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 Synpcc7942_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 212 bits (540), Expect = 2e-59 Identities = 114/271 (42%), Positives = 170/271 (62%), Gaps = 15/271 (5%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL + L++ F G A+ G+ + GES+GIVGESGSGKSV+ L++ L+ + R Sbjct: 5 LLEIRQLQICF----GEAIALQGLDLVVQPGESVGIVGESGSGKSVACLAIPGLLPKTAR 60 Query: 64 IVDGEAIFLG------KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI 117 G+ F +DLL L + ELR +RG + IFQ P++SLNP+ G Q++E I Sbjct: 61 C-SGQIAFRSVAGQSSRDLLTLPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQLLEAI 119 Query: 118 IWHRLMKNEEARERAIELLERVGIPESPKR----FLNYPFQFSGGMRQRVMIAMALACHP 173 H + EA++R I LL+ V + P + YP Q SGG RQR+MIA+ALA +P Sbjct: 120 QQHLPLSQAEAQQRVIALLQEVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIALAANP 179 Query: 174 KLLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKI 233 LL+ADEPTTALD T+QA +++LL+ L+++ M++IF++HDL V DR++ +Y G++ Sbjct: 180 DLLLADEPTTALDATVQASVLQLLRRLQQQRQMAMIFVSHDLGVIAEVADRVVVLYRGQV 239 Query: 234 VEEAPVEEILKTPLHPYTKGLLNSTLEIGSR 264 VE+ V ++L +P HPYT+GL+ +I R Sbjct: 240 VEQGRVADVLNSPQHPYTQGLVACRPQINPR 270 Score = 155 bits (392), Expect = 2e-42 Identities = 92/253 (36%), Positives = 149/253 (58%), Gaps = 8/253 (3%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL V L + + +AV +S+ L G +LG+VGESG GKS L+ L+ + Sbjct: 300 LLQVEQLGITYRGRSTAFQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCLVGLVPAS-- 357 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 +G+ I+L + L L R + + ++FQ+P +L+P VG ++EP+ + Sbjct: 358 --EGQ-IWLDQQPLDLRSSRDRQRLRQTVQMVFQDPAAALDPRWTVGSAILEPLRIKQPR 414 Query: 124 KNEEARERAI-ELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 ++ A +R + + L+RV +P YP +FSGG RQR+ IA AL P+LLI DE Sbjct: 415 RDRTADQRLLKQWLQRVDLPTDIGD--RYPHEFSGGQRQRICIARALIGQPRLLICDESV 472 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 +ALDV++QAQI+ LL++L+ E G++ +FI+HDL+V DRI+ M G++ E++P E++ Sbjct: 473 SALDVSVQAQILNLLKQLQAELGLTYLFISHDLAVVRYMSDRILVMNQGQLEEDSPTEQL 532 Query: 243 LKTPLHPYTKGLL 255 + P YT+ L+ Sbjct: 533 FQRPQSDYTRRLI 545 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: 416 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 554 Length adjustment: 32 Effective length of query: 292 Effective length of database: 522 Effective search space: 152424 Effective search space used: 152424 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: 50 (23.9 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