RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781082|ref|YP_003065495.1| hypothetical protein
CLIBASIA_04920 [Candidatus Liberibacter asiaticus str. psy62]
(108 letters)
>gnl|CDD|178486 PLN02898, PLN02898, HMP-P kinase/thiamin-monophosphate
pyrophosphorylase.
Length = 502
Score = 30.1 bits (68), Expect = 0.13
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 21 SIVEALRKAKPSMSDLAMLSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLRDL 75
SI+ ALR+ ++ + +V+E A+L V D+ K L L
Sbjct: 126 SILSALREELLPLATIVTPNVKEASALLGGDPLE------TVADMRSAAKELHKL 174
>gnl|CDD|183311 PRK11780, PRK11780, isoprenoid biosynthesis protein with
amidotransferase-like domain; Provisional.
Length = 217
Score = 27.8 bits (63), Expect = 0.57
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 19 RNSIVEALRKAKPSMSDLAMLSVEERDAIL 48
RN +VE+ R A+ + DLA E+ DA++
Sbjct: 61 RNVLVESARIARGEIKDLAEADAEDFDALI 90
>gnl|CDD|177604 PHA03367, PHA03367, single-stranded DNA binding protein; Provisional.
Length = 1115
Score = 27.7 bits (62), Expect = 0.77
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 39 LSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLRDLPVYNFSLDYVSRF 88
L DD+ + + E+L+ L D V ++SL+
Sbjct: 1018 LGDRCASLTSDDVLFYLGGYEILADSVMEKLQTLADSGV-DWSLENARSV 1066
>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 26.8 bits (59), Expect = 1.4
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 9 REFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEE 43
EF++ ++E +EAL+K KPS+S ML E
Sbjct: 690 EEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYER 724
>gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
Length = 520
Score = 26.5 bits (59), Expect = 1.7
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAKPSMSDLAMLS 40
M D+ +N W+L I +AL+KA SD+A +S
Sbjct: 46 MEFDLEKN------WQLACQCIRQALQKAGIPASDIAAVS 79
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 26.3 bits (58), Expect = 1.7
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 31/83 (37%)
Query: 14 YWRLERNSIVEALRKAKPSMSDLAMLSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLR 73
Y RL++ + E L+ A PS+ ++ L +R+ +R
Sbjct: 110 YQRLQKRGLPERLKHA-PSLEEI----------------------------LSQRIDRMR 140
Query: 74 DLPVYNFSLDYVSRF--HSFVSD 94
+ Y FSLD+V+ S +
Sbjct: 141 SIADYIFSLDHVAETSSESLMRA 163
>gnl|CDD|179957 PRK05183, hscA, chaperone protein HscA; Provisional.
Length = 616
Score = 26.3 bits (59), Expect = 1.9
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 9 REFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEERDAI 47
R E ++E ++EAL+ A +D +LS ER AI
Sbjct: 527 RALAE-QKVEAERVLEALQAA--LAADGDLLSAAERAAI 562
>gnl|CDD|178924 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
Length = 417
Score = 26.2 bits (59), Expect = 2.1
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 19 RNSIVEALRKAKPSMSDLAMLSVEERDAIL----DDLEKN 54
+ E R+AK + LA LS +++ L D LE N
Sbjct: 3 MEYLEELGRRAKAASRKLAQLSTAQKNRALLAIADALEAN 42
>gnl|CDD|132460 TIGR03419, NifU_clost, FeS cluster assembly scaffold protein NifU,
Clostridium type. NifU and NifS form a pair of
iron-sulfur (FeS) cluster biosynthesis proteins much
simpler than the ISC and SUF systems. Members of this
protein family are a distinct group of NifU-like
proteins, found always to a NifS-like protein and
restricted to species that lack a SUF system. Typically,
NIF systems service a smaller number of FeS-containing
proteins than do ISC or SUF. Members of this particular
branch typically are found, almost half the time, near
the mnmA gene, involved in the carboxymethylaminomethyl
modification of U34 in some tRNAs (see GenProp0704).
While other NifU proteins are associated with nitrogen
fixation, this family is not.
Length = 121
Score = 25.9 bits (57), Expect = 2.3
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEE-RDAILDDLEKNG 55
M T++ + + E W L ++ EAL P ++L+ E AI D EKNG
Sbjct: 66 MATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121
>gnl|CDD|149673 pfam08691, Nse5, DNA repair protein Nse5. Nse5 is a non essential
nuclear protein that is critical for chromosome
segregation in fission yeast. Nse5 forms a dimer with
Nse6 and facilitates DNA repair as part of the Smc5-Smc6
holocomplex.
