RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4327
(187 letters)
>gnl|CDD|189906 pfam01247, Ribosomal_L35Ae, Ribosomal protein L35Ae.
Length = 95
Score = 150 bits (381), Expect = 1e-47
Identities = 64/101 (63%), Positives = 78/101 (77%), Gaps = 6/101 (5%)
Query: 81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKR 140
LY +A+F G++RG+RNQHPNTSLL IE NTKEDA+FY+GKR ++YKAK K K
Sbjct: 1 LYVKAVFLGYRRGKRNQHPNTSLLKIEGVNTKEDAQFYLGKRVAYVYKAKKK------KN 54
Query: 141 KSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIM 181
S++R IWGKVTRPHG+SG VRAKF RNLP MG +VR+M
Sbjct: 55 GSKIRVIWGKVTRPHGNSGVVRAKFRRNLPPQAMGARVRVM 95
>gnl|CDD|240239 PTZ00041, PTZ00041, 60S ribosomal protein L35a; Provisional.
Length = 120
Score = 139 bits (353), Expect = 4e-43
Identities = 64/125 (51%), Positives = 88/125 (70%), Gaps = 6/125 (4%)
Query: 63 KKVKKTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKR 122
++ K KK + + RLY +A+F G+KR + NQ+PN +LL IE NT+EDARFY+GKR
Sbjct: 2 HQLTKKKKKTNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKR 61
Query: 123 CVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIML 182
++YKAK K ++ RAIWGK+TRPHG+SG VRA+F++NLP +G +VR+ L
Sbjct: 62 VAYVYKAKKL------KNGTKFRAIWGKITRPHGNSGVVRARFNKNLPPKAIGSRVRVFL 115
Query: 183 YPSNI 187
YPSNI
Sbjct: 116 YPSNI 120
>gnl|CDD|225295 COG2451, COG2451, Ribosomal protein L35AE/L33A [Translation,
ribosomal structure and biogenesis].
Length = 100
Score = 106 bits (265), Expect = 4e-30
Identities = 46/108 (42%), Positives = 65/108 (60%), Gaps = 13/108 (12%)
Query: 80 RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
RL + + ++R +R QHPN SL+ IE ++ E+A+FY+GKR + Y++
Sbjct: 6 RLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSG-------- 57
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
R I GKV R HG+SG+VRA+F RNLP +G V + LYPSNI
Sbjct: 58 -----RVIKGKVVRTHGNSGAVRARFERNLPGQALGTSVEVKLYPSNI 100
>gnl|CDD|179831 PRK04337, PRK04337, 50S ribosomal protein L35Ae; Validated.
Length = 87
Score = 58.5 bits (142), Expect = 7e-12
Identities = 23/98 (23%), Positives = 43/98 (43%), Gaps = 14/98 (14%)
Query: 83 ARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKS 142
+ + ++RG+ Q+ ++ + +E+A +G++ + +K T
Sbjct: 3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVI--WKDPTGNK-------- 52
Query: 143 RLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRI 180
GK+ R HG+ G VRA+F LP +G V I
Sbjct: 53 ----YVGKIVRVHGNRGEVRARFKPGLPGQALGDYVEI 86
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 33.3 bits (76), Expect = 0.061
Identities = 19/51 (37%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 33 PKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRHGRLYA 83
TPKT EKK K + + A T KK K K K + R G LY
Sbjct: 740 AGTPKTPYEKKTKAKKKSASTKGKAAKT-VKKKSKAKSKKTTKKRAGPLYT 789
Score = 32.9 bits (75), Expect = 0.100
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 26 EKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLR 75
K PKTP E+K AKK +A+T K AK K K+KK + R
Sbjct: 736 ITKYAGTPKTPY--EKKTKAKKKSASTKGKAAKTVKKKSKAKSKKTTKKR 783
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 32.2 bits (74), Expect = 0.13
Identities = 13/42 (30%), Positives = 18/42 (42%)
Query: 32 KPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKR 73
K K P + K +KK A K K + KVKK + +
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTK 420
Score = 30.3 bits (69), Expect = 0.62
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
+ K KK +AK K E++K K + DTK + K +K
Sbjct: 387 KTGKPSKKVLAKRAEKKEKEKEKPKVKK---------RHRDTKNIGKRRK 427
Score = 29.9 bits (68), Expect = 0.75
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 27 KKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRH 78
K +V PKT + PSK A +K +K K+ +++ RH
