RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2414
(114 letters)
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 28.6 bits (64), Expect = 0.24
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 36 MYKCVIC-LKSVRSRWHHLQTHFSRNH---KCPYCESVYSRVD 74
M+KC IC +V L+ H RNH KCP C Y R++
Sbjct: 1 MFKCPICGFTTVT--LFALKQHARRNHTLTKCPVCNKSYRRLN 41
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 26.1 bits (57), Expect = 0.79
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 61 HKCPYCESVYSRVDTLKLHAKRVH 84
KCP C +S D LK H ++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 25.9 bits (57), Expect = 1.4
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 11/41 (26%)
Query: 37 YKCVICLKSVRSR------WHH-----LQTHFSRNHKCPYC 66
+C ICL +R H + + + KCP C
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPIC 43
>gnl|CDD|234242 TIGR03519, Bac_Flav_fam_1, Bacteroidetes-specific putative membrane
protein. This model describes a protein family unique
to, and greatly expanded in, the Bacteriodetes. Species
in this lineage include several, such as Cytophaga
hutchinsonii and Flavobacterium johnsoniae, that exhibit
a poorly understood rapid gliding phenotype. Several
members of this protein family are found in operons with
other genes whose loss leads to a loss a this motility.
Length = 292
Score = 27.6 bits (62), Expect = 1.5
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 6 SRYPPTSPIQPFITRNNTDSIFYPDPASPGMY 37
S+ T P I NN + FYPD G+Y
Sbjct: 131 SKLTFTDANDPSIASNNGSNNFYPD-FGAGIY 161
>gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
Length = 498
Score = 26.9 bits (60), Expect = 2.3
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 43 LKSVRSRWHHLQTHFSRNHKCPYCES 68
L+ + S W T FS C + S
Sbjct: 450 LEELESDWRQQHTLFSEQQPCLFIPS 475
>gnl|CDD|223063 PHA03374, PHA03374, hypothetical protein; Provisional.
Length = 730
Score = 26.9 bits (60), Expect = 2.7
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 7 RYPPTSPIQPFITRNNTDSIFY-PDPASPGMYKCVICL---KSVRSRWHHLQTHFSRNH 61
R P P++ ++ + F+ P S M + +C+ V L + +
Sbjct: 284 RDPGKRPLKIAVSTPGGPASFWLQYPPSGAMLRVAMCMAVAPHVSHECTELSPGWDQLG 342
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 26.0 bits (57), Expect = 3.6
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 37 YKCVICL---KSVRSRWHHLQTHFSRNHKCPYCESVYSRVDTLKLHAKRVHGLGIS 89
Y C +CL S S H++ + + CP C + D+ H + H + +S
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIR-YTEHSKVCPVCGKEFRNTDSTLDHVCKKHNICVS 128
>gnl|CDD|223369 COG0292, RplT, Ribosomal protein L20 [Translation, ribosomal
structure and biogenesis].
Length = 118
Score = 25.7 bits (57), Expect = 4.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 80 AKRVHGLGISRYIHGL 95
A R +GL SR+I+GL
Sbjct: 68 AARENGLSYSRFINGL 83
>gnl|CDD|214968 smart01004, ALAD, Delta-aminolevulinic acid dehydratase. This
entry represents porphobilinogen (PBG) synthase (PBGS,
or 5-aminoaevulinic acid dehydratase, or ALAD, ), which
functions during the second stage of tetrapyrrole
biosynthesis. This enzyme catalyses a Knorr-type
condensation reaction between two molecules of ALA to
generate porphobilinogen, the pyrrolic building block
used in later steps. The structure of the enzyme is
based on a TIM barrel topology made up of eight
identical subunits, where each subunit binds to a metal
ion that is essential for activity, usually zinc (in
yeast, mammals and certain bacteria) or magnesium (in
plants and other bacteria). A lysine has been implicated
in the catalytic mechanism. The lack of PBGS enzyme
causes a rare porphyric disorder known as ALAD
porphyria, which appears to involve conformational
changes in the enzyme.
Length = 321
Score = 26.2 bits (59), Expect = 4.2
Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 7/37 (18%)
Query: 73 VDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTS 109
VD L A+ LGI + +LF P K
Sbjct: 56 VDLLVEEAEEAVELGI-PAV------ILFGVPEKKDE 85
>gnl|CDD|227440 COG5109, COG5109, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 396
Score = 26.1 bits (57), Expect = 4.9
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 34 PGMYKC--VICLKSVRSRWHHLQTHFSRNHKCPYCESVYSRVDTLKLH 79
P M +C VI +++ L + + KCPYC + + L++
Sbjct: 352 PVMLECGHVISKEALS----VLSQNGVLSFKCPYCPEMSKYENILRVR 395
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 25.7 bits (57), Expect = 5.8
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 73 VDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTSPVDR 113
VD L + + LG+SRY+ P SP +
Sbjct: 94 VDGL-VDDGELVFLGVSRYLGPPPPDFSEGVELGSVSPGED 133
>gnl|CDD|224272 COG1353, COG1353, Predicted CRISPR-associated polymerase [Defense
mechanisms].
