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 Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 111 bits (278), Expect = 2e-29 Identities = 74/245 (30%), Positives = 132/245 (53%), Gaps = 15/245 (6%) Query: 3 ELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNG 62 +++ V LK F ++ ++ G+ L KGE++ ++G+SG+GKSV + ++ L+ ++ Sbjct: 4 KVVEVRGLKKSFGELDVLM----GVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQD- 58 Query: 63 RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWH-R 121 +G LGK++ L ++L +R K I FQ + +R ++ P++ + + Sbjct: 59 ---EGTMNVLGKEVSNLGAKDLNELRLK-IGFSFQASALYDSMTVRENLEF--PLVRNVK 112 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 + E + E+LE VG+ ++ + P + SGG R+R+ IA L P++++ DEP Sbjct: 113 GLSRTEKDKMVEEVLEAVGLSQTINQM---PSELSGGQRKRIGIARTLILKPEIMLYDEP 169 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 T LD + I L+ E++E Y S I ITHDL+ A + DR+ + G+ E EE Sbjct: 170 TAGLDPITCSDINNLINEVRENYNTSSIIITHDLTCARDTGDRVAVLLDGQFGAEGKFEE 229 Query: 242 ILKTP 246 + KTP Sbjct: 230 VFKTP 234 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: 169 Number of extensions: 7 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: 324 Length of database: 249 Length adjustment: 26 Effective length of query: 298 Effective length of database: 223 Effective search space: 66454 Effective search space used: 66454 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