RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780980|ref|YP_003065393.1| hypothetical protein
CLIBASIA_04405 [Candidatus Liberibacter asiaticus str. psy62]
(121 letters)
>gnl|CDD|35385 KOG0163, KOG0163, KOG0163, Myosin class VI heavy chain
[Cytoskeleton].
Length = 1259
Score = 31.9 bits (72), Expect = 0.042
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 22 DIVIGRTEDLLNKLQKNSTQMIKEANF--KISETHRLAQERVEAAEKRVKEVEERATASR 79
D+ + E L+ +L Q I+E KI E ++R EA EKR +E EE+ A
Sbjct: 899 DVAVKNYEKLVKRLDSKEQQQIEELERLRKIQELAEAERKRREAEEKRRREEEEKKRAKA 958
Query: 80 KL 81
++
Sbjct: 959 EM 960
>gnl|CDD|146000 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 28.1 bits (62), Expect = 0.55
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 55 RLAQERVEAAEKRVKEVEERATASRK 80
+LA++R EA EK +E E++A R+
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREERE 601
>gnl|CDD|34624 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 27.9 bits (62), Expect = 0.61
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 4/77 (5%)
Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQ----ERVEAAEKRVKEVEERATASRKLS 82
RTE L + + +++E R + E++ EKR++E+E+ RK
Sbjct: 288 RTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKEL 347
Query: 83 VDELANAFWDLSDEDKN 99
+L L D +K
Sbjct: 348 NSKLEEIQKKLEDLEKR 364
>gnl|CDD|147016 pfam04654, DUF599, Protein of unknown function, DUF599. This
family includes several uncharacterized proteins.
Length = 216
Score = 27.5 bits (62), Expect = 0.91
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 7 MTSAF--STTLLTIGGCDIVIGRTEDL 31
M + F ST +L I G ++G T+ L
Sbjct: 61 MGTTFFASTAILLIAGIAALLGSTDRL 87
>gnl|CDD|38820 KOG3614, KOG3614, KOG3614, Ca2+/Mg2+-permeable cation channels (LTRPC
family) [Inorganic ion transport and metabolism, Signal
transduction mechanisms].
Length = 1381
Score = 27.6 bits (61), Expect = 0.94
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 16/80 (20%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER---------ATASR 79
E+ L K + E N E R RV+ R+ E+E+R + +R
Sbjct: 1125 ENFLRKREM-------EQNSSTEERIRRTANRVDLILNRLIELEQREKTLKDSVQNSETR 1177
Query: 80 KLSVDELANAFWDLSDEDKN 99
SV + + + ++ N
Sbjct: 1178 LASVLQFSEEYVNILKILVN 1197
>gnl|CDD|38830 KOG3624, KOG3624, KOG3624, M13 family peptidase [Amino acid
transport and metabolism].
Length = 687
Score = 26.7 bits (58), Expect = 1.5
Identities = 9/40 (22%), Positives = 24/40 (60%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRV 68
+++ L+K +M++E ++ ET + A +++ A +K +
Sbjct: 381 SEMIEDLKKAFEEMLQELDWLDEETRKSAIKKLNAMKKNI 420
>gnl|CDD|33777 COG4018, COG4018, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 505
Score = 26.5 bits (58), Expect = 1.6
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 74 RATASRKLSVDELANAFWDLSDEDKNAFTGNVK 106
+ KL VDE+ +A DLSDE+ N++
Sbjct: 20 KLAYEGKLDVDEVVDAVGDLSDEELEKLGDNLR 52
>gnl|CDD|36445 KOG1231, KOG1231, KOG1231, Proteins containing the FAD binding
domain [Energy production and conversion].
Length = 505
Score = 26.5 bits (58), Expect = 1.8
Identities = 13/57 (22%), Positives = 24/57 (42%)
Query: 42 MIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELANAFWDLSDEDK 98
+I A K+ + QER+ + VE A +R + + ++L DE +
Sbjct: 227 IITRARIKLEPAPKRDQERLISVCGSFDTVEGAAIVARNGLQSNIRVSRFELLDEVQ 283
>gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome
protein 2 (chromosome condensation complex Condensin,
subunit E) [Chromatin structure and dynamics, Cell cycle
control, cell division, chromosome partitioning].
