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 WP_084933101.1 HA51_RS05940 dipeptide ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_002095475.1:WP_084933101.1 Length = 328 Score = 292 bits (747), Expect = 9e-84 Identities = 153/316 (48%), Positives = 211/316 (66%), Gaps = 1/316 (0%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LLNV L V F + +AVD ISY++ +G+ +GIVGESGSGKSVS L+++ LI+ Sbjct: 1 MALLNVEKLSVHFGDEKTPFRAVDRISYQVEQGQVVGIVGESGSGKSVSSLAIMGLIDYP 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 GR++ + F +DL K++++E R + G ++++IFQ+PMTSLNP VG Q+ME + H+ Sbjct: 61 GRVMAEKLEFNQRDLQKISEKERRQLVGAEVAMIFQDPMTSLNPCYTVGFQIMEALKVHQ 120 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 R+RAI+LL++VGIP+ R YP Q SGGM QRVMIAMA+AC PKLLIADEP Sbjct: 121 GGSKSTRRQRAIDLLDQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACKPKLLIADEP 180 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDVTIQAQI+ELL +L+++ M++I ITHDL++ II MYAG++VE + Sbjct: 181 TTALDVTIQAQIIELLLDLQKQENMALILITHDLALVAEAAQHIIVMYAGQVVETGKAVD 240 Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301 I K P HPYT+ +L + E + +L +PG P P+GC +PRC + E C+RE Sbjct: 241 IFKAPRHPYTQAMLRALPEFAADKARLASLPGVVPGKYDRPTGCLLNPRCPYVTERCRRE 300 Query: 302 EPPLVNISENHRVACH 317 EP L +I + CH Sbjct: 301 EPELRDI-PGRQSKCH 315 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: 263 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: 328 Length adjustment: 28 Effective length of query: 296 Effective length of database: 300 Effective search space: 88800 Effective search space used: 88800 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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