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 WP_094506525.1 CEV31_RS05660 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_002252445.1:WP_094506525.1 Length = 535 Score = 176 bits (446), Expect = 9e-49 Identities = 105/254 (41%), Positives = 150/254 (59%), Gaps = 17/254 (6%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP-----PTSGEIYFEGKDIWKDIK 79 +V VSF++ E E V+LVGESGSGK+ +A IL+LLP SG+I GKD+ Sbjct: 24 SVDRVSFDIAEGETVALVGESGSGKSVSALSILKLLPYPAASHPSGQILLNGKDLMS--- 80 Query: 80 DRESLVEFRR----KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKE 135 S E RR V +FQ+P S NP + VER + + + + + A L E Sbjct: 81 --ASEPELRRVRGNDVTMIFQEPMTSLNPLHTVERQIAEILKMHQGMSDQAARARTL--E 136 Query: 136 SLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 L VGI +P+ L +PHQ+SGGQ+QR+MIA +P L++ADEPT+ +D + + I+ Sbjct: 137 LLHEVGIREPEKRLNAFPHQLSGGQRQRVMIAMALANKPKLLIADEPTTALDVTVQAQIL 196 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +LL +L+ QG S++FITHDLG+ ++D + VM G+IVE G ++ P HEYTK L Sbjct: 197 QLLADLKTAQGMSMLFITHDLGIVRKIADRVCVMSKGKIVEAGPTSEIFDNPQHEYTKHL 256 Query: 255 VGSIPKLYRKLEDL 268 + + PK L DL Sbjct: 257 LAAEPKGEPPLADL 270 Score = 148 bits (374), Expect = 2e-40 Identities = 88/245 (35%), Positives = 142/245 (57%), Gaps = 9/245 (3%) Query: 16 GFFSKR--RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKD 73 GF K ++AV + ++ + + +VGESGSGKTT + R++ + GEI F+G+D Sbjct: 290 GFLRKTVDHVKAVDGIDVTLRAGQTLGVVGESGSGKTTLGLALSRMIS-SKGEIRFDGRD 348 Query: 74 IWK-DIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALEL 132 I K D L RR++ VFQDPF S +P + + + + + E K S E E Sbjct: 349 IAKFSFSDMRPL---RREMQIVFQDPFGSLSPRMTIADIIAEGLLVHEPKLS-ADERDER 404 Query: 133 IKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGG 192 + +L V +DP+ +YPH+ SGGQ+QRI IAR +L P ++ DEPTS +D S + Sbjct: 405 VVAALKEVNLDPETRF-RYPHEFSGGQRQRIAIARAMVLNPKFVMLDEPTSALDMSVQAQ 463 Query: 193 IIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTK 252 ++ LL L+++ + +FI+HDL + +++++ VM+NG++VE G V P +YTK Sbjct: 464 VVDLLRALQKKHDLAYLFISHDLKVVRALANDVLVMRNGKVVEYGTSKDVFANPKTDYTK 523 Query: 253 LLVGS 257 L+ + Sbjct: 524 ALMAA 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: 375 Number of extensions: 20 Number of successful extensions: 7 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: 535 Length adjustment: 30 Effective length of query: 238 Effective length of database: 505 Effective search space: 120190 Effective search space used: 120190 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 24 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