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 PP_0879 PP_0879 dipeptide ABC transporter - putative ATP binding subunit
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Putida:PP_0879 Length = 322 Score = 191 bits (485), Expect = 2e-53 Identities = 118/316 (37%), Positives = 179/316 (56%), Gaps = 13/316 (4%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG- 71 LLQ +L F + VDG+ +++ GE L +VGESG GKS ++ L+ G Sbjct: 3 LLQINNLNVRFGDANAV-PVVDGLDLKVDAGEILAIVGESGSGKSVTMMALMGLIDAPGR 61 Query: 72 ---GKIFFEGKDITNLNDKEM-KPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 + F+G D+ L+ ++ K K + ++FQDP+ +LNP TVG IE+ L H +G Sbjct: 62 ITADSLTFDGTDMLKLSGRQRRKVVGKDIAMVFQDPMTALNPSYTVGFQIEEVLRQH-LG 120 Query: 128 TK-KERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 K K R+R ELL V I ++++PH+ SGG QR+ IA A+A PK ++ DEP Sbjct: 121 LKGKAARQRALELLKKVEIPAAESRLDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPT 180 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 +ALDV+IQAQI++LL +Q++ ++ + I H+LAVV + +V VMY G+ VE G V ++ Sbjct: 181 TALDVTIQAQIMELLVNLQKERNMALILITHDLAVVAETARRVCVMYAGQAVEVGQVPEL 240 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 F P HPY+ ALL ++P+ +R +L G +P D P GC RC + C Sbjct: 241 FDVPAHPYSEALLAAIPEHSIGA--ERLATLPGIVPGRYDRPVGCLLSPRCPYVQDNCRR 298 Query: 305 KEPELTEVEKNHFVSC 320 + P L + + + V C Sbjct: 299 QRPPL-DPQAHSLVRC 313 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: 282 Number of extensions: 11 Number of successful extensions: 4 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: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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: 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