RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780815|ref|YP_003065228.1| hypothetical protein
CLIBASIA_03530 [Candidatus Liberibacter asiaticus str. psy62]
(232 letters)
>gnl|CDD|34102 COG4395, COG4395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 281
Score = 122 bits (306), Expect = 1e-28
Identities = 56/239 (23%), Positives = 94/239 (39%), Gaps = 21/239 (8%)
Query: 6 MDSGDFLILLFAFITFFVFLQLRGVLGKKTGNEKPF---------------SGFFSGKYV 50
+ F L F F +FL L ++G E F + YV
Sbjct: 44 LSGMFFGGLFFGIAAFLIFLLLITLIGFVIMLEMRFFDPYRPQRPAYDAAQASVAPDNYV 103
Query: 51 FS-KRDERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARN 109
+ E + D + + + G L R + + FDP FLN AR
Sbjct: 104 TLPRAPEAQPAS-----AADIPAAGDAIGGAGGPLAAGARAVHNADPSFDPARFLNGARA 158
Query: 110 SYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLVGIDDMKIINASI 169
+YE I ++ G + +L+ V + ++ R+S + +SS V I I A +
Sbjct: 159 AYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQSSFVTILQADIARADV 218
Query: 170 EENTVYITIRIVGQFISASYDKDNLLISSDPEIFGKVIDIWTFVRNIPPSNPNWVLIST 228
E + Y T+ I Q I + D+ ++ DP+ + ++WTF R+ +PNW L +
Sbjct: 219 EGDEDYATVAIRYQGIDVTRDRSGKVVDGDPDKPEEFAELWTFTRDTGSRDPNWKLAAI 277
>gnl|CDD|146752 pfam04280, Tim44, Tim44-like domain. Tim44 is an essential
component of the machinery that mediates the
translocation of nuclear-encoded proteins across the
mitochondrial inner membrane. Tim44 is thought to bind
phospholipids of the mitochondrial inner membrane both
by electrostatic interactions and by penetrating the
polar head group region. This family includes the
C-terminal region of Tim44 that has been shown to form a
stable proteolytic fragment in yeast. This region is
also found in a set of smaller bacterial proteins. The
molecular function of the bacterial members of this
family is unknown but transport seems likely. The
crystal structure of the C terminal of Tim44 has
revealed a large hydrophobic pocket which might play an
important role in interacting with the acyl chains of
lipid molecules in the mitochondrial membrane.
Length = 146
Score = 111 bits (280), Expect = 1e-25
Identities = 42/144 (29%), Positives = 80/144 (55%)
Query: 85 NKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSLST 144
+ I + FD ++FL AR +YE I +++ G + + +L+ VY++F ++
Sbjct: 1 ASALAAIKAADPSFDVEEFLEGAREAYEMIQEAWANGDLETLRELLTPEVYEEFAAEIAE 60
Query: 145 RKSNEKNVKSSLVGIDDMKIINASIEENTVYITIRIVGQFISASYDKDNLLISSDPEIFG 204
R++ +++VGI D +++ A +E NT +T+R V Q IS + D ++ DP+
Sbjct: 61 REAQGLTNDATIVGIRDAELLEAKMEGNTAVVTVRFVTQQISVTDDASGEVVEGDPDEPV 120
Query: 205 KVIDIWTFVRNIPPSNPNWVLIST 228
+V ++WTF R++ +PNW L+
Sbjct: 121 EVTEVWTFERDLGSPDPNWRLVGI 144
>gnl|CDD|37791 KOG2580, KOG2580, KOG2580, Mitochondrial import inner membrane
translocase, subunit TIM44 [Intracellular trafficking,
secretion, and vesicular transport].
Length = 459
Score = 37.6 bits (87), Expect = 0.002
Identities = 28/150 (18%), Positives = 60/150 (40%), Gaps = 5/150 (3%)
Query: 82 TRLNKVMRDIVSVYTDFDPKDFLNEARNSY-EAIVDSFFEGKVHAIEKLVDSRVYQDFND 140
T +++V+ +I + FD +DFL E +++++ +G + ++K +
Sbjct: 299 TEMSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAA 358
Query: 141 SLSTRKSNEKNVKSSLVGIDDMKIINASIEENTVYITIRIVGQFISASYDKDNLLISSDP 200
+ K + S ++ I + I + + E+ + I Q I D ++ DP
Sbjct: 359 PIKEYKKHGVYFDSKILDIRGVDIASGKMMEDGPVLIITFQAQEIMCVRDAKGEVVEGDP 418
Query: 201 EIFGKVIDIWTFVRNI----PPSNPNWVLI 226
+ +V W R+ P W L+
Sbjct: 419 DKILRVYYAWVLCRDQDELNPDEYAAWRLL 448
>gnl|CDD|145924 pfam03034, PSS, Phosphatidyl serine synthase. Phosphatidyl serine
synthase is also known as serine exchange enzyme. This
family represents eukaryotic PSS I and II which are
membrane bound proteins which catalyses the replacement
of the head group of a phospholipid (phosphotidylcholine
or phosphotidylethanolamine) by L-serine.