Length = 1174
Score = 26.1 bits (57), Expect = 2.7
Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 9/102 (8%)
Query: 23 IVIGRTEDLLNKLQKNSTQMIKEANFKIS---ETHRLAQERVEAAEKRVKEVEERATASR 79
I I + +KNS I+E KI+ E+ + +E+ EK +KE+E++ A
Sbjct: 233 ICIAYEYLQAEEKRKNSAHEIEEMKDKIAKLDESLGKTDKEIESLEKEIKEIEQQRDAEM 292
Query: 80 KLSVDELANAFWDLSDE------DKNAFTGNVKQEVCKVKKI 115
V L + L +E N + E K+++I
Sbjct: 293 GGEVKALEDKLDSLQNEITREETSLNLKKETLNGEEEKLEEI 334
>gnl|CDD|31753 COG1565, COG1565, Uncharacterized conserved protein [Function
unknown].
Length = 370
Score = 26.0 bits (57), Expect = 2.7
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETH----RLAQERVEAAEKRVKEVEERATASRKLSVD 84
D+L L++ ++ + ++ I E +E ++A E ++ VE +K
Sbjct: 93 SDILRTLRRLYPELYEALSYYIIEPSPELRARQKETLKATEDLIRWVEWVEDLPKKFPGI 152
Query: 85 ELANAFWD 92
++N +D
Sbjct: 153 VVSNELFD 160
>gnl|CDD|30092 cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup.
The yeast kinesin KIP3 plays a role in positioning the
mitotic spindle. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward..
Length = 338
Score = 26.0 bits (57), Expect = 2.8
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 30 DLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELA 87
+LL K +N TQ EAN S +H + Q V ++ ++ KLS+ +LA
Sbjct: 188 ELLMKGNRNRTQEPTEANATSSRSHAVLQITVRQKDRTASINQQVRIG--KLSLIDLA 243
>gnl|CDD|37332 KOG2121, KOG2121, KOG2121, Predicted metal-dependent hydrolase
(beta-lactamase superfamily) [General function
prediction only].
Length = 746
Score = 25.7 bits (56), Expect = 3.3
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 13/63 (20%)
Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDEL 86
R + L K K++T +I EA + EA EK +T S +SV +
Sbjct: 629 RPCEDLVKAGKDATLLIHEATLEDDLEE-------EAVEK------GHSTTSEAISVAKK 675
Query: 87 ANA 89
NA
Sbjct: 676 MNA 678
>gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl
cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1
[Signal transduction mechanisms].
Length = 3738
Score = 25.5 bits (55), Expect = 3.9
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 57 AQERVEAAEKRVKEVEERATASRKLSV----DELANAFWDLSDEDKN 99
++E K + + + T+SR + D FW+ DEDKN
Sbjct: 2874 SEESFVMCLKDLTSIVDIKTSSRPAMIGSLTDGSTETFWESGDEDKN 2920
>gnl|CDD|33327 COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope
biogenesis, outer membrane].
Length = 372
Score = 25.3 bits (55), Expect = 3.9
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 35 LQKNSTQMIKEANFKI-SETHRLAQERVEAAEKRVKEVEERATASR 79
+ K S ++I + + + +T R A+E V+ AE+RVK+ T R
Sbjct: 161 ILKQSEKLINQLSERARRDTVRFAEEEVQKAEERVKKASNDLTDYR 206
>gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin
subunit beta [Extracellular structures].
Length = 1758
Score = 25.5 bits (55), Expect = 4.2
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 41 QMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELANAFWD-LSDEDKN 99
M++EA SE AQ+ + A ++ + S + + L D L+ D +
Sbjct: 1436 SMVREAKLSASE----AQQSAQRALEQANASRSQMEESNRE-LRNLIQQVRDFLTQPDAD 1490
Query: 100 AFT-GNVKQEV 109
+ V +EV
Sbjct: 1491 PDSIEEVAEEV 1501
>gnl|CDD|35462 KOG0241, KOG0241, KOG0241, Kinesin-like protein [Cytoskeleton].
Length = 1714
Score = 25.4 bits (55), Expect = 4.4
Identities = 11/52 (21%), Positives = 25/52 (48%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRK 80
E L +L++ + E K+ E+ +L +E E+++++ EE +
Sbjct: 374 EKLREQLEQAEAMKLPELKEKLEESEKLIKEITVTWEEKLRKTEEINQERQA 425
>gnl|CDD|111928 pfam03087, DUF241, Arabidopsis protein of unknown function. This
family represents a number of Arabidopsis proteins.
