RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16324
(251 letters)
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 35.3 bits (81), Expect = 0.005
Identities = 16/32 (50%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
+++E+ +EDDEE EGE EE+ E E EE+T
Sbjct: 49 DEMEEEEEVDEDDEEEEGEGEEE-EGEEEEET 79
Score = 31.1 bits (70), Expect = 0.15
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKF 47
+E+ + + + +E+ E++EE EG ++ + E+ +K K
Sbjct: 57 VDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDAETKKQKT 102
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The
domain is found in the primary vegetative sigma factor.
The function of this domain is unclear and can be
removed without loss of function.
Length = 211
Score = 36.4 bits (85), Expect = 0.007
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
E + +D+D +++DE+ + E+E L +PEE
Sbjct: 42 AAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 36.2 bits (84), Expect = 0.012
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEE----GEGEKEEKL-EVEPEEQTTLQKAK 46
E E L+ SD D + E DDE E E E V P+ +T Q+ K
Sbjct: 235 DEMSEGLLEESDDDGEEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNK 285
Score = 29.3 bits (66), Expect = 1.8
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 1 MEEEETKLQNSDK--DEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
M E ++L + E+S++D EE ++ E E + + +
Sbjct: 227 MAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGFESEYEPINKPVR 274
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 34.3 bits (79), Expect = 0.028
Identities = 11/38 (28%), Positives = 24/38 (63%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
ME+E ++ + +ED +++E E +K ++ ++E EE
Sbjct: 1 MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEE 38
Score = 32.8 bits (75), Expect = 0.12
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
+E E K ++ K+ED E ++ E E E+ E + L+
Sbjct: 19 KENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61
Score = 29.7 bits (67), Expect = 1.1
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 3 EEETKLQNSDKDEDSE-EDDEEGEGEKEEKLEVEPEE 38
EE+ +N +K+ED E+D E E ++E++ + EE
Sbjct: 14 EEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEE 50
Score = 28.2 bits (63), Expect = 3.1
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
+EE K + D + + E +E E + EE EV+ EE
Sbjct: 23 NKEEDKGKEEDLEFEEIEKEEIIE-DSEESNEVKIEELKDENN 64
Score = 27.8 bits (62), Expect = 4.8
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPE 37
EE K + + E+S E E ++ KL+ E +
Sbjct: 36 FEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENK 71
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 34.8 bits (80), Expect = 0.034
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTL 42
E++E +++ ++ EE+ EEGE ++EE+ E E EE L
Sbjct: 65 EDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPL 105
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 35.0 bits (81), Expect = 0.039
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
++++ + + D D EE+DEE E +E E E EE+ +K K
Sbjct: 338 DDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKK 382
Score = 31.5 bits (72), Expect = 0.47
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+EEE + D+DE+ ++DD E E E + + E +E
Sbjct: 322 DEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDE 358
Score = 30.7 bits (70), Expect = 0.74
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE+E + ++ DED E+DD++ E E+E+ + EE
Sbjct: 320 EEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEE 356
Score = 28.4 bits (64), Expect = 3.9
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
+ + ++ + ++ +EDDEE E E++EK + + E T
Sbjct: 349 VDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAEST 387
Score = 28.4 bits (64), Expect = 4.4
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 11 SDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
D D+D EE++E+ + EE+ E + +
Sbjct: 336 EDDDDDLEEEEEDVDLSDEEEDEEDEDS 363
