Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Synpcc7942_2454 Synpcc7942_2454 adenine phosphoribosyltransferase
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__SynE:Synpcc7942_2454 Length = 424 Score = 145 bits (367), Expect = 1e-39 Identities = 110/317 (34%), Positives = 161/317 (50%), Gaps = 30/317 (9%) Query: 52 LAPGNFFELQRVRDAIARVTTPDDPAY-----QATLKGFE---ERYGLNN---PLWKQIL 100 LAPG+ + V D IA T A ATL GF E GLN P +Q Sbjct: 108 LAPGD--RVVVVDDLIATGGTASATATLIDRCSATLAGFAFVIELEGLNGRDRPWLEQYG 165 Query: 101 MYLKGAVVF-KFGPSFSDPARNIEDLIKEKFPITFTLALSSILFALVVGVPLGILAALKK 159 +L V + FG SF R + DL+ E+ P T LA+ S++ + +PLGI AA+ + Sbjct: 166 RWLWQVVRYGNFGSSFVYQ-RPVADLLWERVPNTLLLAICSLITTWAIALPLGIQAAVAQ 224 Query: 160 NTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEGI-------------- 205 N D +S +G PS++ A+ L+ + LP G + Sbjct: 225 NQRSDRILQLISYLGQGTPSFITALLLLFLAQFLTPLLPIGGMTSLDFEDLTPLQQMADL 284 Query: 206 -RTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMI 264 R ILP +AL L AS+ R +R +L+ L QD+IRTA AKG ++ VI HALR ++ Sbjct: 285 GRHLILPVLALTLSGFASLQRISRGEMLEVLRQDYIRTARAKGLPEQRVIYVHALRNAIN 344 Query: 265 PLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMN 324 PL+T++G + A L+ G E F PGLG+L A +D L++ S + A+ +++ N Sbjct: 345 PLITLLGFEFATLLSGAFIAEYFFNWPGLGRLILQAVFAQDLYLVMASLMMGAVMLILGN 404 Query: 325 LIVDVLYAILDPRIKLD 341 L+ D+L +DPRI+LD Sbjct: 405 LLADLLLRWVDPRIRLD 421 Lambda K H 0.328 0.143 0.429 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: 353 Number of extensions: 17 Number of successful extensions: 2 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: 341 Length of database: 424 Length adjustment: 30 Effective length of query: 311 Effective length of database: 394 Effective search space: 122534 Effective search space used: 122534 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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