Their functions are unknown.
Length = 230
Score = 25.1 bits (55), Expect = 4.4
Identities = 7/38 (18%), Positives = 19/38 (50%)
Query: 36 QKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73
++ + E + +E + +R+E E ++E+E+
Sbjct: 174 IRSELSRLDEEKRRDNEEVKDILKRLEELENSIEELED 211
>gnl|CDD|36302 KOG1086, KOG1086, KOG1086, Cytosolic sorting
protein/ADP-ribosylation factor effector GGA
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 594
Score = 25.4 bits (55), Expect = 4.5
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 31 LLNKLQK-NSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73
LL +L K N + ++ AN I + + ++E KRVK +EE
Sbjct: 177 LLARLLKSNHPEDLQAANKLIKTLVKEEEHKLEKISKRVKALEE 220
>gnl|CDD|38926 KOG3722, KOG3722, KOG3722, Lipocalin-interacting membrane receptor
(LIMR) [Defense mechanisms].
Length = 538
Score = 24.9 bits (54), Expect = 4.9
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATAS 78
RT ++ K K+ + K NF E E V+ + +E+R TAS
Sbjct: 289 RTTPIVRKWDKDVPKK-KNPNFDYRELK----EYVKELRTQRSSLEKRRTAS 335
>gnl|CDD|73362 cd00311, TIM, Triosephosphate isomerase (TIM) is a glycolytic
enzyme that catalyzes the interconversion of
dihydroxyacetone phosphate and
D-glyceraldehyde-3-phosphate. The reaction is very
efficient and requires neither cofactors nor metal ions.
TIM, usually homodimeric, but in some organisms
tetrameric, is ubiqitous and conserved in function
across eukaryotes, bacteria and archaea..
Length = 242
Score = 25.2 bits (55), Expect = 5.2
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 11/71 (15%)
Query: 46 ANFKISETHRLAQERVEAAEKRVKEVEER-----------ATASRKLSVDELANAFWDLS 94
N+K++ T A E +A +K+ A + L ++ ++S
Sbjct: 5 GNWKMNGTLAEALELAKALNAVLKDESGVEVVVAPPFTYLAAVAEALEGSKIKVGAQNVS 64
Query: 95 DEDKNAFTGNV 105
ED AFTG +
Sbjct: 65 PEDSGAFTGEI 75
>gnl|CDD|32264 COG2081, COG2081, Predicted flavoproteins [General function
prediction only].
Length = 408
Score = 24.8 bits (54), Expect = 5.8
Identities = 10/53 (18%), Positives = 18/53 (33%)
Query: 30 DLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLS 82
L K +K + T + V A KE++ + S+K+
Sbjct: 317 QLSPKELAQLAAALKAWPITPNGTEPYREAEVTAGGVDTKEIDSKTMESKKVP 369
>gnl|CDD|40045 KOG4848, KOG4848, KOG4848, Extracellular matrix-associated
peroxidase [Extracellular structures, Defense
mechanisms].
Length = 225
Score = 24.7 bits (53), Expect = 6.1
Identities = 7/47 (14%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEE 73
R ++ ++K Q + + + + + A + E+ ++E++E
Sbjct: 133 REAEIAKNMKK-YPQTLAKYEASLVKQEQEADAKEVRLERLIREIQE 178
>gnl|CDD|145274 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.
This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA.
The TRM1 gene of Saccharomyces cerevisiae is necessary
for the N2,N2-dimethylguanosine modification of both
mitochondrial and cytoplasmic tRNAs. The enzyme is found
in both eukaryotes and archaebacteria.
Length = 375
Score = 24.6 bits (54), Expect = 6.2
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 15/68 (22%)
Query: 56 LAQERVEAAEKRVKEVEERATASRKLSVDELANA--FWDLSDEDKNAFTGNVKQEVCKVK 113
+E +E AE +E +R KL +EL + ++DL ++ V
Sbjct: 284 FVEEMLEIAESPPEEFSKRILGLLKLIKEELLDVPLYYDLH-------------QLASVL 330
Query: 114 KITVPPSN 121
K++VPP
Sbjct: 331 KLSVPPLQ 338
>gnl|CDD|38122 KOG2911, KOG2911, KOG2911, Uncharacterized conserved protein
[Function unknown].
