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 GFF3769 PGA1_262p01730 putative glutathione import ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Phaeo:GFF3769 Length = 325 Score = 195 bits (495), Expect = 1e-54 Identities = 120/336 (35%), Positives = 187/336 (55%), Gaps = 17/336 (5%) Query: 1 MKEILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMV 60 M E LL+ +++ Y+ + +KA+ +SF++ + E++G+VGESGCGK+TL + I + Sbjct: 1 MSEKLLEIDDLSVDYETARGDLKALRSISFDVNKGEIVGIVGESGCGKSTLISAILRLIA 60 Query: 61 KPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR 120 +G++ R GE + ++S D R G +I+I+ Q M P I + K + Sbjct: 61 PNTRFRNGEV--RFKGEDLLVAS---DRHIRDLRGDDISIVFQDPMQTHNPVISIGKQMV 115 Query: 121 HLAESHGIDEEELLDKARRRFEEVGL-DP-LWIKRYPFELSGGMRQRAVIAIATILNPSL 178 + + E L A + VG+ DP + +K+YP E SGGMRQR IA+A + P L Sbjct: 116 DIQHRSKASKAEKLATAAKMLGAVGIPDPEMRLKQYPHEFSGGMRQRIAIAMALMSEPDL 175 Query: 179 LIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIV 238 LIADEPT+ALD + +++ L +++ + +I+FI+H + + ++ DR+++MYAG +V Sbjct: 176 LIADEPTTALDATLEVQIIERLKELQSE-FGCAILFISHHLGVIAELCDRVVVMYAGAVV 234 Query: 239 EFAPVESLLEKPLHPYTQGLFNSVLTPEP---EVKKRGITTIPGAPPNLINPPSGCRFHP 295 E V + P HPYT+ L +P + + R + TIPG P+L N P GC F Sbjct: 235 ESGTVREIFHNPKHPYTRRLIEC----DPGHLKERARVLPTIPGEVPDLANLPEGCIFRD 290 Query: 296 RCPHAMDVCKEKEPPLTEIEPGRRVACWL-YMEERA 330 RC AMD C PPL + G ACWL + EE A Sbjct: 291 RCDQAMDRC-ASVPPLARLSEGHNAACWLNHAEEMA 325 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: 260 Number of extensions: 8 Number of successful extensions: 6 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: 325 Length adjustment: 28 Effective length of query: 302 Effective length of database: 297 Effective search space: 89694 Effective search space used: 89694 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: 48 (23.1 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