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)