Length = 278
Score = 32.3 bits (74), Expect = 0.12
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 179 RIVGQFISASYDKDNLLISSDPEIFGKVIDIWT-------------FVRNIPPSNP 221
R++ QF AS+DK + P+ F +V+ + + IPPS+P
Sbjct: 167 RVLLQFTPASWDKYEWKVFKSPKRFLQVLFLVFLILLAELNTFFLKHILWIPPSHP 222
>gnl|CDD|73314 cd02568, PseudoU_synth_PUS1_PUS2, PseudoU_synth_PUS1_PUS2:
Pseudouridine synthase, PUS1/ PUS2 like. This group
consists of eukaryotic pseudouridine synthases similar
to Saccharomyces cerevisiae Pus1p, S. cerevisiae
Pus2p, Caenorhabditis elegans Pus1p and human PUS1.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus1p catalyzes the formation of psi34 and
psi36 in the intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia
(MLASA)..
Length = 245
Score = 30.2 bits (68), Expect = 0.53
Identities = 23/129 (17%), Positives = 50/129 (38%), Gaps = 17/129 (13%)
Query: 60 ITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSF- 118
G G +D ++ +N P R+ + R V F+ + + +YE ++ +F
Sbjct: 75 DPEGLGIGEDLVEKLNSHLPEDIRVFGITR----VTKSFNARKACD--SRTYEYLLPTFA 128
Query: 119 FEGKVH---AIEKLVDSRVYQDF-NDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENTV 174
E ++ V + + +F S + + S + + +I +E
Sbjct: 129 LETLDRFNEILKLYVGTHNFHNFTVRKKFEDPSANRFIIS--FYVSEPFVIEEGLE---- 182
Query: 175 YITIRIVGQ 183
+++I I GQ
Sbjct: 183 WVSIEIHGQ 191
>gnl|CDD|39459 KOG4258, KOG4258, KOG4258, Insulin/growth factor receptor (contains
protein kinase domain) [Signal transduction mechanisms].
Length = 1025
Score = 29.6 bits (66), Expect = 0.70
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 117 SFFEGKVHAIEKLVDSRVYQD---FNDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENT 173
E I+ + D++ + N SL+ N N+ S L + IEE T
Sbjct: 332 KVCEPGTKTIDSVADAQNLRGCTIINGSLTINIRNGNNIASEL------ENALGLIEEIT 385
Query: 174 VYITIRIVGQFISASYDKDNLLISSDPEIFGK 205
Y+ +R +S S+ ++ LI DP G
Sbjct: 386 GYLKVRHSSALVSLSFLRNLRLIRGDPLEEGN 417
>gnl|CDD|36513 KOG1299, KOG1299, KOG1299, Vacuolar sorting protein VPS45/Stt10
(Sec1 family) [Intracellular trafficking, secretion, and
vesicular transport].
Length = 549
Score = 28.3 bits (63), Expect = 2.0
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 63 GKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDP 100
G ++ +L N+L PI R K ++ + +VYT P
Sbjct: 429 GLHVRQGDLFGPNDLVPIARRFIKGLKGVENVYTQHQP 466
>gnl|CDD|146065 pfam03246, Pneumo_ncap, Pneumovirus nucleocapsid protein.
Length = 391
Score = 27.9 bits (62), Expect = 2.3
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 83 RLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVDSRVYQDFNDSL 142
R N V++D + Y D KD A + YE FE K + I+ V+ +F +
Sbjct: 185 RANNVLKDEMKRYPRMDIKDI---ANSFYE-----LFEKKPYYID------VFIEFGKAQ 230
Query: 143 STRKSNEKNVKSSLVGI 159
S+ + V+ VG+
Sbjct: 231 SSTSGGSR-VEGLFVGL 246
>gnl|CDD|112214 pfam03389, MobA_MobL, MobA/MobL family. This family includes of
the MobA protein from the E. coli plasmid RSF1010, and
the MobL protein from the Thiobacillus ferrooxidans
plasmid PTF1. These sequences are mobilisation proteins,
which are essential for specific plasmid transfer.
Length = 219
Score = 27.9 bits (62), Expect = 2.5
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 56 ERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVSVYTDFDPKDFLNEARNSYEAIV 115
R + G G KK + I L G ++ I D+ K+ + E R ++
Sbjct: 123 LRPLDPDGFGGKKKKSEYI--LDENGNKIRTKRGKIK--TEDWGSKELVEEWRKAWADHA 178
Query: 116 DSFFEGKVHAIEKLVDSRVYQ 136
++ E I+ +D R Y+
Sbjct: 179 NAHLEL--AGIDARIDHRSYE 197
>gnl|CDD|143487 cd06812, PLPDE_III_DSD_D-TA_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
and D-Threonine Aldolase, Unknown Group 1. This
subfamily is composed of uncharacterized bacterial
proteins with similarity to eukaryotic D-serine
dehydratases (DSD) and D-threonine aldolases (D-TA). DSD
catalyzes the dehydration of D-serine to aminoacrylate,
which is rapidly hydrolyzed to pyruvate and ammonia.
