ++ L+ P +GEI F+G DI K Sbjct: 300 AVHSANLSIAPGETLALVGGSGSGKTTLGRALVGLVKPCAGEIRFKGVDILK-----AGQ 354 Query: 85 VEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDP 144 + R + +FQDP++S +P + TL + + L +K + I +L +G+ Sbjct: 355 RDHRLQCQMIFQDPYSSLDPRMRIGETLAEPLRHLPELSEEQKR--QRIATTLVDIGLS- 411 Query: 145 KDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQ 204 + + ++PHQ+SGGQ+QR+ I R + P L++ADEP S +D + + I++L E L+ + Sbjct: 412 EAFMERFPHQLSGGQRQRVAIGRALVRHPQLVIADEPISALDMTIQKQILELFERLQAQY 471 Query: 205 GTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPKL 261 G + +FI+HDL ++ + VM G IVE G + V P H YT+ L+ + L Sbjct: 472 GFACLFISHDLAAVERIAHRVAVMHQGHIVEIGSREAVFDNPLHPYTRQLLAAASPL 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: 359 Number of extensions: 23 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: 549 Length adjustment: 30 Effective length of query: 238 Effective length of database: 519 Effective search space: 123522 Effective search space used: 123522 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