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 H281DRAFT_04047 H281DRAFT_04047 glutathione transport system permease protein
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Burk376:H281DRAFT_04047 Length = 306 Score = 211 bits (537), Expect = 2e-59 Identities = 117/315 (37%), Positives = 191/315 (60%), Gaps = 12/315 (3%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L FL+KRL + ++ +V V+ ++ + L PG D PD A +AT+ Sbjct: 2 LNFLVKRLFGLLPTLFIVAVLVFLFVHLLPG---------DPARLAAGPD--ADEATVAL 50 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 GL+ P+ +Q + FG S + R + I E+F T L L+S+++A Sbjct: 51 VRADLGLDKPMPQQFAHFFVKIAHGDFGTS-TRSKRPVSQEIGERFMPTLLLTLASMVWA 109 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204 +V+G+ +GI++A+ +N W D MT++V G++ P++ + + L+ IFS+ LGWLP G Sbjct: 110 VVMGMGIGIVSAVWRNRWPDRLGMTLAVSGISFPAFALGMLLMEIFSVKLGWLPIVGDGS 169 Query: 205 IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMI 264 ++ ILP++ L A +ARFTR S ++ +N+DF+RTA AKG +R VI+KH LR +MI Sbjct: 170 WQSYILPSLTLGAAVAAVMARFTRASFVEVMNEDFVRTARAKGVPERLVIVKHCLRNAMI 229 Query: 265 PLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMN 324 P+VT++G Q +L+ G++ VE +F PGLG+L +A RDYP++ + +L +I+N Sbjct: 230 PVVTMMGLQFGFLLGGSIVVEVVFNWPGLGRLLVDAVSMRDYPVIQAEVLLFSLEFIIIN 289 Query: 325 LIVDVLYAILDPRIK 339 L+VDVLYA+++P I+ Sbjct: 290 LVVDVLYAVINPTIR 304 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: 271 Number of extensions: 10 Number of successful extensions: 1 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: 306 Length adjustment: 28 Effective length of query: 313 Effective length of database: 278 Effective search space: 87014 Effective search space used: 87014 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: 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