RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9210
(234 letters)
>gnl|CDD|218229 pfam04722, Ssu72, Ssu72-like protein. The highly conserved and
essential protein Ssu72 has intrinsic phosphatase
activity and plays an essential role in the
transcription cycle. Ssu72 was originally identified in
a yeast genetic screen as enhancer of a defect caused by
a mutation in the transcription initiation factor TFIIB.
It binds to TFIIB and is also involved in mRNA
elongation. Ssu72 is further involved in both poly(A)
dependent and independent termination. It is a subunit
of the yeast cleavage and polyadenylation factor (CPF),
which is part of the machinery for mRNA 3'-end
formation. Ssu72 is also essential for transcription
termination of snRNAs.
Length = 193
Score = 260 bits (667), Expect = 5e-89
Identities = 110/234 (47%), Positives = 145/234 (61%), Gaps = 44/234 (18%)
Query: 4 NLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIPL 63
LK AVVC+SN NRSMEAH L+K G +V+SFGTG
Sbjct: 1 KLKFAVVCASNQNRSMEAHKVLAKAGFNVRSFGTGSA----------------------- 37
Query: 64 FFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLHM 123
V L G ++DKPNVYDF T Y++IY DL ++D+ YT+NGLLHM
Sbjct: 38 -----------VKL-----PGPSIDKPNVYDF-GTPYDEIYNDLESQDEELYTQNGLLHM 80
Query: 124 LERNKRIKLKPEKFQE-SKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQ 182
L+RN+RIK PE++Q+ ++ KFD++ITCEERV+D V+E N+ SL N PVH+IN+DI+
Sbjct: 81 LDRNRRIKEAPERWQDNTELKFDVVITCEERVFDAVVEDLMNRGSSL-NQPVHVINVDIK 139
Query: 183 DNQEEATLGAFLASELMSMFIKC-EDLDNEIDEIMQEFEEKC-SRPLLHTILFY 234
DN EEA +GA +L M EDL++EIDEI+ EF+EK PLL+T+ FY
Sbjct: 140 DNHEEAIIGAKAILDLAQMLEAASEDLEDEIDEILAEFQEKHPGLPLLYTVAFY 193
>gnl|CDD|227536 COG5211, SSU72, RNA polymerase II-interacting protein involved in
transcription start site selection [Transcription].
Length = 197
Score = 176 bits (449), Expect = 6e-56
Identities = 87/234 (37%), Positives = 126/234 (53%), Gaps = 43/234 (18%)
Query: 3 SNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTGDKKPQQWESVVIFHCCDFCSELIP 62
NLK+AV C+SN NRSME H L+K G VKSFGTG S V
Sbjct: 5 PNLKLAVTCASNQNRSMETHDVLAKAGYPVKSFGTG--------SAV------------- 43
Query: 63 LFFHKVFVFQISVNLFFQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLLH 122
+ G ++DKPNVY+F Y+ IY DL +++ Y NGLL+
Sbjct: 44 ------------------RLPGESIDKPNVYNF-GVPYQQIYDDLCMQNEDHYRENGLLY 84
Query: 123 MLERNKRIKLKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQ 182
ML+RN+R+K PE +Q+ + FD++ITCEER +D + E + SL N V +IN+DI+
Sbjct: 85 MLDRNRRVKEAPENWQQRSEDFDLVITCEERCFDAICEDLYARGPSL-NQCVFMINVDIK 143
Query: 183 DNQEEATLGAFLASELMSMFIKCED-LDNEIDEIMQEFEEKCSR-PLLHTILFY 234
D E+A GA EL+ + K E+ L+ +D I++ ++ PLL+T++
Sbjct: 144 DTPEDAIAGAKAILELVDVLAKEEERLEYAVDSILRRYQSNHKGLPLLYTVVNL 197
>gnl|CDD|223680 COG0607, PspE, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 110
Score = 28.7 bits (64), Expect = 0.99
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 1 MPSNLKVAVVCSSNMNRSMEAHAYLSKKGVDVKSFGTG 38
+P + + V C+S RS A A L G G
Sbjct: 58 LPDDDPIVVYCAS-GVRSAAAAAALKLAGFTNVYNLDG 94
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 29.7 bits (67), Expect = 1.3
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 5/80 (6%)
Query: 143 KFDIIITCEERV-YDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFLASELMSM 201
++ T R +V + L+ L+++ + D LG + L +
Sbjct: 265 SYESKTTKLLRPDPKKVFSKI---RLVLKTLSKMLLSVSVDDCSLFEILGDLIWERLSEL 321
Query: 202 FIKCEDLDNEIDEIMQEFEE 221
IK + L I E E +E
Sbjct: 322 LIK-DCLVKSIPETSSELQE 340
>gnl|CDD|221530 pfam12322, T4_baseplate, T4 bacteriophage base plate protein. This
protein is found in viruses. Proteins in this family are
typically between 208 to 249 amino acids in length. This
protein has a single completely conserved residue S that
may be functionally important. This family includes the
two base plate proteins in T4 bacteriophages. These are
gp51 and gp26, encoded by late genes.