Score = 28.4 bits (64), Expect = 4.5
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 2 EEEETKLQNSDKDEDSEEDDEE--GEGEKEEKLEVEPEE 38
EEE++K D D++ E DD++ G G+ EE E E +
Sbjct: 291 EEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDG 329
Score = 28.4 bits (64), Expect = 4.7
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFY 48
+ + + ED EED+EE K+ K EV E + K+KFY
Sbjct: 145 DLASDDRAAHFGGGEDDEEDEEEQPERKKSKKEVMKE---VIAKSKFY 189
Score = 28.0 bits (63), Expect = 5.0
Identities = 8/47 (17%), Positives = 26/47 (55%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFY 48
E+ + + D++++ +D+++ E E+EEK + + + + + +
Sbjct: 347 EDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSELPF 393
Score = 27.7 bits (62), Expect = 8.4
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
EEEE + + +ED ++D EE E + + E E EE
Sbjct: 322 DEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEED 360
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 35.0 bits (80), Expect = 0.042
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 14/56 (25%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTL------QKAKFYVSL 51
EEEE +E+ EE++EE E E+EE+ E E EE +L QK Y+ L
Sbjct: 864 EEEE--------EEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQAIYLFL 911
Score = 33.0 bits (75), Expect = 0.16
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 12 DKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
D +E+ EE++EE E E+EE+ E E EE+
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEE 889
Score = 32.3 bits (73), Expect = 0.24
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 10 NSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTL 42
+S+++E+ EE++EE E E+EE+ E E E + L
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPL 894
Score = 31.5 bits (71), Expect = 0.52
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 11 SDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
SD + EE++EE E E+EE+ E E EE+
Sbjct: 858 SDGGDSEEEEEEEEEEEEEEEEEEEEEEE 886
Score = 28.4 bits (63), Expect = 4.3
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
EE E + ++ + + E EGE E K E E E +
Sbjct: 647 EEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEI 685
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 34.4 bits (79), Expect = 0.051
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
EEEE + + ++E+ D EE E+EEK E + + +
Sbjct: 37 DEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKK 76
Score = 31.7 bits (72), Expect = 0.33
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
E+E K +++E+ +E+ +E E + +K E EE+ +K K
Sbjct: 28 EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKK 72
Score = 30.9 bits (70), Expect = 0.75
Identities = 22/71 (30%), Positives = 28/71 (39%), Gaps = 21/71 (29%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGE---------KEEKLEVE------------PEEQT 40
E+EE K + + EE DEE E E KE E E P++ T
Sbjct: 43 EKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPIWTRNPKDVT 102
Query: 41 TLQKAKFYVSL 51
+ A FY SL
Sbjct: 103 KEEYAAFYKSL 113
Score = 30.5 bits (69), Expect = 0.78
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
E E ++ + +++E+ EE EE E +++ EV+ EE+ +K K
Sbjct: 30 EVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKK 73
Score = 28.2 bits (63), Expect = 4.6
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 1 MEEEETKLQNSDKDE-DSEEDDEEGEGEKEEKLEVEP 36
E E KL N K+ EE +EE + +E K E E
Sbjct: 331 KEFEGKKLVNVTKEGLKLEESEEEKKKREELKKEFEE 367
Score = 27.8 bits (62), Expect = 6.8
Identities = 12/45 (26%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
E+E + ++ E+ +E++E+ +KEE+++ E E++ +K K
Sbjct: 32 EKEVPDEEEEEEKEEKKEEEEKTT-DKEEEVDEEEEKEEKKKKTK 75
Score = 27.4 bits (61), Expect = 8.4
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 10 NSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+ D+DE+ EE+DEE E E E E + E+
Sbjct: 494 SIDEDEEVEEEDEEAEVETTEPAEEDAED 522