Length = 439
Score = 24.5 bits (53), Expect = 6.7
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDEL 86
EDL +KN ++ + RL+ + E +++ E K V++L
Sbjct: 380 EDLEADEKKNEDLVLPLNSVSRDFLKRLSDLELLTNEDSLEKTEGPLNQISKSLVEQL 437
>gnl|CDD|112811 pfam04012, PspA_IM30, PspA/IM30 family. This family includes
PspA a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator
of the Escherichia coli phage shock psp operon, is
produced when virulence factors are exported through
secretins in many Gram-negative pathogenic bacteria and
its homologue in plants, VIPP1, plays a critical role
in thylakoid biogenesis, essential for photosynthesis.
Activation of transcription by the enhancer-dependent
bacterial sigma(54) containing RNA polymerase occurs
through ATP hydrolysis-driven protein conformational
changes enabled by activator proteins that belong to
the large AAA(+) mechanochemical protein family. It has
been shown that PspA directly and specifically acts
upon and binds to the AAA(+) domain of the PspF
transcription activator.
Length = 220
Score = 24.3 bits (53), Expect = 8.2
Identities = 8/38 (21%), Positives = 20/38 (52%)
Query: 53 THRLAQERVEAAEKRVKEVEERATASRKLSVDELANAF 90
+ + ++E +++ K++E +A A+ +ELA
Sbjct: 52 RQKQLERKLEEQKEQAKKLENKARAALTKGNEELAREA 89
>gnl|CDD|145010 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme
methylmalonyl-CoA mutase is a member of a class of
enzymes that uses coenzyme B12 (adenosylcobalamin) as a
cofactor. The enzyme induces the formation of an
adenosyl radical from the cofactor. This radical then
initiates a free-radical rearrangement of its substrate,
succinyl-CoA, to methylmalonyl-CoA.
Length = 517
Score = 24.3 bits (53), Expect = 9.0
Identities = 20/117 (17%), Positives = 36/117 (30%), Gaps = 36/117 (30%)
Query: 17 TIGGCDIV--------IGRTEDLLNKLQKNSTQMIKEANFKISETH-------------- 54
+GG + +G D ++ +N+ +++E E+
Sbjct: 319 VLGGTQSLHTNPFDEALGLPTDFSARIARNTQLILQE------ESGVARVIDPWGGSYYV 372
Query: 55 -RLAQERVEAAEKRVKEVEER-------ATASRKLSVDELANAFWDLSDEDKNAFTG 103
L E A K +E+EE KL ++E A D + G
Sbjct: 373 EELTDRIAEEAWKLFQEIEEAGGMAKAIEDGLPKLRIEESAARRQARIDSGREVIVG 429
>gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA
ligases catalyze the crucial step of joining the breaks
in duplex DNA during DNA replication, repair and
recombination, utilizing either ATP or NAD(+) as a
cofactor, but using the same basic reaction mechanism.
The enzyme reacts with the cofactor to form a
phosphoamide-linked AMP with the amino group of a
conserved Lysine in the KXDG motif, and subsequently
transfers it to the DNA substrate to yield adenylated
DNA. This alignment contains members of the NAD+
dependent subfamily only..
Length = 307
Score = 24.4 bits (53), Expect = 9.0
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 25 IGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER 74
+G E L K Q + +KE F +S RL + +E E+E +
Sbjct: 218 LGEAEGLGPKTQSEALAFLKEWGFPVSPETRLC-KNIEEVLAFYDEIEAK 266
>gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 24.1 bits (52), Expect = 9.2
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 30 DLLNKLQKNSTQMIKE-ANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELA 87
+ ++ L++ + +I E + F + + +R E+ ER A R L+ ELA
Sbjct: 1203 EAISLLERLNLSLITELSRFISTLEAKGLLDREVEFLPSDAELAERNAAGRGLTRPELA 1261
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
0.312 0.126 0.337
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: 1,255,070
Number of extensions: 53647
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 243
Number of HSP's successfully gapped: 80
Length of query: 121
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 39
Effective length of database: 4,491,799
Effective search space: 175180161
Effective search space used: 175180161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.3 bits)