D-TA reversibly catalyzes the aldol cleavage of
D-threonine into glycine and acetaldehyde, and the
synthesis of D-threonine from glycine and acetaldehyde.
DSD and D-TA are fold type III PLP-dependent enzymes,
similar to bacterial alanine racemase (AR), which
contains an N-terminal PLP-binding TIM barrel domain and
a C-terminal beta-sandwich domain. AR exists as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Based on
their similarity to AR, it is possible members of this
family also form dimers in solution.
Length = 374
Score = 27.7 bits (62), Expect = 2.5
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 5/29 (17%)
Query: 56 ERGIITLGKGKKKDNLDSINELFPIGTRL 84
E GII L + D PIGTRL
Sbjct: 315 EHGIIAL-----RGGSDLSLPDLPIGTRL 338
>gnl|CDD|39890 KOG4692, KOG4692, KOG4692, Predicted E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 489
Score = 27.7 bits (61), Expect = 3.0
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 98 FDPKDFLNEARNSYEAIVDSFFEGKVHAIEKLVD 131
F P+ ++N +A++D F + A + D
Sbjct: 24 FVPEVYVNTLPILLDAVMD--FSHDLKAQFEASD 55
>gnl|CDD|31697 COG1508, RpoN, DNA-directed RNA polymerase specialized sigma
subunit, sigma54 homolog [Transcription].
Length = 444
Score = 26.8 bits (59), Expect = 4.8
Identities = 29/132 (21%), Positives = 50/132 (37%), Gaps = 26/132 (19%)
Query: 34 KTGNEKPFSGFFSGKYVFSKRDERGIITLGKGKKKDNLDSINELFPIGTRLNKVMRDIVS 93
++ + +P F SG+ + D G+ + N DS+ + RLN+ +VS
Sbjct: 220 RSLDPRPGLEFSSGEAEYVVPDVLVRKHNGEWTVELNDDSLPRI-----RLNQEYAALVS 274
Query: 94 VYTDFDPKDFLNEARNSYEAIVDS---------------------FFEGKVHAIEKLVDS 132
+ + +DFL E + ++ S FFEG A++ LV
Sbjct: 275 RAENDEDQDFLKEKLQEAKWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLR 334
Query: 133 RVYQDFNDSLST 144
V + ST
Sbjct: 335 DVADEIGMHEST 346
>gnl|CDD|39760 KOG4560, KOG4560, KOG4560, Transcription factor IIIC box B binding
(alpha) subunit [Transcription].
Length = 1897
Score = 26.6 bits (58), Expect = 5.5
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 1/71 (1%)
Query: 99 DPKDFLNEARNSYEAIV-DSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLV 157
DP + ++ + K + L +Y+ F++ + N+ S LV
Sbjct: 1166 DPASETDLQVAVAHGVLHSNICCAKDKTLLNLQTFEIYKHFSEEVLNSAFNKARADSLLV 1225
Query: 158 GIDDMKIINAS 168
+ I +A+
Sbjct: 1226 AVKRRNIQSAA 1236
>gnl|CDD|109933 pfam00895, ATP-synt_8, ATP synthase protein 8.
Length = 55
Score = 26.1 bits (58), Expect = 7.6
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 11 FLILLFAFITFFVFLQL 27
FLI L +++T + +QL
Sbjct: 10 FLIFLSSWLTLLIIIQL 26
>gnl|CDD|153131 cd01581, AcnB, Aconitate hydratase B catalyses the formation of
cis-aconitate from citrate as part of the TCA cycle.
Aconitase B catalytic domain. Aconitate hydratase B
catalyses the formation of cis-aconitate from citrate as
part of the TCA cycle. Aconitase has an active (4FE-4S)
and an inactive (3FE-4S) form. The active cluster is
part of the catalytic site that interconverts citrate,
cis-aconitase and isocitrate. The domain architecture of
aconitase B is different from other aconitases in that
the catalytic domain is normally found at C-terminus for
other aconitases, but it is at N-terminus for B family.
It also has a HEAT domain before domain 4 which plays a
role in protein-protein interaction. This alignment is
the core domain including domains 1,2 and 3.
Length = 436
Score = 25.9 bits (57), Expect = 8.6
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 116 DSFFEGKVHAIEKLVDSRVYQDFNDSLSTRKSNEKNVKSSLVGIDDMKIINASIEENTVY 175
+ F G++ IE L D +V Q F T S E++ + V +D +I +E N V
Sbjct: 188 KNVFNGRILEIEGLPDLKVEQAFE---LTDASAERSAAACTVRLDKEPVIE-YLESNVVL 243
Query: 176 ITIRI 180
+ I I
Sbjct: 244 MKIMI 248
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
0.321 0.140 0.401
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,864,349
Number of extensions: 152240
Number of successful extensions: 468
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 22
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)