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 RR42_RS18195 RR42_RS18195 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS18195 Length = 332 Score = 278 bits (710), Expect = 2e-79 Identities = 144/317 (45%), Positives = 203/317 (64%), Gaps = 6/317 (1%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L V LK +F G+ +AVD +S+ + +GE +G+VGESGSGKS++ S++ LI+ G++ Sbjct: 6 LVVEGLKTQFFTRGGVARAVDDVSFSVGRGEIMGLVGESGSGKSMTGYSIMGLIDPPGKV 65 Query: 65 VDGEAIFLGKD-----LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIW 119 VDG +D L L ++R++RG I++IFQ+PM +LNP++R+ Q++E ++ Sbjct: 66 VDGRIELTSRDGVTRDLRNLTPAQMRDVRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVLA 125 Query: 120 HRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIAD 179 H + ARER+ L RVGIP +R YP QFSGGMRQRV IA+AL P L+IAD Sbjct: 126 HEKVDKAVARERSRNALARVGIPSPDERLRAYPHQFSGGMRQRVAIAIALLNKPDLIIAD 185 Query: 180 EPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPV 239 EPTTALDVTIQ QI+ +Q+L E G ++I+ITHDLSV D + MYAGKIVE V Sbjct: 186 EPTTALDVTIQGQILYEMQKLCRESGTALIWITHDLSVVAGLADTVCVMYAGKIVEAGDV 245 Query: 240 EEILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQ 299 ++L+ P HPYT GL++S RG L IPG P+ P+GC F RC++A ++C Sbjct: 246 RQVLERPEHPYTHGLISSAPSRNPRGAPLRQIPGMTPSLLNLPAGCAFRERCTYATDVC- 304 Query: 300 REEPPLVNISENHRVAC 316 + PPL ++ R+ C Sbjct: 305 KTAPPLDTAADGRRLRC 321 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: 288 Number of extensions: 12 Number of successful extensions: 2 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: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 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: 49 (23.5 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