RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027746
(219 letters)
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 213 bits (546), Expect = 1e-69
Identities = 86/168 (51%), Positives = 109/168 (64%), Gaps = 11/168 (6%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
PK V D ++ DI + G+ +PL + +GT +HNIE+ PG+GG+L R+AGTSA+
Sbjct: 107 PKGLKVGDTVV-SGPDADI--KPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQ 163
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
++ KE + +RLPSG + + CRATIG V N H L KAG+SRWLG RP VR
Sbjct: 164 LVAKE--GKYATLRLPSGEVRKVLAECRATIGEVGNEEHSNISLGKAGRSRWLGIRPTVR 221
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKKK 214
GVAMNPVDHPHGGGEGR+ GR +TPWGKP K GYKT K+
Sbjct: 222 GVAMNPVDHPHGGGEGRTSG----GRHPVTPWGKPTK-GYKTRKKNKR 264
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 194 bits (496), Expect = 3e-64
Identities = 74/133 (55%), Positives = 96/133 (72%), Gaps = 4/133 (3%)
Query: 69 QIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKL 128
+IG+ +PL + IGT+IHNIE+ PG+GG+L R+AGT A+I+ + + ++LPSG +L
Sbjct: 2 KIGNALPLKNIPIGTVIHNIELIPGKGGQLARSAGTYAQIIAK-EGKYVTLKLPSGEVRL 60
Query: 129 IDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRSKSSG 188
+ + CRATIG VSN H K L KAG+SRWLG RP VRGVAMNPVDHPHGGGEGR+
Sbjct: 61 VSSNCRATIGVVSNIDHNNKPLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTSIGR 120
Query: 189 NHGRCSLTPWGKP 201
++PWGKP
Sbjct: 121 PP---PVSPWGKP 130
>gnl|CDD|162234 TIGR01171, rplB_bact, ribosomal protein L2, bacterial/organellar.
This model distinguishes bacterial and organellar
ribosomal protein L2 from its counterparts in the
archaea nad in the eukaryotic cytosol. Plant
mitochondrial examples tend to have long, variable
inserts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 273
Score = 191 bits (487), Expect = 7e-61
Identities = 87/168 (51%), Positives = 110/168 (65%), Gaps = 11/168 (6%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
PK V D ++ + + + G+ +PL + +GT +HNIE+ PG+GG+L R+AGTSA+
Sbjct: 105 PKGLKVGDTVI---SGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQ 161
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
IL KE + +RLPSG +++ CRATIG V N H L KAG+SRWLG RP VR
Sbjct: 162 ILAKE--GGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRSRWLGIRPTVR 219
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKKK 214
GVAMNPVDHPHGGGEGR+ GR +TPWGKP K GYKT KK
Sbjct: 220 GVAMNPVDHPHGGGEGRTPG----GRHPVTPWGKPTK-GYKTRKKKKY 262
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 189 bits (482), Expect = 4e-60
Identities = 82/169 (48%), Positives = 103/169 (60%), Gaps = 12/169 (7%)
Query: 47 KPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSA 106
P+ + D I+ + + +IG+ +PL + +GT IHNIE+ PG+GG+L RAAG A
Sbjct: 104 HPRGLKIGDTIV---SGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVA 160
Query: 107 KIL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVV 165
K++ KE ++LPSG +LI C ATIG V N K L KAG RWLG+RP V
Sbjct: 161 KLIAKE--GKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAGSKRWLGKRPKV 218
Query: 166 RGVAMNPVDHPHGGGEGRSKSSGNHGRCS-LTPWGKPCKSGYKTASPKK 213
RGV MNPVDHPHGGGEGR+ GR +TPWGKP G KT KK
Sbjct: 219 RGVVMNPVDHPHGGGEGRAPI----GRKKPVTPWGKPAL-GRKTRKRKK 262
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 188 bits (479), Expect = 1e-59
Identities = 78/168 (46%), Positives = 106/168 (63%), Gaps = 11/168 (6%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
P+ V D I + D + + G+ +PL + GTI+HN+E+ PG GG+L R+AGT A+
Sbjct: 107 PEGLKVGDVIE---SGKDADIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQ 163
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
++ KE ++ +VRLPSG + + + CRATIG V+N H K L KAG++R G+RP VR
Sbjct: 164 VVGKE--GNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKPLGKAGRARHKGKRPTVR 221
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKKK 214
GVAMNPVDHPHGGGEG+ G+ PWGKP G KT K+
Sbjct: 222 GVAMNPVDHPHGGGEGQHPG----GKPPTVPWGKPTP-GKKTRIAAKR 264
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
Length = 317
Score = 140 bits (354), Expect = 2e-40
Identities = 71/149 (47%), Positives = 92/149 (61%), Gaps = 8/149 (5%)
