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_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 207 bits (527), Expect = 5e-58 Identities = 103/242 (42%), Positives = 160/242 (66%), Gaps = 5/242 (2%) Query: 20 IVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKL 79 IV+AVDG+S ++ GE+LG++GESG GKS + ++L+L+ R G+ +F G+DL +L Sbjct: 296 IVRAVDGLSLEVWPGETLGLIGESGCGKSTLLRTILQLL----RPSQGKVLFQGQDLTQL 351 Query: 80 NKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERV 139 LR++R +++ +IFQ+P LNP + +G + +P+ L + A+++ + +LE+V Sbjct: 352 PDRRLRSLR-RELQLIFQDPAACLNPRLTIGDAIADPLKIQGLARGAAAKQQVLAILEQV 410 Query: 140 GIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQE 199 G+ +P YP Q SGG +QRV IA AL PKL++ DEP + LD T+QAQ++ L+QE Sbjct: 411 GLTPAPTWIDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQAQVLALMQE 470 Query: 200 LKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNSTL 259 LK++ ++ +F+THDL VA FCDR+ + GKIVE P ++L P HPYT+ LL S Sbjct: 471 LKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKIVEIGPAAQVLTQPEHPYTRSLLASLP 530 Query: 260 EI 261 E+ Sbjct: 531 EL 532 Score = 192 bits (488), Expect = 2e-53 Identities = 108/257 (42%), Positives = 160/257 (62%), Gaps = 6/257 (2%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL+++ L V + E A+ +S +L GE LG+VGESG GKS ++LRL+ Sbjct: 1 MTLLSIDQLSVTYPGSEQ--PALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPP- 57 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 G G+ G+ L +L L+ RG + ++FQ+PMT L+P+ +G ++E + HR Sbjct: 58 GSHQQGDIRLAGQALGQLQGRSLQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQVHR 117 Query: 122 L-MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADE 180 + +A+++A+ LERV IP + R+ YP QFSGGMRQRV IA+AL P+L++ADE Sbjct: 118 PHLSRRQAKQQALSWLERVRIPAN--RWSQYPHQFSGGMRQRVAIALALLLQPRLVVADE 175 Query: 181 PTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVE 240 PTT+LDVT+ A+I++ L L E S++ I+HDL + +CDRI +Y G++VE P Sbjct: 176 PTTSLDVTVAAEILQELTRLCSEENTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTT 235 Query: 241 EILKTPLHPYTKGLLNS 257 +L P HPYT+ LL S Sbjct: 236 AVLTRPQHPYTQTLLQS 252 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: 388 Number of extensions: 18 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: 536 Length adjustment: 31 Effective length of query: 293 Effective length of database: 505 Effective search space: 147965 Effective search space used: 147965 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