Align TM0028, 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 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Dino:3610414 Length = 331 Score = 183 bits (465), Expect = 5e-51 Identities = 111/326 (34%), Positives = 175/326 (53%), Gaps = 20/326 (6%) Query: 5 LLKAENVRAYYKL-----EKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNM 59 +L A N+ ++ L + V+AVD ++FE+ E +GVVGESGCGK+T + ++ Sbjct: 10 VLSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLL---- 65 Query: 60 VKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYV 119 V+ L G++ R G + E+ K + + + ++ Q + +L P + M + Sbjct: 66 VQLLGADSGEV--RFQGH------VAGTEMPLKEFRRHVQMVFQDSYASLNPRMSMLDAI 117 Query: 120 RHLAESHGIDEEELLDKARRRFEEVGLDPLWI-KRYPFELSGGMRQRAVIAIATILNPSL 178 HG+ E E AR + VGLDP RYP ELSGG RQR IA A P + Sbjct: 118 AFGPTVHGVSEAEAQRIARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEV 177 Query: 179 LIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIV 238 ++ DE SALD + +L +LM +KR+ + + +FI+HD+ VR ++DR+++MY G++ Sbjct: 178 IVLDEAVSALDKSVEAQVLNLLMDLKRERNL-TYVFISHDLNVVRHVSDRVMVMYLGEVA 236 Query: 239 EFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCP 298 E P + P HPYT+ L ++ + +P+ ++ + G PPN I+PPSGCRFH RC Sbjct: 237 EIGPTAEMYADPRHPYTRALLAAMPSLDPD-RRTTEAPLSGDPPNPIDPPSGCRFHTRCA 295 Query: 299 HAMDVCKEKEPPLTEIEPGRRVACWL 324 A C + P + G +C L Sbjct: 296 EAFGACSAQRPSNLRVGAGHYASCHL 321 Lambda K H 0.321 0.138 0.405 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: 266 Number of extensions: 12 Number of successful extensions: 5 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: 330 Length of database: 331 Length adjustment: 28 Effective length of query: 302 Effective length of database: 303 Effective search space: 91506 Effective search space used: 91506 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 (21.8 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