Query: 71 GSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLID 130
G+ +PL + +G+I+HN+E+ PG GG+++RA GT A ++ F ++L S +
Sbjct: 158 GNSLPLRNIPVGSIVHNVEMRPGAGGQIIRAGGTYATVV-SKDEQFATLKLKSTEIRKFP 216
Query: 131 TRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRSKSSGNH 190
C ATIG VSN H + L KAG +RWLG+RPVVRGVAMNP HPHGGG SK
Sbjct: 217 LDCWATIGQVSNLEHHMRILGKAGVNRWLGKRPVVRGVAMNPSKHPHGGGT--SKKGTKR 274
Query: 191 GRCSLTPWGKPCKSGYKTASPKKKKKLAF 219
+CSL WG C+ GYKT S KKK L
Sbjct: 275 PKCSL--WGI-CRDGYKTRS--KKKPLGL 298
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 111 bits (281), Expect = 2e-30
Identities = 54/127 (42%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 70 IGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEKL 128
G+ +PL + GT + NIE PG GGK R++GT A ++ E +V+LPSG K
Sbjct: 91 PGNTLPLGEIPEGTPVCNIESRPGDGGKFARSSGTYALVVGHEGDKV--IVQLPSGKIKE 148
Query: 129 IDTRCRATIGTVSNPSHGAKKLRKAGQSRWL----GRR-PVVRGVAMNPVDHPHGGGE-- 181
++ RCRATIG V+ K KAG+ ++ P VRGVAMN VDHPHGGG
Sbjct: 149 LNPRCRATIGVVAGGGRKEKPFLKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQ 208
Query: 182 --GRSKS 186
GR +
Sbjct: 209 HPGRPST 215
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional.
Length = 260
Score = 99.8 bits (249), Expect = 1e-25
Identities = 51/117 (43%), Positives = 69/117 (58%), Gaps = 6/117 (5%)
Query: 70 IGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEKL 128
IG+ +PL + GTI+ N+E PG G L RA+G A I+ +RLPSG +K
Sbjct: 98 IGNVLPLGQIPEGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKT 157
Query: 129 IDTRCRATIGTVSNPSHGAKKLRKAGQS--RWLGRR---PVVRGVAMNPVDHPHGGG 180
+ + RA IG V+ K + KAG + ++ G+R P VRGVAMNPV+HPHGGG
Sbjct: 158 VSSLSRAMIGIVAGGGRIDKPVLKAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGG 214
>gnl|CDD|130386 TIGR01319, glmL_fam, conserved hypothetical protein. This small
family includes, so far, an uncharacterized protein from
E. coli O157:H7 and GlmL from Clostridium tetanomorphum
and Clostridium cochlearium. GlmL is located between the
genes for the two subunits, epsilon (GlmE) and sigma
(GlmS), of the coenzyme-B12-dependent glutamate mutase
(methylaspartate mutase), the first enzyme in a pathway
of glutamate fermentation. Members shows significant
sequence similarity to the hydantoinase branch of the
hydantoinase/oxoprolinase family (pfam01968).
Length = 463
Score = 31.2 bits (70), Expect = 0.42
Identities = 18/99 (18%), Positives = 39/99 (39%), Gaps = 4/99 (4%)
Query: 8 SASSTLFNRLLCPSVLNNNTTYRYQSSETELVGD-PSKQEKPKKETVRDKIMRQMA---H 63
+++ N+ + + + Y + P+ E+ K + + MA H
Sbjct: 306 ASAKEKLNKNFADNPADLDACCHYLRHLAAHIDMLPANAEEIKFDEALAGLATDMAMERH 365
Query: 64 VDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAA 102
++ +CM ++IG + N++ G GG L A+
Sbjct: 366 AGTIEEMCTCMGNIDLQIGKDLLNVKCVIGSGGVLSHAS 404
>gnl|CDD|238621 cd01296, Imidazolone-5PH,
Imidazolonepropionase/imidazolone-5-propionate hydrolase
(Imidazolone-5PH) catalyzes the third step in the
histidine degradation pathway, the hydrolysis of
(S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to
N-formimidoyl-L-glutamate. In bacteria, the enzyme is
part of histidine utilization (hut) operon.
Length = 371
Score = 30.3 bits (69), Expect = 0.67
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 97 KLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSH 145
+ AGT A +L P ++F L KLID +GT NP
Sbjct: 245 AALAEAGTVAVLL--PGTAFSLRETYPPARKLIDAGVPVALGTDFNPGS 291
>gnl|CDD|213340 cd05391, RasGAP_p120GAP, Ras-GTPase Activating Domain of p120.
p120GAP is a negative regulator of Ras that stimulates
hydrolysis of bound GTP to GDP. Once the Ras regulator
p120GAP, a member of the GAP protein family, is
recruited to the membrane, it is transiently immobilized
to interact with Ras-GTP. The down-regulation of Ras by
p120GAP is a critical step in the regulation of many
cellular processes, which is disrupted in approximately
30% of human cancers. p120GAP contains SH2, SH3, PH,
calcium- and lipid-binding domains, suggesting its
involvement in a complex network of cellular
interactions in vivo.