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 33.6 bits (77), Expect = 0.055
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFYVS 50
E++E K +DE+SEE++EE + E ++ E E EE+T K +
Sbjct: 76 EDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITN 124
Score = 30.5 bits (69), Expect = 0.57
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 2 EEEETKLQNSDKDED---SEEDDEEGEGEKEEKLEVEPEEQTT 41
+EEE + NS+ ED +E++DEE E E EE+ E +E
Sbjct: 66 KEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEK 108
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 34.4 bits (79), Expect = 0.057
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE+ + D D+ ED E G E E E E +E
Sbjct: 228 EEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDE 264
Score = 28.3 bits (63), Expect = 5.3
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEP 36
EE E + +D +S+E DE+ E E+ P
Sbjct: 272 GEEGEMDAAEASEDSESDESDEDTETPGEDARPATP 307
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 33.9 bits (77), Expect = 0.066
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
+ + K+++S+ED+EE E E+EE+ EVE EQ T
Sbjct: 127 KKATKEDESDEDEEEEEEEEEEEAEVEENEQGT 159
Score = 30.4 bits (68), Expect = 0.68
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEE 30
++ TK SD+DE+ EE++EE E E EE
Sbjct: 126 GKKATKEDESDEDEEEEEEEEEEEAEVEE 154
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 32.3 bits (74), Expect = 0.077
Identities = 12/45 (26%), Positives = 22/45 (48%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
EEE ++++ ++ + +D+E EG E + EE K K
Sbjct: 80 EEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYK 124
Score = 28.4 bits (64), Expect = 2.1
Identities = 10/39 (25%), Positives = 15/39 (38%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
EE D + + ED E+ E E + V E+
Sbjct: 78 LLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEE 116
Score = 26.5 bits (59), Expect = 9.0
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFY 48
+E KL + D++ + + E+ E ++++ E PE T + ++
Sbjct: 73 KEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYI 118
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 32.7 bits (75), Expect = 0.11
Identities = 31/177 (17%), Positives = 55/177 (31%), Gaps = 40/177 (22%)
Query: 65 LFLIPFIIEPAIKTIMADYEAEPVTCNISRHDINLGISNCNWASCREGCTAQMIKCHQIS 124
L +I A++ + A+ ++ R L + A +++ H I
Sbjct: 9 LIDFDPVIFEALRDLAAERLGLDISAEELREAGGLP---------FDEALADLLREHPID 59
Query: 125 VHYSRMFFKDYNKSHSPGPIPWDHEDIRFLINT-EGCGYPPG--TNCT-----NFVKQYG 176
+YN P P D+ L+ + G +N + +++ G
Sbjct: 60 PDEILEALLEYNLESRLEPFP----DVVELLRRLKAKGVKLVILSNGSREAVERLLEKLG 115
Query: 177 LPESP-----SQKSSPPKPFPCYYSKVF------P--TLHVVAKYNWDDNLRYLILA 220
L + S KP P Y +V P L + DD+ L A
Sbjct: 116 LLDLFDAVFTSDDVGARKPDPEAYERVLERLGLPPEEILFI------DDSPEDLEAA 166
>gnl|CDD|218673 pfam05642, Sporozoite_P67, Sporozoite P67 surface antigen. This
family consists of several Theileria P67 surface
antigens. A stage specific surface antigen of Theileria
parva, p67, is the basis for the development of an
anti-sporozoite vaccine for the control of East Coast
fever (ECF) in cattle. The antigen has been shown to
contain five distinct linear peptide sequences
recognised by sporozoite-neutralising murine monoclonal
antibodies.
Length = 727
Score = 33.5 bits (76), Expect = 0.11
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 3 EEETKLQNSDK--DEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFYVSLCSGVTA 57
++ T+ K DSEEDD++ E E + + + +K + VS SG T
Sbjct: 100 QDNTEQNQDTKGSKTDSEEDDDDSEEEDNKSTSSKDGKG--SKKTQPGVSTSSGSTT 154
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM).
This family consists of several Plasmodium falciparum
SPAM (secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the
alanine heptad-repeat domain. Heptad repeats in which
the a and d position contain hydrophobic residues
generate amphipathic alpha-helices which give rise to
helical bundles or coiled-coil structures in proteins.
