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 15605 b1484 D-ala-D-ala transporter subunit (NCBI)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Keio:15605 Length = 328 Score = 266 bits (681), Expect = 4e-76 Identities = 135/314 (42%), Positives = 197/314 (62%), Gaps = 1/314 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L++ L + F G V A++ +S ++N+GE +G+VGESGSGKSV+ + ++RL+ Sbjct: 5 VLDIQQLHLSFPGFNGDVHALNNVSLQINRGEIVGLVGESGSGKSVTAMLIMRLLPTGSY 64 Query: 64 IVD-GEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 V G+ LG+D+L +++LR RG +++IFQ PMT+LNP R+G+Q+M+ I H+ Sbjct: 65 CVHRGQISLLGEDVLNAREKQLRQWRGARVAMIFQEPMTALNPTRRIGLQMMDVIRHHQP 124 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 + EAR +AI+LLE + IP++ + YPF+ SGGMRQRVMIA+A +C P+L+IADEPT Sbjct: 125 ISRREARAKAIDLLEEMQIPDAVEVMSRYPFELSGGMRQRVMIALAFSCEPQLIIADEPT 184 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVT+Q Q++ LL+ G +V+FI+HD++V + CD + MYAG ++E ++ Sbjct: 185 TALDVTVQLQVLRLLKHKARASGTAVLFISHDMAVVSQLCDSVYVMYAGSVIESGVTADV 244 Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302 + P HPYT GLL E G + L IPG PN T P GC F RC A C+ Sbjct: 245 IHHPRHPYTIGLLQCAPEHGVPRQLLPAIPGTVPNLTHLPDGCAFRDRCYAAGAQCENVP 304 Query: 303 PPLVNISENHRVAC 316 N R AC Sbjct: 305 ALTACGDNNQRCAC 318 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: 259 Number of extensions: 14 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: 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 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