Sbjct: 369 KARVIDELRPKTKAPSEKKTG----KPSKKVLAKRAEKKEKEKEKPKVKKRH 416
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 31.9 bits (72), Expect = 0.17
Identities = 15/60 (25%), Positives = 19/60 (31%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRL 76
A + P P K A A A S D+ T V+K K K + L
Sbjct: 224 EPAPDPAARAPHAAPDPPAPAPAPAKTAAPAAAAPVSSGDSGPYVTPLVRKLAKDKGVDL 283
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 31.7 bits (73), Expect = 0.21
Identities = 11/49 (22%), Positives = 16/49 (32%)
Query: 16 MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKK 64
A +K EK + K KK A K + T + + K
Sbjct: 809 EALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857
Score = 27.4 bits (62), Expect = 5.4
Identities = 8/44 (18%), Positives = 14/44 (31%)
Query: 29 KVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
KP+ + + A K ++ T + V K K
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857
Score = 27.1 bits (61), Expect = 7.2
Identities = 13/44 (29%), Positives = 14/44 (31%), Gaps = 8/44 (18%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKAT 60
A K KK A + KT K KD KAT
Sbjct: 824 LADAPAKDPAGKKAAVKFSRKT--------KQQYVASEKDGKAT 859
Score = 27.1 bits (61), Expect = 8.0
Identities = 6/46 (13%), Positives = 12/46 (26%), Gaps = 1/46 (2%)
Query: 24 KDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTK 69
EK + + ++ KKA K + +
Sbjct: 814 LAEKPEKLRYLADAPAKDPA-GKKAAVKFSRKTKQQYVASEKDGKA 858
Score = 27.1 bits (61), Expect = 8.0
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 40 EEKKVAKKATATTPSKDAKATDTKKVKKTKKHKR 73
EK + A P+KD VK ++K K+
Sbjct: 815 AEKPEKLRYLADAPAKDPAGKKAA-VKFSRKTKQ 847
>gnl|CDD|239430 cd03314, MAL, Methylaspartate ammonia lyase (3-methylaspartase,
MAL) is a homodimeric enzyme, catalyzing the
magnesium-dependent reversible alpha,beta-elimination of
ammonia from L-threo-(2S,3S)-3-methylaspartic acid to
mesaconic acid. This reaction is part of the main
catabolic pathway for glutamate. MAL belongs to the
enolase superfamily of enzymes, characterized by the
presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and is
stabilized by coordination to the essential Mg2+ ion.
Length = 369
Score = 30.8 bits (70), Expect = 0.42
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 95 RNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
+ ++A E CNT ED R + + + KT +L
Sbjct: 256 DRRGVGVRIVADEWCNTLEDIRDFADAGAAHMVQIKTPDL 295
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 30.7 bits (69), Expect = 0.42
Identities = 16/52 (30%), Positives = 20/52 (38%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
E KK KKK + K P + + A +K KK K KK K
Sbjct: 3 ETKKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTK 54
Score = 30.3 bits (68), Expect = 0.57
Identities = 18/55 (32%), Positives = 22/55 (40%)
Query: 16 MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
T+ K E+KK A K + E K K A T+ KA KK K K
Sbjct: 4 TKKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKT 58
>gnl|CDD|224668 COG1754, COG1754, Uncharacterized C-terminal domain of
topoisomerase IA [General function prediction only].
Length = 298
Score = 29.7 bits (67), Expect = 0.78
Identities = 15/42 (35%), Positives = 17/42 (40%)
Query: 29 KVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
+ AK K +K A KA TT K A K K KK
Sbjct: 255 RRAKGGPGKKPAKKATAAKAKKTTAKKAAAKKAAKTKKAAKK 296
>gnl|CDD|116097 pfam07476, MAAL_C, Methylaspartate ammonia-lyase C-terminus.
Methylaspartate ammonia-lyase EC:4.3.1.2 catalyzes the
second step of fermentation of glutamate. It is a
homodimer. This family represents the C-terminal region
of Methylaspartate ammonia-lyase and contains a TIM
barrel fold similar to the pfam01188. This family
represents the catalytic domain and contains a metal
binding site.
