RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780259|ref|YP_003064672.1| 50S ribosomal protein L23 [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|180228 PRK05738, rplW, 50S ribosomal protein L23; Reviewed. Length = 92 Score = 105 bits (265), Expect = 2e-24 Identities = 53/105 (50%), Positives = 59/105 (56%), Gaps = 14/105 (13%) Query: 7 YDTIISPVIAEKSTLLA-GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65 YD I PVI EKSTLL QN+ VF V D++K EIK+AVE LF VKV SVNTL KGK Sbjct: 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKT 60 Query: 66 KRLSRISAARSRVRSSRDMYVSRKDVKRAFVTLAKGYSIDISAGV 110 KR R R D K+A VTLA+G ID G Sbjct: 61 KRFGRRIG-------------KRSDWKKAIVTLAEGQKIDFFGGA 92 >gnl|CDD|183398 PRK12280, rplW, 50S ribosomal protein L23; Reviewed. Length = 158 Score = 65.6 bits (160), Expect = 3e-12 Identities = 37/97 (38%), Positives = 51/97 (52%), Gaps = 13/97 (13%) Query: 10 IISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLS 69 I P++ EKS L +N F V + ++K EIK AVE +F VKV+ VN K KRL Sbjct: 7 IKKPILTEKSYSLMSKNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLG 66 Query: 70 RISAARSRVRSSRDMYVSRKDVKRAFVTLAKGYSIDI 106 R + K+A+VTLA+GYSI++ Sbjct: 67 RFPGFTNS-------------YKKAYVTLAEGYSINL 90 >gnl|CDD|184736 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional. Length = 84 Score = 60.3 bits (147), Expect = 1e-10 Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 2/62 (3%) Query: 7 YDTIISPVIAEKSTLLA-GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIR-KGK 64 Y I P++ EK+ L +N++ F V + ++K +IK AVE LF VKV VNTLI KG+ Sbjct: 2 YSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGE 61 Query: 65 VK 66 K Sbjct: 62 KK 63 >gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts. Length = 77 Score = 52.6 bits (127), Expect = 2e-08 Identities = 23/51 (45%), Positives = 34/51 (66%), Gaps = 1/51 (1%) Query: 13 PVIAEKST-LLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRK 62 P++ EK+ L+ +N++ F V + ++K +IK AVE LF VKV VNTLI Sbjct: 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP 51 >gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional. Length = 145 Score = 46.6 bits (111), Expect = 1e-06 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 2/70 (2%) Query: 6 FYDTIISPVIAEKST-LLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIR-KG 63 Y I P+ EK+ + N +VF V + ++K++IK AVE L+ VKVV VNTLI G Sbjct: 62 KYSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDG 121 Query: 64 KVKRLSRISA 73 K R+S Sbjct: 122 LKKAYIRLSP 131 >gnl|CDD|181432 PRK08453, fliD, flagellar capping protein; Validated. Length = 673 Score = 28.7 bits (64), Expect = 0.32 Identities = 15/30 (50%), Positives = 17/30 (56%) Query: 80 SSRDMYVSRKDVKRAFVTLAKGYSIDISAG 109 SSRD S+ D F T K Y+IDI AG Sbjct: 118 SSRDDVFSQVDTTLKFYTQGKDYAIDIKAG 147 >gnl|CDD|178741 PLN03200, PLN03200, cellulose synthase-interactive protein; Provisional. Length = 2102 Score = 26.6 bits (59), Expect = 1.6 Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 7/81 (8%) Query: 29 VFNVKKDSSKSEIKSAVEALFSV-KVVSVNTLIRKGKVKRLSRISAARSR-VRSSRDMYV 86 +F+ ++D +S E + K+++ NT + + +R AA SR ++ +R + Sbjct: 636 IFSSRQDLCESLA--TDEIINPCIKLLTNNT---EAVATQSARALAALSRSIKENRKVSY 690 Query: 87 SRKDVKRAFVTLAKGYSIDIS 107 + +D + + LAK SI+++ Sbjct: 691 AAEDAIKPLIKLAKSSSIEVA 711 >gnl|CDD|152098 pfam11662, DUF3263, Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria. Length = 77 Score = 25.4 bits (56), Expect = 3.4 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 65 VKRLSRISAARSRVRSSR 82 VKRL R+ ++R R RS+R Sbjct: 60 VKRLRRLRSSRQRARSAR 77 >gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional. Length = 386 Score = 25.1 bits (55), Expect = 3.9 Identities = 9/27 (33%), Positives = 17/27 (62%) Query: 83 DMYVSRKDVKRAFVTLAKGYSIDISAG 109 D + +++K+A+ LAK Y D++ G Sbjct: 14 DRNATEEEIKKAYRRLAKKYHPDLNPG 40 >gnl|CDD|169383 PRK08329, PRK08329, threonine synthase; Validated. Length = 347 Score = 24.8 bits (54), Expect = 4.7 Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 12/74 (16%) Query: 24 GQNQVVFNVKKDSS-KSEIKSAVEALFS-VKV---VSVNTLIRKGKVKRLSRISAARSRV 78 G N+VV DSS + + A+ +L +KV VS N K K+ LSR+ A V Sbjct: 103 GINEVVI----DSSGNAALSLALYSLSEGIKVHVFVSYNA--SKEKISLLSRLGAELHFV 156 Query: 79 RSSRDMYVSRKDVK 92 R M V + VK Sbjct: 157 EGDR-MEVHEEAVK 169 >gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed. Length = 1034 Score = 25.0 bits (55), Expect = 4.9 Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%) Query: 27 QVVFNVKKDSSKSE-IKSAVEALFSVKVVSVNTLIRKGKVKR 67 V +++ + S S+ I A+E F V +S+NT+ K++ Sbjct: 704 AVFYDIMLNYSSSDYITDALEFGFEVAKLSINTIPYHDKIEN 745 >gnl|CDD|184602 PRK14280, PRK14280, chaperone protein DnaJ; Provisional. Length = 376 Score = 24.7 bits (54), Expect = 5.4 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 8/36 (22%) Query: 80 SSRDMY--------VSRKDVKRAFVTLAKGYSIDIS 107 + RD Y S+ ++K+A+ L+K Y DI+ Sbjct: 2 AKRDYYEVLGVSKSASKDEIKKAYRKLSKKYHPDIN 37 Score = 24.3 bits (53), Expect = 7.5 Identities = 10/20 (50%), Positives = 11/20 (55%) Query: 29 VFNVKKDSSKSEIKSAVEAL 48 V V K +SK EIK A L Sbjct: 9 VLGVSKSASKDEIKKAYRKL 28 >gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional. Length = 365 Score = 24.5 bits (53), Expect = 6.3 Identities = 11/27 (40%), Positives = 17/27 (62%) Query: 83 DMYVSRKDVKRAFVTLAKGYSIDISAG 109 D S++D+K+AF LAK + D+ G Sbjct: 12 DRNASQEDIKKAFRELAKKWHPDLHPG 38 >gnl|CDD|162033 TIGR00770, Dcu, anaerobic c4-dicarboxylate membrane transporter family protein. These proteins are members of th C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most proteins in this family have 12 GES predicted transmembrane regions; however one member has 10 experimentally determined transmembrane regions with both the N- and C-termini localized to the periplasm. The two Escherichia coli proteins, DcuA and DcuB, transport aspartate, malate, fumarate and succinate, and function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively. Length = 430 Score = 24.3 bits (53), Expect = 7.1 Identities = 10/26 (38%), Positives = 16/26 (61%) Query: 7 YDTIISPVIAEKSTLLAGQNQVVFNV 32 Y TI++P + T+LAG VV++ Sbjct: 83 YITILAPSVTYFLTILAGTGHVVYST 108 >gnl|CDD|184385 PRK13905, murB, UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional. Length = 298 Score = 24.3 bits (54), Expect = 7.6 Identities = 8/18 (44%), Positives = 11/18 (61%) Query: 53 VVSVNTLIRKGKVKRLSR 70 + SV L R G++K LS Sbjct: 146 LESVEVLDRDGEIKTLSN 163 >gnl|CDD|173334 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional. Length = 421 Score = 24.0 bits (52), Expect = 8.2 Identities = 10/20 (50%), Positives = 12/20 (60%) Query: 29 VFNVKKDSSKSEIKSAVEAL 48 V N+ KD + SEIK A L Sbjct: 33 VLNLSKDCTTSEIKKAYRKL 52 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.130 0.329 Gapped Lambda K H 0.267 0.0780 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,603,660 Number of extensions: 84234 Number of successful extensions: 238 Number of sequences better than 10.0: 1 Number of HSP's gapped: 233 Number of HSP's successfully gapped: 39 Length of query: 110 Length of database: 5,994,473 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,352,265 Effective search space: 147977010 Effective search space used: 147977010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (22.9 bits)