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 GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Marino:GFF2860 Length = 672 Score = 265 bits (677), Expect = 2e-75 Identities = 133/299 (44%), Positives = 198/299 (66%), Gaps = 5/299 (1%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86 ++ L+A+D +S+ +K+GE L LVGESGCGK+TL RTI+ L P G + G+ I NL Sbjct: 372 RKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAPSTGSVTLNGQRIENLPP 431 Query: 87 KEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIG 146 + + +Q IFQDP SLNP+ T+G II PL +H IG+ +E+ ++V +++++VG+ Sbjct: 432 MDRA---RMIQPIFQDPYSSLNPRKTIGEIIAKPLFVHGIGSNQEQHQQVRKMMELVGLP 488 Query: 147 REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKM 206 NS+P + SGGQ+QR I RAL LNP+ ++CDEP SALDVS+QAQI++LL +++ ++ Sbjct: 489 SRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQILNLLLDLRDEL 548 Query: 207 GISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWD 266 ++YLF+ HNL+VV+H++ +VAVMYLG+IVE G+ D++ +P HPYT AL+ S I Sbjct: 549 DLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMSDPKHPYTHALMNSALSIS-P 607 Query: 267 GQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHLVRS 325 G+ L G+ P+P++ P GC F RC C E+ P E+ N V C R+ Sbjct: 608 GESVPDPGLSGDFPNPMNRPSGCPFHPRCPLADQQCREQAPG-PELIDNTLVQCWKART 665 Score = 224 bits (572), Expect = 4e-63 Identities = 123/322 (38%), Positives = 185/322 (57%), Gaps = 9/322 (2%) Query: 8 IKMKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67 + M +L DL P L AV GIS+E+ GETLG+VGESG GKS ++ LL Sbjct: 1 MNMASILDIQDLSVDIPTDSSTLHAVRGISLELNRGETLGIVGESGSGKSMTALALMNLL 60 Query: 68 RPDGGK----IFFEGKDITNLNDKEM--KPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPL 121 P + I F+G D+T+ ++E+ K +++ +IFQ+P+ SLNP ++GR +++ + Sbjct: 61 PPAAKRQASCIDFDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETM 120 Query: 122 IIHKIGTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIV 179 +H+ + E R LL+ VG+ + +PHE SGGQ+QR+ IA AL P+ ++ Sbjct: 121 TLHRKVSDTEAENRAVYLLEKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLI 180 Query: 180 CDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYG 239 DEP +ALDV+IQAQI+ LL E+QQ+ G+S + I H+L VV + +AVMY G IVE G Sbjct: 181 ADEPTTALDVTIQAQILHLLRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETG 240 Query: 240 DVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKK 299 ++ NP HPYT+ LL+ VP Q QR ++ G +P+ GC F +RC Sbjct: 241 KTGEVLENPRHPYTKGLLECVPGYKGQSQ-QRLGAIPGIVPAMTGDISGCAFASRCPRAA 299 Query: 300 AICFEKEPELTEVEKNHFVSCH 321 +C P ++ + + CH Sbjct: 300 GVCRTTNPPTKKLHQGRYFVCH 321 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: 622 Number of extensions: 24 Number of successful extensions: 7 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: 672 Length adjustment: 33 Effective length of query: 295 Effective length of database: 639 Effective search space: 188505 Effective search space used: 188505 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