Length = 249
Score = 29.6 bits (67), Expect = 0.85
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 99 PNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
++A E CNT ED R +V + + KT +L
Sbjct: 138 IGVEIVADEWCNTLEDIREFVDAGAADMVQIKTPDL 173
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 29.4 bits (66), Expect = 1.1
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 12 RVSVMAAATEVKKDEKKKVAK-PKTPKTGEEKKVAKKATATTPSKDAKATDTK 63
+V V++A T+ KK K V + PK + + + PS + K
Sbjct: 94 KVKVVSAPTKKKKAMPKSVVRAPKPLENPVPAQAESSGSKPVPSIPVSTPEVK 146
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 29.2 bits (66), Expect = 1.3
Identities = 10/54 (18%), Positives = 15/54 (27%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
++ + K E + KK T T A KK K +
Sbjct: 47 KTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDEL 100
Score = 28.8 bits (65), Expect = 1.9
Identities = 9/56 (16%), Positives = 14/56 (25%), Gaps = 2/56 (3%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEE--KKVAKKATATTPSKDAKATDTKKVKKTKK 70
E+K+ + K P+ + K T S K K
Sbjct: 33 ITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAA 88
Score = 27.7 bits (62), Expect = 4.4
Identities = 12/51 (23%), Positives = 14/51 (27%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKK 67
T K K AK K + K A+K A D V
Sbjct: 78 KTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLN 128
Score = 26.9 bits (60), Expect = 8.7
Identities = 12/47 (25%), Positives = 15/47 (31%)
Query: 26 EKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
K + E KK KK A + SK + K K K
Sbjct: 1 MTTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKK 47
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 28.6 bits (64), Expect = 1.3
Identities = 18/54 (33%), Positives = 23/54 (42%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
E + + KK K K K EK KK+T TT + KAT KK +
Sbjct: 104 KETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKEEG 157
Score = 28.2 bits (63), Expect = 1.8
Identities = 18/52 (34%), Positives = 25/52 (48%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
+ +EK+ + K K +EKKVA+K +K K T K KKT K
Sbjct: 103 SKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKK 154
Score = 26.3 bits (58), Expect = 8.6
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
+ TE K+ K K K + + +K+AKK + T K K K ++ K
Sbjct: 103 SKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKEEGK 158
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 29.1 bits (65), Expect = 1.5
Identities = 23/59 (38%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 12 RVSVMAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
S A+ K KKV+K K KT K A K TA +K AK T K +KK K
Sbjct: 208 AKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAK-TAAKAAKKAKKTAKKALKKAAK 265
Score = 28.3 bits (63), Expect = 2.3
Identities = 20/92 (21%), Positives = 27/92 (29%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRL 76
A KK K V+ K KT + K TA K A K KK K
Sbjct: 223 AKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAA 282
Query: 77 RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEK 108
+ + K+ + + A K
Sbjct: 283 KGAAKATKGKAKAKKKAGKKAAAGSKAKATAK 314
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 29.2 bits (66), Expect = 1.6
Identities = 16/41 (39%), Positives = 19/41 (46%)
Query: 33 PKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKR 73
P+ PK KK A KATA +K KA K K K+
Sbjct: 815 PREPKAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKK 855
Score = 26.9 bits (60), Expect = 8.0
Identities = 14/50 (28%), Positives = 15/50 (30%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
E + E K A KT K A AK T KK K
Sbjct: 812 EFEPREPKAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKKTAARKT 861
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 28.9 bits (64), Expect = 1.7
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 11 YRVSVMAAATEVKK--DEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKT 68
Y + +M T K+ DE ++ K + GEE KV + + K TKKVK+
Sbjct: 201 YDIELMVEKTTEKEVTDEDEEDTKKAD-EDGEEPKVEE----VKEGDEGKKKKTKKVKEV 255
Query: 69 KKHKRLRLRHGRLYAR 84
K ++ +H L+ R
Sbjct: 256 TKEYEVQNKHKPLWTR 271
>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional.
