RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780146|ref|YP_003064559.1| 50S ribosomal protein L1 [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >gnl|CDD|144329 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This family includes prokaryotic L1 and eukaryotic L10. Length = 203 Score = 290 bits (745), Expect = 2e-79 Identities = 124/203 (61%), Positives = 161/203 (79%), Gaps = 1/203 (0%) Query: 21 LYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFA 80 LY + +A+ +LKE AT +FDETVE+A+NLG+DP+ A+Q VRG V +P+GTG V+VAVFA Sbjct: 1 LYAIKEALELLKETATRKFDETVELAINLGVDPKKADQRVRGTVVLPHGTGKTVKVAVFA 60 Query: 81 TSSKADEAREAGADIVGGEDLFE-IVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMP 139 KA EA+ AGAD VGG++L E I K G +DFD IATPDMMP VG+LGRILGPRG+MP Sbjct: 61 KGEKAKEAKAAGADYVGGDELLEKIKKDGWLDFDVFIATPDMMPQVGKLGRILGPRGLMP 120 Query: 140 NLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVK 199 N + GTVT DVA AV+E KSG+V+FR++KAGIIH +GKVSF+++K+ EN+ A ++A+VK Sbjct: 121 NPKTGTVTPDVAKAVKELKSGSVEFRADKAGIIHVPVGKVSFDDEKLAENIKAVLNALVK 180 Query: 200 AKPSVAKGDYVKRVTLSSTMGCG 222 KPS+ KG Y+K V + STMG G Sbjct: 181 LKPSLKKGWYIKSVYIKSTMGPG 203 >gnl|CDD|30430 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]. Length = 228 Score = 282 bits (723), Expect = 6e-77 Identities = 136/227 (59%), Positives = 178/227 (78%), Gaps = 1/227 (0%) Query: 3 SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62 +K SKR + S+ +DR+ LY L +AV +LKE + +FDETVE+A+NL +DPR +Q VRG Sbjct: 2 AKKSKRYRAASEKVDRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRG 61 Query: 63 VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQ-IDFDRCIATPDM 121 V +PNGTG VRVAVFA KA+EA+ AGAD VGGEDL E++K G+ DFD IATPDM Sbjct: 62 SVVLPNGTGKTVRVAVFADGEKAEEAKAAGADYVGGEDLIELIKNGRAKDFDVFIATPDM 121 Query: 122 MPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSF 181 MPLVG+LG++LGPRG+MPN + GTVT DVA AV E K G V+FR++KAG+IH IGKVSF Sbjct: 122 MPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADKAGVIHVPIGKVSF 181 Query: 182 ENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLS 228 +++K+ EN+ A ++A+VKAKP+ AKG Y+K V +S+TMG G+KVDL+ Sbjct: 182 DDEKLAENIEALLNAIVKAKPAGAKGQYIKSVYVSTTMGPGVKVDLA 228 >gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed. Length = 229 Score = 258 bits (660), Expect = 1e-69 Identities = 103/230 (44%), Positives = 155/230 (67%), Gaps = 1/230 (0%) Query: 2 VSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVR 61 + K+S+R +++ I++ LY +A+ +LKE ATA+F ET E ++L IDP++A+Q +R Sbjct: 1 MKKLSRRTKELRSKIEKK-LYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLR 59 Query: 62 GVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDM 121 VT+P GTG +R+AV K EA+ AGADIVG +DL E + G +DFD IATPDM Sbjct: 60 TTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADIVGSDDLIEEITKGNLDFDLLIATPDM 119 Query: 122 MPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSF 181 MP + +LGR+LGPRG+MP+ + GTVTTD+A+A+ E K G +++R++K GI+H GK +F Sbjct: 120 MPKLAKLGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLEYRADKTGIVHVLFGKSNF 179 Query: 182 ENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231 + + EN+ A ++ + +PS KG Y K + STMG I++D+S Sbjct: 180 TEEDLLENLQAIYESIEQNRPSGVKGKYWKSFYICSTMGPSIQIDISLLR 229 >gnl|CDD|88601 cd00403, Ribosomal_L1, Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.. Length = 208 Score = 200 bits (511), Expect = 2e-52 Identities = 95/210 (45%), Positives = 137/210 (65%), Gaps = 10/210 (4%) Query: 24 LSDAVVMLKERA--TARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81 L +A+ LK+ + +FDETVE+ +NL D R +Q +RG V +P+G G +V+V VFA Sbjct: 1 LEEAIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAK 60 Query: 82 SSKADEAREAGADIVGGEDLFEIVKGGQ-----IDFDRCIATP-DMMPLVGRLGRILGPR 135 +A EA+ AGAD+VGGEDL + +K G+ DFD +A P MM L LG++LGPR Sbjct: 61 DEQAKEAKAAGADVVGGEDLKKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPR 120 Query: 136 GIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVS 195 G MPN + GTVT D+A A+ E+KS +V+FR +K G IH +GKVS +++ EN+ A ++ Sbjct: 121 GKMPNPKTGTVTEDLAKAIEEAKS-SVEFRLDKGGCIHVPVGKVSMSPEQLVENIEAVIN 179 Query: 196 AVVKAKPSVAKGDYVKRVTLSSTMGCGIKV 225 A+VK PS KG +K + L +TMG + + Sbjct: 180 ALVKKLPS-KKGQNIKSIYLKTTMGPSLPI 208 >gnl|CDD|36782 KOG1569, KOG1569, KOG1569, 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]. Length = 323 Score = 153 bits (387), Expect = 5e-38 Identities = 68/209 (32%), Positives = 106/209 (50%), Gaps = 10/209 (4%) Query: 26 DAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT-SSK 84 A + K+ R + + A V P G ++AVF +SK Sbjct: 106 SAYNVPKQPVNLRIELNMLAE---KETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDASK 162 Query: 85 ADEAREAGADIVGGEDLFEIVKGGQI--DFDRCIATPDMMPLVGRLGRILGPRGIMPNLR 142 +EAREAGA + GG DL + +K G+I D+D +A PD+MP + RL +ILGPR PN + Sbjct: 163 VEEAREAGAALAGGTDLIKKIKSGEIVADYDFYVAHPDIMPELNRLRKILGPR--FPNPK 220 Query: 143 VGTVTTDVATAVRESKSG-AVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAK 201 GTV ++ + E K+G + F E+ I+ +GK+ +++I N+ A ++AV + Sbjct: 221 RGTVGRNIPEMIEEFKNGHEIKFDEERENILQIKVGKLDMTSEQILANIQAVIAAVCTHR 280 Query: 202 PSVAKGDYVKRVTLSSTMGCGIKVDLSSF 230 P A G +V R L S+ G GI + + Sbjct: 281 PK-ALGPFVVRALLRSSPGEGILLKIDPL 308 >gnl|CDD|39568 KOG4367, KOG4367, KOG4367, Predicted Zn-finger protein [Function unknown]. Length = 699 Score = 28.5 bits (63), Expect = 1.4 Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 3/65 (4%) Query: 52 DPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQID 111 + +H++ V+ + M + A+ S +A EA+E +V ++ + ++ ++ Sbjct: 252 EGKHSSHEVKALGAMWKLHKSQLSQALNGLSDRAKEAKE---FLVQLRNMVQQIQENSVE 308 Query: 112 FDRCI 116 F+ C+ Sbjct: 309 FEACL 313 >gnl|CDD|35079 COG5520, COG5520, O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]. Length = 433 Score = 28.5 bits (63), Expect = 1.6 Identities = 11/67 (16%), Positives = 26/67 (38%) Query: 30 MLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAR 89 ML + E + + ++ ++ +Q++RG M + A + + A Sbjct: 17 MLCLPFVSGSTEVLAASEDITVNVAAKHQVIRGFGGMNSSAWAGDLSAAQLETLFGNGAN 76 Query: 90 EAGADIV 96 + G I+ Sbjct: 77 QLGFSIL 83 >gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related proteins. Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes, or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Length = 330 Score = 28.1 bits (63), Expect = 2.4 Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 14/68 (20%) Query: 75 RVAVFATS-SKADEAREAGADIV---GGEDLFEIVKGGQIDFDRCIAT-------PDMMP 123 S K + AR+ GAD V G E + GG D + T + Sbjct: 188 ETVAITRSPDKRELARKLGADEVVDSGAELDEQAAAGG---ADVILVTVVSGAAAEAALG 244 Query: 124 LVGRLGRI 131 + R GRI Sbjct: 245 GLRRGGRI 252 >gnl|CDD|34243 COG4623, COG4623, Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]. Length = 473 Score = 28.0 bits (62), Expect = 2.6 Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 12/100 (12%) Query: 53 PRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDF 112 PR Q+ +T+ G+ + + +K E D +G EDL E+V G++D+ Sbjct: 121 PRSLGQLKGRQITVAKGSAHVEDLKL-LKETKYPELIWKVDDKLGVEDLLEMVAEGKLDY 179 Query: 113 DRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVAT 152 T + R+ P L V TD Sbjct: 180 -----TIADSVEISLFQRVH------PELAVAFDLTDEQP 208 >gnl|CDD|176229 cd08268, MDR2, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Length = 328 Score = 27.6 bits (62), Expect = 3.4 Identities = 22/72 (30%), Positives = 26/72 (36%), Gaps = 14/72 (19%) Query: 76 VAVFATSSKADEAREAGADIV---GGEDLFEIV------KGGQIDFDRCIATPDMMPLVG 126 +A TS K D GA V EDL V KG + FD P P Sbjct: 173 IATTRTSEKRDALLALGAAHVIVTDEEDLVAEVLRITGGKGVDVVFD-----PVGGPQFA 227 Query: 127 RLGRILGPRGIM 138 +L L P G + Sbjct: 228 KLADALAPGGTL 239 >gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Length = 337 Score = 26.3 bits (59), Expect = 7.4 Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%) Query: 75 RVAVFATS-SKADEAREAGAD 94 V F+ S SK ++A + GAD Sbjct: 195 EVTAFSRSPSKKEDALKLGAD 215 >gnl|CDD|37314 KOG2103, KOG2103, KOG2103, Uncharacterized conserved protein [Function unknown]. Length = 910 Score = 26.1 bits (57), Expect = 7.7 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 4/46 (8%) Query: 151 ATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKI----EENVLA 192 A AV E ++G D+R + G+ ++K++ E+ VLA Sbjct: 15 AAAVYEDQAGKFDWRQQLVGVKKVNFLVYDTKSKRLIVSTEKGVLA 60 >gnl|CDD|34204 COG4566, TtrR, Response regulator [Signal transduction mechanisms]. Length = 202 Score = 26.0 bits (57), Expect = 9.3 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 2/52 (3%) Query: 115 CIATPDMMPLVGRLG--RILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDF 164 C+ MP + L L RGI + T D+ AV+ K+GAVDF Sbjct: 51 CLLLDVRMPGMSGLELQDRLAERGIRLPVIFLTGHGDIPMAVQAMKAGAVDF 102 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 0.318 0.134 0.367 Gapped Lambda K H 0.267 0.0783 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,539,060 Number of extensions: 131636 Number of successful extensions: 432 Number of sequences better than 10.0: 1 Number of HSP's gapped: 422 Number of HSP's successfully gapped: 35 Length of query: 232 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 141 Effective length of database: 4,297,318 Effective search space: 605921838 Effective search space used: 605921838 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 (21.7 bits) S2: 56 (25.2 bits)