Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 254 bits (649), Expect = 3e-72 Identities = 123/265 (46%), Positives = 184/265 (69%), Gaps = 12/265 (4%) Query: 12 PLLQTVDLKKYFPQ----------GKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGR 61 PLLQ ++ ++F G I++AVDG+S+E+ GETLGL+GESGCGKSTL R Sbjct: 269 PLLQLENVTQHFRVAQSWLQGWRGGGEIVRAVDGLSLEVWPGETLGLIGESGCGKSTLLR 328 Query: 62 TILKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPL 121 TIL+LLRP GK+ F+G+D+T L D+ ++ R+++Q+IFQDP LNP++T+G I DPL Sbjct: 329 TILQLLRPSQGKVLFQGQDLTQLPDRRLRSLRRELQLIFQDPAACLNPRLTIGDAIADPL 388 Query: 122 IIHKIGTKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIV 179 I + +++V +L+ VG+ +I+ +PH+ SGGQQQR+ IARAL PK ++ Sbjct: 389 KIQGLARGAAAKQQVLAILEQVGLTPAPTWIDRYPHQLSGGQQQRVAIARALITRPKLVL 448 Query: 180 CDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYG 239 CDEPVS LD ++QAQ++ L++E++Q++ ++YLF+ H+L V +VAV+ GKIVE G Sbjct: 449 CDEPVSMLDATVQAQVLALMQELKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKIVEIG 508 Query: 240 DVDKIFLNPIHPYTRALLKSVPKIP 264 ++ P HPYTR+LL S+P++P Sbjct: 509 PAAQVLTQPEHPYTRSLLASLPELP 533 Score = 167 bits (423), Expect = 5e-46 Identities = 89/233 (38%), Positives = 145/233 (62%), Gaps = 5/233 (2%) Query: 32 AVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG---GKIFFEGKDITNLNDKE 88 A+ +S+E+ GE LGLVGESGCGKSTLGR IL+LL P G I G+ + L + Sbjct: 20 ALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQQGDIRLAGQALGQLQGRS 79 Query: 89 MKPYRK-KMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG-TKKERRKRVEELLDMVGIG 146 ++ +R ++ ++FQDP+ L+P T+G + + L +H+ ++++ +++ L+ V I Sbjct: 80 LQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQVHRPHLSRRQAKQQALSWLERVRIP 139 Query: 147 REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKM 206 + +PH+FSGG +QR+ IA AL L P+ +V DEP ++LDV++ A+I+ L + + Sbjct: 140 ANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVAAEILQELTRLCSEE 199 Query: 207 GISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKS 259 S L I+H+L +V ++AV+Y G++VE G + P HPYT+ LL+S Sbjct: 200 NTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAVLTRPQHPYTQTLLQS 252 Lambda K H 0.321 0.142 0.417 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: 448 Number of extensions: 13 Number of successful extensions: 5 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: 328 Length of database: 536 Length adjustment: 32 Effective length of query: 296 Effective length of database: 504 Effective search space: 149184 Effective search space used: 149184 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