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 Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 139 bits (350), Expect = 2e-37 Identities = 89/271 (32%), Positives = 143/271 (52%), Gaps = 24/271 (8%) Query: 5 LLKAENVRAYYKLEKV----------SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNV 54 LL+ ENV ++++ + V+AVDGLS E+ E +G++GESGCGK+TL Sbjct: 270 LLQLENVTQHFRVAQSWLQGWRGGGEIVRAVDGLSLEVWPGETLGLIGESGCGKSTLLRT 329 Query: 55 IFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIR 114 I + +++P GK+ + + +L ++R E+ +I Q L P + Sbjct: 330 I-LQLLRPS---QGKVLFQ-GQDLTQLPDRRLRSLRR-----ELQLIFQDPAACLNPRLT 379 Query: 115 MEKYVRHLAESHGIDEEELL-DKARRRFEEVGLDPL--WIKRYPFELSGGMRQRAVIAIA 171 + + + G+ + E+VGL P WI RYP +LSGG +QR IA A Sbjct: 380 IGDAIADPLKIQGLARGAAAKQQVLAILEQVGLTPAPTWIDRYPHQLSGGQQQRVAIARA 439 Query: 172 TILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMII 231 I P L++ DEP S LD Q +L ++ ++K+Q + + +F+THD+ R+ DR+ + Sbjct: 440 LITRPKLVLCDEPVSMLDATVQAQVLALMQELKQQ-LNLTYLFVTHDLRVAREFCDRVAV 498 Query: 232 MYAGKIVEFAPVESLLEKPLHPYTQGLFNSV 262 + GKIVE P +L +P HPYT+ L S+ Sbjct: 499 LQRGKIVEIGPAAQVLTQPEHPYTRSLLASL 529 Score = 124 bits (312), Expect = 4e-33 Identities = 83/248 (33%), Positives = 136/248 (54%), Gaps = 25/248 (10%) Query: 24 AVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSS 83 A+ LS E+ E +G+VGESGCGK+TL I + ++ P + G I R+ G+ + Sbjct: 20 ALQQLSLELAAGERLGLVGESGCGKSTLGRAI-LRLLPPGSHQQGDI--RLAGQAL---G 73 Query: 84 MTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEE 143 + ++F G ++ ++ Q M L P ++ HL E+ + L +RR+ ++ Sbjct: 74 QLQGRSLQRFRGGQVGLVFQDPMTRLDP---LQTIGDHLLETLQVHRPHL---SRRQAKQ 127 Query: 144 VGLDPLWIKR----------YPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQ 193 L W++R YP + SGGMRQR IA+A +L P L++ADEPT++LDV Sbjct: 128 QALS--WLERVRIPANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVA 185 Query: 194 KVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHP 253 +L+ L ++ + S++ I+HD+ V DR+ ++Y G++VE P ++L +P HP Sbjct: 186 AEILQELTRLCSEENT-SLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAVLTRPQHP 244 Query: 254 YTQGLFNS 261 YTQ L S Sbjct: 245 YTQTLLQS 252 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: 389 Number of extensions: 18 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: 330 Length of database: 536 Length adjustment: 32 Effective length of query: 298 Effective length of database: 504 Effective search space: 150192 Effective search space used: 150192 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: 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