Length = 328
Score = 30.1 bits (68), Expect = 0.82
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 2 ALCRVRSASSTLFNRLLCPSVLN 24
R R S +F RL+CP++LN
Sbjct: 176 TTVRTRVVSGFVFLRLICPAILN 198
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 27.7 bits (62), Expect = 4.3
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 84 IIHNIEVN----PGQGGKLVRA--AGTSAKILKEPTSSFCLVRLPSGNEKLIDTR 132
I + V PG +++ + +GT ++L+ + VR P G E + +R
Sbjct: 2 ISDELFVYMRSGPGNQYRILGSLKSGTPVEVLERSDDGYSRVRTPKGREGWVLSR 56
>gnl|CDD|180167 PRK05620, PRK05620, long-chain-fatty-acid--CoA ligase; Validated.
Length = 576
Score = 27.8 bits (62), Expect = 5.3
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 10/34 (29%)
Query: 136 TIGTVSNPSHGAKKLRKAGQSRWL-----GRRPV 164
+GTV+ P G +G++RW GR P
Sbjct: 337 PVGTVARPPSGV-----SGEARWAYRVSQGRFPA 365
>gnl|CDD|217617 pfam03567, Sulfotransfer_2, Sulfotransferase family. This family
includes a variety of sulfotransferase enzymes.
Chondroitin 6-sulfotransferase catalyzes the transfer
of sulfate to position 6 of the N-acetylgalactosamine
residue of chondroitin. This family also includes
Heparan sulfate 2-O-sulfotransferase (HS2ST) and
Heparan sulfate 6-sulfotransferase (HS6ST). Heparan
sulfate (HS) is a co-receptor for a number of growth
factors, morphogens, and adhesion proteins. HS
biosynthetic modifications may determine the strength
and outcome of HS-ligand interactions. Mice that lack
HS2ST undergo developmental failure only after
midgestation,the most dramatic effect being the
complete failure of kidney development. Heparan
sulphate 6- O -sulfotransferase (HS6ST) catalyzes the
transfer of sulphate from adenosine 3'-phosphate,
5'-phosphosulphate to the 6th position of the N
-sulphoglucosamine residue in heparan sulphate.
Length = 238
Score = 27.4 bits (61), Expect = 5.6
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 1 MALCRVRSASSTLFNRLLCPSVLNNNTTY---RYQSSETEL 38
+ CRV +ST + R+LC VL + ++T
Sbjct: 6 IVYCRVPKVASTSWKRILC--VLYGENKFLADNRSINDTWA 44
>gnl|CDD|201944 pfam01735, PLA2_B, Lysophospholipase catalytic domain. This family
consists of Lysophospholipase / phospholipase B
EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which
also has a C2 domain pfam00168. Phospholipase B enzymes
catalyze the release of fatty acids from
lysophsopholipids and are capable in vitro of
hydrolysing all phospholipids extractable form yeast
cells. Cytosolic phospholipase A2 associates with
natural membranes in response to physiological increases
in Ca2+ and selectively hydrolyses arachidonyl
phospholipids, the aligned region corresponds the the
carboxy-terminal Ca2+-independent catalytic domain of
the protein as discussed in.
Length = 490
Score = 27.7 bits (62), Expect = 5.8
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 8 SASSTLFNRLLCPSVLNNNTTYRYQSSETEL----VGDPSK 44
SSTLFN+ L L N+T S L + D S+
Sbjct: 229 GTSSTLFNQFL----LVINSTSSLPSFLNILIKHFLKDLSE 265
>gnl|CDD|236285 PRK08554, PRK08554, peptidase; Reviewed.
Length = 438
Score = 27.0 bits (60), Expect = 9.3
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 35 ETELVGDPSKQEKPKKETVRDKIMRQMAHVDINSQI 70
E V DPSK KP KE + I + I S++
Sbjct: 12 SFETVNDPSKGIKPSKECPK-FIKDTLESWGIESEL 46
>gnl|CDD|224417 COG1500, COG1500, Predicted exosome subunit [Translation, ribosomal
structure and biogenesis].
Length = 234
Score = 26.5 bits (59), Expect = 9.5
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 1/62 (1%)
Query: 74 MPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRC 133
+ ++ I +E G L + + +E S C++ +P+GN+
Sbjct: 159 IRFERAKVAVKI-PVEYAGKAYGLLRKFGEIKKEEWQEDGSWICVLEIPAGNQDEFYELL 217
Query: 134 RA 135
Sbjct: 218 NE 219
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
0.316 0.131 0.397
Gapped
Lambda K H
0.267 0.0813 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,600,276
Number of extensions: 935195
Number of successful extensions: 680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 663
Number of HSP's successfully gapped: 18
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
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 (21.6 bits)
S2: 57 (25.6 bits)