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 6939374 Sama_3467 cell division ABC transporter, ATP-binding protein FtsE (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__SB2B:6939374 Length = 229 Score = 110 bits (276), Expect = 3e-29 Identities = 73/229 (31%), Positives = 120/229 (52%), Gaps = 18/229 (7%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGG 72 +++ + K +P G+ KA+ ++ ++ GE L G SG GKSTL + I + R G Sbjct: 1 MIRFEQVSKVYPGGQ---KALSDVNFHLRRGEMAFLTGHSGAGKSTLLKLITVIERASAG 57 Query: 73 KIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIED----PLIIHKIGT 128 K+F G DI +++ + R+++ +IFQ N + + R + D PL+I + Sbjct: 58 KVFINGHDIADISRHHVPYLRREIGMIFQ------NHHLLMDRSVFDNVALPLVIEGF-S 110 Query: 129 KKERRKRVEELLDMVGI-GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSAL 187 E +KRV LDMVG+ G+E N P SGG+QQR+GIARA+ P ++ DEP L Sbjct: 111 HGEIKKRVAAALDMVGLYGKERHN--PIMLSGGEQQRVGIARAIVNKPALLLADEPTGNL 168 Query: 188 DVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIV 236 D + I+ L E G S L H+L ++ + ++ + G+++ Sbjct: 169 DPKLSMDILRLFETFND-AGTSVLIATHDLGLIARMKYRTLTLRQGRML 216 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: 220 Number of extensions: 18 Number of successful extensions: 3 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: 328 Length of database: 229 Length adjustment: 25 Effective length of query: 303 Effective length of database: 204 Effective search space: 61812 Effective search space used: 61812 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: 47 (22.7 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