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 GFF205 HP15_204 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Marino:GFF205 Length = 336 Score = 207 bits (528), Expect = 2e-58 Identities = 113/308 (36%), Positives = 181/308 (58%), Gaps = 8/308 (2%) Query: 14 FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 F R + V A++G+ ++ KGE+L +VGESG GKS +++ L++ + GE + G Sbjct: 32 FRRKQEAVHAINGVDLEVQKGEALCVVGESGCGKSTVARTVMGLLSPSA----GEIHYDG 87 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL-MKNEEARERA 132 + + L +++ R K + +IFQNP SLNP + + + EPI +H + R++ Sbjct: 88 QRIDNLERKDSLPYRRK-MQMIFQNPYASLNPRMTIQQTLEEPIRFHHPDWSPVQVRDKI 146 Query: 133 IELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQ 192 E++ VGI + + +FSGG RQR+ IA ALA P+ ++ADEP +ALDV+IQAQ Sbjct: 147 HEVMHSVGIDQDWGN--RFGHEFSGGQRQRIAIARALAVDPEFIVADEPISALDVSIQAQ 204 Query: 193 IMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTK 252 ++ LL + +E G++ +FITHDL+V +F R+ MY G++ E A + + P HPYT+ Sbjct: 205 VLNLLMDAQESRGLTYLFITHDLAVVEHFGTRVAVMYLGRVCELADTKTLFSAPRHPYTQ 264 Query: 253 GLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENH 312 LL++ ++ + + G P P PSGC FH RC +A E C++E P L+ Sbjct: 265 ALLSAIPKLEDDRPNHIRLKGEVPTPVNLPSGCVFHGRCPYANERCRQELPQLITTDGGT 324 Query: 313 RVACHLIK 320 +VACH ++ Sbjct: 325 QVACHAVE 332 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: 279 Number of extensions: 9 Number of successful extensions: 3 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: 336 Length adjustment: 28 Effective length of query: 296 Effective length of database: 308 Effective search space: 91168 Effective search space used: 91168 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