Length = 799
Score = 25.9 bits (57), Expect = 6.1
Identities = 10/50 (20%), Positives = 13/50 (26%), Gaps = 6/50 (12%)
Query: 26 IFYPD--PASPGMYKCVICLKSVRSRWHHLQTHFSRN-HKCPYCESVYSR 72
I +P PG C +C R C C +Y
Sbjct: 383 ILFPRYELDGPGERTCSVCGNKRAK---GDSEKEMRAETLCDVCRVLYEL 429
>gnl|CDD|130104 TIGR01032, rplT_bact, ribosomal protein L20. This model
describes bacterial ribosomal protein L20 and its
chloroplast equvalent. This protein binds directly to
23s ribosomal RNA and is necessary for the in vitro
assembly process of the 50s ribosomal subunit. It is
not involved in the protein synthesizing functions of
that subunit. GO process changed accordingly (SS
5/09/03) [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 113
Score = 25.0 bits (55), Expect = 6.2
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 80 AKRVHGLGISRYIHGL 95
A R HGL SR+I+GL
Sbjct: 67 AARQHGLSYSRFINGL 82
>gnl|CDD|224246 COG1327, COG1327, Predicted transcriptional regulator, consists
of a Zn-ribbon and ATP-cone domains [Transcription].
Length = 156
Score = 25.3 bits (56), Expect = 6.8
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 62 KCPYCESVYSRV 73
KCP+C ++V
Sbjct: 2 KCPFCGHEDTKV 13
>gnl|CDD|227579 COG5254, ARV1, Predicted membrane protein [Function unknown].
Length = 239
Score = 25.6 bits (56), Expect = 7.1
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 8/35 (22%)
Query: 37 YKCVICLKSVRSRWHHLQTHFSRNH----KCPYCE 67
C+ C V L T +S + +CP C
Sbjct: 1 MVCIECGSRVD----SLYTRYSTSAIQLSRCPSCN 31
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 25.6 bits (57), Expect = 7.7
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 4/19 (21%)
Query: 59 RNHKCPYCES----VYSRV 73
++CP C S VYSR+
Sbjct: 499 ELNRCPVCGSEDVEVYSRI 517
>gnl|CDD|188476 TIGR03961, rSAM_PTO1314, archaeal radical SAM protein, PTO1314
family. Members of this protein family average about
340 residues in length, with a radical SAM domain in the
N-terminal 200 residues. The taxonomic distribution is
restricted to non-methanogenic archaea, including
Picrophilus torridus (locus PTO1314), Sulfolobus sp.,
Thermoplasma sp., Picrophilus torridus, and
Metallosphaera sedula. The gene neighborhood is not
conserved, and the function of this family is unknown
[Unknown function, Enzymes of unknown specificity].
Length = 332
Score = 25.5 bits (56), Expect = 7.7
Identities = 11/22 (50%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 7 RYPPTSPIQPFITRNNTDSIFY 28
RY P S I IT N D IF
Sbjct: 153 RYLPVS-ISFTITNENLDQIFD 173
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 25.2 bits (56), Expect = 8.5
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 67 ESVYSRVDTLKLHA---KRVHGLGISRYIHGL 95
E V + D +K+ A + VHG+ IS +I+ L
Sbjct: 277 EFVVTDPDAVKIRAEDGRSVHGVDISPFINNL 308
>gnl|CDD|236450 PRK09283, PRK09283, delta-aminolevulinic acid dehydratase;
Validated.
Length = 323
Score = 25.0 bits (56), Expect = 9.4
Identities = 10/37 (27%), Positives = 13/37 (35%), Gaps = 7/37 (18%)
Query: 73 VDTLKLHAKRVHGLGISRYIHGLIPQLLFPTPHAKTS 109
+D L A+ LGI + LF P K
Sbjct: 58 IDLLVKEAEEAVELGIP----AVA---LFGVPELKDE 87
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 23.2 bits (50), Expect = 9.7
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 61 HKCPYCESVYSRVDTLKLHAKRVH 84
++CP C V+ L+ H R H
Sbjct: 1 YRCPECGKVFKSKSALREH-MRTH 23
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 24.9 bits (55), Expect = 9.8
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 9 PPTSPIQPFITRNNTDSIFYPDPASPGMYK 38
PI + +I+ P PG+ K
Sbjct: 267 VEAEPIVVLDYNDRCLAIYEHHPKKPGLLK 296
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 24.5 bits (54), Expect = 9.8
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 63 CPYCESVYSRVDTLKLHAKRVHGL 86
C +C V+ H + HG
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHGF 25
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.325 0.140 0.465
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,764,779
Number of extensions: 451276
Number of successful extensions: 594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 592
Number of HSP's successfully gapped: 41
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (23.9 bits)