Length = 209
Score = 28.6 bits (64), Expect = 1.7
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 18 AATEVKKDEKKKVAKPKTPKTGE--EKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
A + + + AK T KK K A A P+ D AT KK K KK K
Sbjct: 152 APAKPRAKSPRPAAKAAPKPTETITAKKAKKTAAAPKPTADKTATPAKKTTKKKKTK 208
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 28.4 bits (64), Expect = 2.2
Identities = 13/53 (24%), Positives = 21/53 (39%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTK 69
AA + K +++ KPK P+ + + K TP D + K K
Sbjct: 124 AAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISELTVGQAVKVK 176
Score = 26.4 bits (59), Expect = 7.7
Identities = 8/51 (15%), Positives = 18/51 (35%)
Query: 17 AAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKK 67
A E +++K + + PK +K K + +D ++
Sbjct: 119 AKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISELTV 169
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 28.4 bits (64), Expect = 2.3
Identities = 11/52 (21%), Positives = 17/52 (32%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
E + + + K KT E+ K A T T + KV +
Sbjct: 771 EKESKSELEALKGVGAKTAEKLKDAGVETVTDLTAADPDAVAAKVDGVSADR 822
>gnl|CDD|206228 pfam14058, PcfK, PcfK-like protein. The PcfK-like protein family
includes the Enterococcus faecalis PcfK protein, which
is functionally uncharacterized. This family of proteins
is found in bacteria and viruses. Proteins in this
family are typically between 137 and 257 amino acids in
length. There are two completely conserved residues (D
and L) that may be functionally important.
Length = 136
Score = 27.7 bits (62), Expect = 2.3
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 21 EVKKDEKKKVAKPKTPK-TGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
+V K +V T + T EEK A+K ++ K+ KK+KK +
Sbjct: 73 KVGKPINCRVTVNHTVELTEEEKAEARKEALKAYQQEELRKIQKRSKKSKKAE 125
>gnl|CDD|235370 PRK05244, PRK05244, Der GTPase activator; Provisional.
Length = 177
Score = 27.6 bits (62), Expect = 3.1
Identities = 14/41 (34%), Positives = 18/41 (43%)
Query: 32 KPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHK 72
K K K +AK T DA+A + K+ KK K K
Sbjct: 1 KKKKSSPKRSKGMAKSKKKTREELDAEARERKRKKKHKGLK 41
>gnl|CDD|145556 pfam02478, Pneumo_phosprot, Pneumovirus phosphoprotein. This
family represents the phosphoprotein of Paramyxoviridae,
a putative RNA polymerase alpha subunit that may
function in template binding.
Length = 266
Score = 27.5 bits (61), Expect = 3.5
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 23 KKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRHGRLY 82
KDE V K K ++ EK V + TP++ + T TKK KK + ++ +L
Sbjct: 62 IKDEIISVNKVKDIESIYEKPVTPTSDGKTPTEKSDDTPTKKKKKVSFKEPEPGKYTKLE 121
Query: 83 ARAI 86
A+
Sbjct: 122 KEAL 125
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 27.8 bits (62), Expect = 3.6
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 19 ATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
+ KK++K +K K+ K ++KK K+ + +K T K K KK
Sbjct: 54 TKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKK 105
>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed.
Length = 327
Score = 27.7 bits (62), Expect = 4.2
Identities = 13/58 (22%), Positives = 16/58 (27%), Gaps = 3/58 (5%)
Query: 16 MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKA---TDTKKVKKTKK 70
A AT K A +T T +K KK A + K K
Sbjct: 176 TAPATVAPSKGAKVPATAETHPTPPQKPATKKPAVNHHKTATVAVPPATSGKPKSGAA 233
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 27.6 bits (62), Expect = 4.3
Identities = 12/55 (21%), Positives = 21/55 (38%)
Query: 16 MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
+AA E+ ++E + + K +K V K K K KK ++
Sbjct: 388 LAAFLELTEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEE 442
Score = 26.4 bits (59), Expect = 9.2
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 21 EVKKDEKKKVAKPKTPKTGEEKKVAKK-ATATTPSKDAKATDTKKVKKTKKHKRL 74
E KK++KKK K + EE++ KK ++A+ ++ +K KK L
Sbjct: 425 EEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQATL 479
>gnl|CDD|213632 TIGR01502, B_methylAsp_ase, methylaspartate ammonia-lyase. This
model describes methylaspartate ammonia-lyase, also
called beta-methylaspartase (EC 4.3.1.2). It follows
methylaspartate mutase (composed of S and E subunits) in
one of several possible pathways of glutamate
fermentation [Energy metabolism, Amino acids and amines,
Energy metabolism, Fermentation].
