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 Pf6N2E2_1813 ABC-type oligopeptide transport system, ATPase component
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1813 Length = 329 Score = 191 bits (484), Expect = 3e-53 Identities = 125/333 (37%), Positives = 183/333 (54%), Gaps = 27/333 (8%) Query: 2 KEILLKAENVRAYYKLEK------VSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVI 55 K+I L+ ++R +++ K ++KAVDG+S ++ E +G+VGESGCGK+TL+ ++ Sbjct: 3 KDIALELCDIRREFRINKGFFKPTATLKAVDGVSLRLMRGETLGLVGESGCGKSTLAKLL 62 Query: 56 FMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM 115 + ++ P + G + +NG+ + + RK + I I Q ++L P + Sbjct: 63 -LGLLAPTS---GDVL--INGKHLAATD-------RKAMARHIQPIFQDPYSSLNPRKTL 109 Query: 116 EKYVRHLAESHGIDEE-ELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174 + + H I E K + VGL I YP +LSGG RQR IA A I+ Sbjct: 110 REIITLPLIVHDIGSPAERRKKTEAMLDVVGLPKRVIDSYPSQLSGGQRQRVAIARALIM 169 Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234 P +LI DEPTSALDV Q +L +L +KR+ + + I+H++A + +ADR+ +MY Sbjct: 170 RPDVLICDEPTSALDVSVQAQILNLLQDLKRE-FGLTYLLISHNLAVIEHLADRVAVMYL 228 Query: 235 GKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTI--PGAPPNLINPPSGCR 292 G+IVE ESL KP HPYT+ L +SVLTP+P + GI I G PN ++PPSGC Sbjct: 229 GRIVEERTRESLFAKPGHPYTRALLDSVLTPDPRL---GIPEIGLHGTFPNPMSPPSGCA 285 Query: 293 FHPRCPHAMDVCKEKEPPLTEIEPGRRVACWLY 325 FHPRCP CK P I G V C L+ Sbjct: 286 FHPRCPSCFAPCKTAYPANDPI-IGGNVRCHLH 317 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: 282 Number of extensions: 11 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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