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_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 194 bits (493), Expect = 4e-54 Identities = 104/257 (40%), Positives = 166/257 (64%), Gaps = 11/257 (4%) Query: 11 KPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD 70 +PLLQ L + +AV +S + G TLGLVGESGCGKS+L R ++ L+ Sbjct: 298 QPLLQVEQLGITYRGRSTAFQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCLVGLVPAS 357 Query: 71 GGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKK 130 G+I+ + + + + ++ + R+ +Q++FQDP +L+P+ TVG I +PL I K+ Sbjct: 358 EGQIWLDQQPLDLRSSRDRQRLRQTVQMVFQDPAAALDPRWTVGSAILEPLRI-----KQ 412 Query: 131 ERRKR------VEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 RR R +++ L V + + + +PHEFSGGQ+QRI IARAL P+ ++CDE V Sbjct: 413 PRRDRTADQRLLKQWLQRVDLPTDIGDRYPHEFSGGQRQRICIARALIGQPRLLICDESV 472 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQI++LL+++Q ++G++YLFI+H+LAVV ++S ++ VM G++ E +++ Sbjct: 473 SALDVSVQAQILNLLKQLQAELGLTYLFISHDLAVVRYMSDRILVMNQGQLEEDSPTEQL 532 Query: 245 FLNPIHPYTRALLKSVP 261 F P YTR L+ ++P Sbjct: 533 FQRPQSDYTRRLIAAIP 549 Score = 159 bits (402), Expect = 2e-43 Identities = 96/268 (35%), Positives = 158/268 (58%), Gaps = 20/268 (7%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71 PLL+ L+ F G+ I A+ G+ + ++ GE++G+VGESG GKS I LL Sbjct: 4 PLLEIRQLQICF--GEAI--ALQGLDLVVQPGESVGIVGESGSGKSVACLAIPGLLPKTA 59 Query: 72 ---GKIFFEG------KDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPL 121 G+I F +D+ L ++E++ R ++ IFQ+PL SLNP + G + + + Sbjct: 60 RCSGQIAFRSVAGQSSRDLLTLPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQLLEAI 119 Query: 122 IIHKIGTKKERRKRVEELLDMVGIGRE------FINSFPHEFSGGQQQRIGIARALALNP 175 H ++ E ++RV LL V + RE + +PH+ SGGQ+QR+ IA ALA NP Sbjct: 120 QQHLPLSQAEAQQRVIALLQEVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIALAANP 179 Query: 176 KFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKI 235 ++ DEP +ALD ++QA ++ LL +QQ+ ++ +F++H+L V+ ++ +V V+Y G++ Sbjct: 180 DLLLADEPTTALDATVQASVLQLLRRLQQQRQMAMIFVSHDLGVIAEVADRVVVLYRGQV 239 Query: 236 VEYGDVDKIFLNPIHPYTRALLKSVPKI 263 VE G V + +P HPYT+ L+ P+I Sbjct: 240 VEQGRVADVLNSPQHPYTQGLVACRPQI 267 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: 497 Number of extensions: 19 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: 554 Length adjustment: 32 Effective length of query: 296 Effective length of database: 522 Effective search space: 154512 Effective search space used: 154512 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: 51 (24.3 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