Length = 408
Score = 27.5 bits (61), Expect = 4.4
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 103 LLAIEKCNTKEDARFYVGKRCVFLYKAKTKEL 134
++A E CNT ED +F+ + + + KT ++
Sbjct: 300 IVADEWCNTVEDVKFFTDAKAGHMVQIKTPDV 331
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 27.3 bits (61), Expect = 5.1
Identities = 14/52 (26%), Positives = 21/52 (40%)
Query: 23 KKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRL 74
KK +KKK K K A ++A + A + KK KK + +
Sbjct: 182 KKKKKKKKKKTKKNNATGSSAEATVSSAVPTELSSGAGQVGEAKKLKKKRSI 233
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 27.2 bits (61), Expect = 5.2
Identities = 16/49 (32%), Positives = 21/49 (42%)
Query: 19 ATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKK 67
E KK KK+ K + E +K A K A +K AK D + K
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV 456
>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2
complex component). RNases H are enzymes that
specifically hydrolyse RNA when annealed to a
complementary DNA and are present in all living
organisms. In yeast RNase H2 is composed of a complex of
three proteins (Rnh2Ap, Ydr279p and Ylr154p), this
family represents the homologues of Ydr279p. It is not
known whether non yeast proteins in this family fulfil
the same function.
Length = 287
Score = 27.3 bits (61), Expect = 5.6
Identities = 14/54 (25%), Positives = 22/54 (40%)
Query: 18 AATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKH 71
+ K+ KKK + + E + KK + K K ++K VK KK
Sbjct: 222 PLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKALKKV 275
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 27.0 bits (60), Expect = 5.9
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 9 QTYRVSVMAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKT 68
+ V E +K+EKK+ + T K E K+ K TKKVK+T
Sbjct: 29 KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEV--------DEEEEKEEKKKKTKKVKET 80
Query: 69 KK 70
Sbjct: 81 TT 82
>gnl|CDD|220838 pfam10659, Trypan_glycop_C, Trypanosome variant surface
glycoprotein C-terminal domain. The trypanosome
parasite expresses these proteins to evade the immune
response.
Length = 98
Score = 25.9 bits (57), Expect = 6.5
Identities = 15/48 (31%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 23 KKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK 70
K E KPK E K A T + T+ K KK KK
Sbjct: 19 DKKEDDGKCKPK-----EGKAKKNGAPVTQTAGTETTTEKCKGKKDKK 61
>gnl|CDD|133091 cd06233, M14-like_6, Peptidase M14-like domain; uncharacterized
subfamily. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 283
Score = 26.8 bits (60), Expect = 7.5
Identities = 6/29 (20%), Positives = 7/29 (24%)
Query: 135 KPHSKRKSRLRAIWGKVTRPHGSSGSVRA 163
R R WG + SV
Sbjct: 231 PDEDGALERARRWWGSSVTLPAAGTSVSY 259
>gnl|CDD|224680 COG1766, fliF, Flagellar basal body M-ring protein [Cell motility
and secretion].
Length = 545
Score = 26.6 bits (59), Expect = 9.3
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 1/55 (1%)
Query: 9 QTYRVSVMAAATEVKKDEKKKVAKPK-TPKTGEEKKVAKKATATTPSKDAKATDT 62
+ + ++ A V + + TP + EE K + DAK D+
Sbjct: 357 EPGTIRRLSVAVVVDGKSLAGTGEKEYTPLSDEELKEIEDLVRDAVGYDAKRGDS 411
>gnl|CDD|236087 PRK07748, PRK07748, sporulation inhibitor KapD; Provisional.
Length = 207
Score = 26.2 bits (58), Expect = 9.6
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 26 EKKKVAKPKTPKTGEEK---KVAKKAT 49
+K+ + KP+ P GE KV KK +
Sbjct: 179 DKEYLVKPEPPTIGERVDFSKVLKKVS 205
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 26.5 bits (58), Expect = 9.7
Identities = 26/73 (35%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 12 RVSVMAAATEVKKDEKKKVAKPKTPKTGEEKKVA--KKATATTPSKD--AKATDTKKVKK 67
R AAAT + KKKVAK K KK A K A +K AK K K
Sbjct: 980 RSVKKAAAT--RAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAK 1037
Query: 68 TKKHKRLRLRHGR 80
K R GR
Sbjct: 1038 KAAKKPARKAAGR 1050
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
0.317 0.129 0.369
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,094,573
Number of extensions: 795018
Number of successful extensions: 1513
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1310
Number of HSP's successfully gapped: 206
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
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: 56 (25.2 bits)