RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781045|ref|YP_003065458.1| outer membrane lipoprotein omp19 [Candidatus Liberibacter asiaticus str. psy62] (162 letters) >gnl|CDD|145888 pfam02974, Inh, Protease inhibitor Inh. The Inh inhibitor is secreted into the periplasm where its presumed physiological function is to protect periplasmic proteins against the action of secreted proteases. A range of proteases including A, B and C from E. chrysanthemi, alkaline protease from Pseudomonas aeruginosa and the 50 kDa protease from Serratia marcescens are inhibited. Length = 98 Score = 48.1 bits (115), Expect = 1e-06 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 3/75 (4%) Query: 77 GAWKVSYRDVDCKMILTLTRFKKNFRGTARSCHGRLASLA--AWNIIDEDSFELKNKSGQ 134 G W++S C + LT T+ + + +C G W D L + SG Sbjct: 13 GQWQLSKGGQVCDIELTQTKLGQGYLAGDLACLGEWLGEVPSGWRP-TPDGLALTDASGS 71 Query: 135 TIIVFYKTAEQSFEG 149 T+ Y++ E +EG Sbjct: 72 TVAFLYRSGEGRYEG 86 >gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD. Length = 215 Score = 28.2 bits (64), Expect = 1.1 Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 6/43 (13%) Query: 7 ILLNLYMLTLFSHGCTQIDFGNIFFKKPE------ISLPPSVE 43 ILLNL + S + + K P I LP VE Sbjct: 68 ILLNLKEIVFKSDSEDEPQVLRLKVKGPGVVTAADIELPSGVE 110 >gnl|CDD|37317 KOG2106, KOG2106, KOG2106, Uncharacterized conserved protein, contains HELP and WD40 domains [Function unknown]. Length = 626 Score = 26.9 bits (59), Expect = 3.1 Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 4/68 (5%) Query: 29 IFFKKPEISLPPSVESEILLPPIPEEEFDQDDISVPSKDNNAIRMGIIGAWKVSYRDVDC 88 FF E + +L +P + + P D + W YR VDC Sbjct: 12 CFFSNGEGNYKNFSRGRPVLVSVPVDPEH----TYPMADVELPTEKLKLEWVYGYRGVDC 67 Query: 89 KMILTLTR 96 + L L Sbjct: 68 RNNLYLLP 75 >gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein. Length = 219 Score = 25.7 bits (57), Expect = 5.7 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 7/38 (18%) Query: 54 EEFDQDDISVPSKDNNAIRMGIIGAWKVSYRDVDCKMI 91 EEF D + +A+R I A+K SYR+VD +I Sbjct: 73 EEFLNDFV-------DALRDNKIEAFKKSYRNVDLLLI 103 >gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3. Length = 199 Score = 25.0 bits (55), Expect = 9.0 Identities = 8/24 (33%), Positives = 12/24 (50%) Query: 97 FKKNFRGTARSCHGRLASLAAWNI 120 FK+ R R H + S+ AW+ Sbjct: 124 FKRLPRKHGRGYHRKPGSIGAWHP 147 >gnl|CDD|36281 KOG1063, KOG1063, KOG1063, RNA polymerase II elongator complex, subunit ELP2, WD repeat superfamily [Chromatin structure and dynamics, Transcription]. Length = 764 Score = 25.0 bits (54), Expect = 9.9 Identities = 11/70 (15%), Positives = 23/70 (32%), Gaps = 2/70 (2%) Query: 65 SKDNNAIRMGIIGAWKVSYRDVDCKMILTLTRFKKNFRGTARSCHGRLASLAAWNIIDED 124 K++ IR+ W + +T F + R R SL + + ++ Sbjct: 548 LKEHAVIRLWNTANWLQVQELEGHSLTVTRLAFSPDGRYLLSVSRDRTVSL--YEVQEDI 605 Query: 125 SFELKNKSGQ 134 E + + Sbjct: 606 KDEFRFACLK 615 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.323 0.139 0.417 Gapped Lambda K H 0.267 0.0775 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,060,131 Number of extensions: 104336 Number of successful extensions: 202 Number of sequences better than 10.0: 1 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 9 Length of query: 162 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 76 Effective length of database: 4,405,363 Effective search space: 334807588 Effective search space used: 334807588 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 (21.9 bits) S2: 53 (24.1 bits)