Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 3607243 Dshi_0658 ABC transporter related (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Dino:3607243 Length = 533 Score = 243 bits (619), Expect = 1e-68 Identities = 127/252 (50%), Positives = 171/252 (67%), Gaps = 1/252 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L V NL+V F + + +AV G+S+ + +GE++ +VGESGSGKSV+ LS + L+ + Sbjct: 5 VLQVRNLRVGFRQDGQVTEAVKGVSFDVAQGETVALVGESGSGKSVTALSTVSLLPDSAE 64 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 V G + G +++ + +LR +RG D+S IFQ PMTSLNP+ + Q+ E + H+ + Sbjct: 65 -VSGSITYAGTEMVGAPERDLRRVRGNDVSFIFQEPMTSLNPLHPLEKQITESLTLHQGL 123 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 + AR R IELLE+VGI ++ R YP Q SGG RQRVMIAMALA P LLIADEPTT Sbjct: 124 TGDAARARVIELLEKVGIRDAESRLGAYPHQLSGGQRQRVMIAMALANGPDLLIADEPTT 183 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVTIQAQI++LL +LKE GMS++FITHDL++ DR+ M G+IVE P EI Sbjct: 184 ALDVTIQAQILDLLADLKEAEGMSLLFITHDLTIVRRIADRVCVMQGGEIVETGPTAEIF 243 Query: 244 KTPLHPYTKGLL 255 P HPYT+ LL Sbjct: 244 ANPQHPYTRKLL 255 Score = 179 bits (455), Expect = 1e-49 Identities = 99/240 (41%), Positives = 146/240 (60%), Gaps = 8/240 (3%) Query: 16 RVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKD 75 R G VKAV+ + + GE+LG+VGESGSGK+ L++LRLI+ GRIV + G++ Sbjct: 292 RTVGHVKAVNNATLNVRAGETLGVVGESGSGKTTLALAILRLISSEGRIV-----YAGEN 346 Query: 76 LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIEL 135 + +LR +R KD+ ++FQ+P SL+P + + + E + H L + R E+ Sbjct: 347 IQGWKSRDLRRLR-KDMQVVFQDPYGSLSPRMTIAQIIAEGLGVHGLEPGADPRRMVAEI 405 Query: 136 LERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIME 195 L VG+ P YP +FSGG RQR+ IA A+ PKL++ DEPT+ALD+T+Q QI+E Sbjct: 406 LVEVGL--DPAMMDRYPHEFSGGQRQRIAIARAMILRPKLVVLDEPTSALDMTVQVQIVE 463 Query: 196 LLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLL 255 LL+ L+ +YG++ IFI+HDL V ++I M G +VE +I + P YTK LL Sbjct: 464 LLRALQRKYGLAYIFISHDLKVVRALSHKVIVMRQGDVVEMGEGRQIFERPRSDYTKQLL 523 Lambda K H 0.320 0.139 0.401 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: 415 Number of extensions: 15 Number of successful extensions: 5 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: 324 Length of database: 533 Length adjustment: 31 Effective length of query: 293 Effective length of database: 502 Effective search space: 147086 Effective search space used: 147086 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: 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