Length = 344
Score = 25.5 bits (56), Expect = 3.5
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 44 RDAILDDLEKNGSSDYSFVNDLWERLKYLRDLPVYNFSLDYVSRFHSFVSDEVAVWYEVT 103
I KN S + + ++L + LD +++ VSD+ W+ +T
Sbjct: 55 EKDINASPRKNKSIVTTPHEERQKQLSKKFTNSIPTRLLDELAK--DRVSDKYKDWHFIT 112
Query: 104 KE 105
+
Sbjct: 113 EN 114
>gnl|CDD|163351 TIGR03607, TIGR03607, patatin-related protein. This bacterial
protein family contains an N-terminal patatin domain,
where patatins are plant storage proteins capable of
phospholipase activity (see pfam01734). Regions of
strong sequence conservation are separated by regions of
significant sequence and length variability. Members of
the family are distributed sporadically among bacteria.
The function is unknown.
Length = 739
Score = 25.5 bits (56), Expect = 3.5
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAK 30
N V R R ++ R E +VEAL
Sbjct: 357 HNRRVRRLRAIVDARRPEVARLVEALFGRT 386
>gnl|CDD|181873 PRK09457, astD, succinylglutamic semialdehyde dehydrogenase;
Reviewed.
Length = 487
Score = 25.3 bits (56), Expect = 3.5
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 20 NSIVEALRKAKPSMSDLAMLSVEERDAIL 48
++ V A R A P A LS EER AI+
Sbjct: 40 DAAVRAARAAFP---AWARLSFEERQAIV 65
>gnl|CDD|132128 TIGR03084, TIGR03084, conserved hypothetical protein TIGR03084.
This family, like Pfam family pfam07398, belongs to the
larger set of probable enzymes modeled by TIGRFAMs
family TIGR03083. Members are found primarily in the
Actinobacteria (Mycobacterium, Streptomyces, etc.). The
family is uncharacterized.
Length = 253
Score = 25.0 bits (55), Expect = 4.7
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 9/41 (21%)
Query: 9 REFIEYWRLERNSIVEALRKAK---------PSMSDLAMLS 40
E + WR R ++ EALR A P MS +M +
Sbjct: 89 AELLARWRAGRAALAEALRAAPPGARVPWFGPPMSAASMAT 129
>gnl|CDD|180205 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 24.7 bits (54), Expect = 4.7
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 33 MSDLAMLSVEERDAILDD 50
+S+L +L +ERD +LD
Sbjct: 3691 LSELPLLGEQERDFLLDG 3708
>gnl|CDD|181878 PRK09463, fadE, acyl-CoA dehydrogenase; Reviewed.
Length = 777
Score = 24.8 bits (55), Expect = 5.1
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 20 NSIVEALRKAKPSMSDLAMLSVEERDAI 47
+++ RK P MS ER+A+
Sbjct: 29 APLLKWFRKVLPPMSQ------TEREAL 50
>gnl|CDD|163284 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 24.6 bits (54), Expect = 5.8
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 23 VEALRKAKPSMSDLAMLSVEERDAILD 49
V A+RK P + + +E D ++
Sbjct: 686 VRAVRKVAPDATGAPVSILESGDTVVG 712
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift.
Length = 360
Score = 24.3 bits (53), Expect = 7.2
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 8 NREFIEYWRLERNSIVEA---LRKAKPSMSDLAMLSVEERDAILDDLEK 53
+ EY + + + I EA L ++ P M ++A +EE + +++LE+
Sbjct: 49 VDCYREYQQAQED-IKEAKEILEESDPEMREMAKEELEELEEKIEELEE 96
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 24.1 bits (53), Expect = 7.7
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 7 RNR-EFIEYWRLERNSIVEALRK 28
RN IE+ RL SIV L++
Sbjct: 149 RNACLMIEFKRLSTRSIVPVLKR 171
>gnl|CDD|173383 PTZ00089, PTZ00089, transketolase; Provisional.
Length = 661
Score = 23.9 bits (52), Expect = 8.6
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 79 NFSLDYVSRFHSFVSDEVAVWYEVTKEKKK 108
F LD +FH VS+EV ++E EKKK
Sbjct: 278 LFGLDPEKKFH--VSEEVRQFFEQHVEKKK 305
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.317 0.132 0.383
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,806,104
Number of extensions: 104107
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 42
Length of query: 108
Length of database: 5,994,473
Length adjustment: 74
Effective length of query: 34
Effective length of database: 4,395,481
Effective search space: 149446354
Effective search space used: 149446354
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: 50 (23.2 bits)