Length = 204
Score = 28.5 bits (64), Expect = 2.1
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 6/44 (13%)
Query: 130 IKLKPEKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTP 173
IK + K E KD F++I C E V D ++++ E+
Sbjct: 113 IKFRYPKLFEDKDPFEMIAECIESVED------NDEVYLWEDLS 150
>gnl|CDD|222565 pfam14133, DUF4300, Domain of unknown function (DUF4300). This
family of lipoproteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 281 and 303 amino
acids in length. There are two conserved sequence
motifs: NCR and PYQ.
Length = 251
Score = 28.7 bits (65), Expect = 2.4
Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 9/84 (10%)
Query: 116 TRNGLLHMLERNKRIKLKPEKF-QESKDKFDIII-------TCEERVY-DQVLEHFDNQM 166
++ L + + F E K+KF + T + +V+ +++ +++ +
Sbjct: 102 DKDDTLLFFDLDAIDNGPDYLFSAEEKEKFTTLFSRIPTEATKDVKVHAEKIEKYWKERG 161
Query: 167 ISLENTPVHLINIDIQDNQEEATL 190
IS +N LI++ + DN + L
Sbjct: 162 ISFKNEKASLISVFLHDNLDGNYL 185
>gnl|CDD|227527 COG5200, LUC7, U1 snRNP component, mediates U1 snRNP association
with cap-binding complex [RNA processing and
modification].
Length = 258
Score = 28.4 bits (63), Expect = 3.5
Identities = 24/145 (16%), Positives = 43/145 (29%), Gaps = 22/145 (15%)
Query: 79 FQSITGTAMDKPNVYDFHTTTYEDIYQDLMNKDKAFYTRNGLL----HMLERNKRIKLKP 134
F T H Y+ Y+ + Y L +L N I+
Sbjct: 44 FDLFRNTKRSLGKCPTSHEEKYKAEYERNGRERAEEYEWEYLRLLVRIVLSCNDGIRAAG 103
Query: 135 EKFQESKDKFDIIITCEERVYDQVLEHFDNQMISLENTPVHLINIDIQDNQEEATLGAFL 194
+ + + ++F I + E F+ S+ + ++ +A L
Sbjct: 104 LEDRTTPEEFGKI--------KEKEELFNRVDESIG-----ELGMEG-----DALAKRKL 145
Query: 195 ASELMSMFIKCEDLDNEIDEIMQEF 219
S F + E L E EI +
Sbjct: 146 VERACSAFNELERLREERKEIKEAV 170
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 27.5 bits (61), Expect = 5.4
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 81 SITGTAM-DKPNVYDFHT----TTYEDIYQDLMNKDKAFYTRNGLLHMLERNK 128
S+TG + DK Y +HT E +D M KD R +L ML RN+
Sbjct: 65 SVTGRKLTDK--FYRWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNR 115
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 27.8 bits (62), Expect = 5.4
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 14/67 (20%)
Query: 89 KPNVYDFHT---TTYEDIYQD--LMNKD-------KAFYTRNGLLHMLERNKRIKLKPEK 136
K +++ HT T ED+ + +M KD KA T GLL + ER R+K+
Sbjct: 359 KRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRER--RMKVTQAD 416
Query: 137 FQESKDK 143
F+++K+K
Sbjct: 417 FRKAKEK 423
>gnl|CDD|238063 cd00115, LMWPc, Low molecular weight phosphatase family;.
Length = 141
Score = 26.5 bits (59), Expect = 7.6
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 6 KVAVVCSSNMNRS-M-EA--HAYLSKKGVDVKSFGTG 38
KV VC+ N+ RS M EA K ++V S GT
Sbjct: 2 KVLFVCTGNICRSPMAEAIFRHLAPKLDIEVDSAGTS 38
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
0.323 0.137 0.406
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,814,856
Number of extensions: 1110535
Number of successful extensions: 1305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1298
Number of HSP's successfully gapped: 29
Length of query: 234
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 140
Effective length of database: 6,768,326
Effective search space: 947565640
Effective search space used: 947565640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.7 bits)