SPAM is an example of a P. falciparum antigen in which
a repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 32.1 bits (73), Expect = 0.13
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
E E+ K +K ED EE++EE E E EE ++E EE+
Sbjct: 39 ENEDVK---DEKQEDDEEEEEEDEEEIEEPEDIEDEEE 73
Score = 29.8 bits (67), Expect = 0.86
Identities = 12/42 (28%), Positives = 27/42 (64%), Gaps = 3/42 (7%)
Query: 2 EEEETKLQNSDKDEDSE--EDDEEGEGEKEEKLEVEPEEQTT 41
+EEE + + D +++ E ED+EE E ++E+ ++++ E+
Sbjct: 58 DEEEIE-EPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKN 98
Score = 28.3 bits (63), Expect = 2.6
Identities = 11/39 (28%), Positives = 25/39 (64%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
++EE + ++ ++ E+ E+ ++E E ++E+ E E EE
Sbjct: 50 DDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDN 88
Score = 26.7 bits (59), Expect = 7.8
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPE 37
+E E +D++ EE+++E E E+ E +E E E
Sbjct: 38 KENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEE 73
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 30.5 bits (69), Expect = 0.16
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE E D DED ++DD++ + + ++ + E +E
Sbjct: 48 EEPEDD----DDDEDDDDDDDKDDKDDDDDDDDEDDE 80
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 31.5 bits (72), Expect = 0.17
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 10 NSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
D+ +D EED+EE + E+++ + EE++ ++K K
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDESEEEESPVKKVK 146
Score = 30.0 bits (68), Expect = 0.62
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 4/35 (11%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVE 35
EE+E+ D +ED EE+D+E + +++E E E
Sbjct: 109 SEEDESD----DDEEDEEEEDDEEDDDEDESEEEE 139
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 32.3 bits (73), Expect = 0.21
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 2 EEEETKLQNSDKDEDSEEDDE-----EGEGEKEEKLEVEPEEQTT 41
EEE +L+ SD E+ EED+E GEG +E E E E + +
Sbjct: 176 NEEEERLEESDGREE-EEDEEVGSDSYGEGNRELNEEEEEEAEGS 219
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 31.6 bits (72), Expect = 0.24
Identities = 13/38 (34%), Positives = 26/38 (68%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+E++ +L+ D DE+ E+D+EE E E+EE + + ++
Sbjct: 156 LEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDD 193
Score = 29.7 bits (67), Expect = 1.2
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
E KL+ + ++ EED+++ E E+EE E E E+
Sbjct: 154 SMLEKKLKELEAEDVDEEDEKDEEEEEEE--EEEDED 188
Score = 28.2 bits (63), Expect = 4.1
Identities = 6/29 (20%), Positives = 18/29 (62%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEE 30
+EE + +++E+ EED++ + + ++
Sbjct: 168 VDEEDEKDEEEEEEEEEEDEDFDDDDDDD 196
Score = 27.8 bits (62), Expect = 5.4
Identities = 6/30 (20%), Positives = 21/30 (70%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEE 30
++EE+ K + +++E+ E++D + + + ++
Sbjct: 168 VDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197
Score = 27.0 bits (60), Expect = 8.1
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 1 MEEEETKLQNSD-KDEDSEEDDEEGEGEKEEKLEVEPEE 38
EEE+ + S + + E + E+ + E E+ E E EE
Sbjct: 144 EEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEE 182
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel,
four-helix bundle structure with a large hydrophobic
patch in which 23 residues of one monomer form van der
Waals contacts with the other monomer. This CENP-B
dimer configuration may be suitable for capturing two
distant CENP-B boxes during centromeric heterochromatin
formation.
Length = 101
Score = 30.5 bits (68), Expect = 0.26
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEK 31
+E EE +SD++ED +++DEE + E +++
Sbjct: 6 LEGEEDSDSDSDEEEDDDDEDEEDDDEDDDE 36
Score = 27.8 bits (61), Expect = 2.4
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEE 30
+ ++ + D DED E+DDE+ + + +E
Sbjct: 13 DSDSDEEEDDDDEDEEDDDEDDDEDDDE 40
Score = 27.4 bits (60), Expect = 3.3
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
++SD D D EEDD++ + E +++ + E +++
Sbjct: 10 EDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40
>gnl|CDD|220496 pfam09972, DUF2207, Predicted membrane protein (DUF2207). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 503
Score = 31.9 bits (73), Expect = 0.29
Identities = 17/70 (24%), Positives = 31/70 (44%)
Query: 181 PSQKSSPPKPFPCYYSKVFPTLHVVAKYNWDDNLRYLILALVVPIVLFFGSLTILGYWYC 240
P +PP +++ AKY + N+R +L +++P++L L IL +
Sbjct: 189 PKGSVTPPNANIISKNRLAEIEKQEAKYAREANIRKNLLLILLPLLLVLLILLILIPYLI 248
Query: 241 PRKSKVQPAY 250
K +P Y
Sbjct: 249 WLKYGREPKY 258
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to
be DNA-binding and may be a transcription factor.
Length = 238
Score = 31.6 bits (72), Expect = 0.30
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPE 37
EEE + +D++ E DDEE EGEKE + E +
Sbjct: 51 EEEVDSDFDDSEDDEPESDDEE-EGEKELQREERLK 85
Score = 30.0 bits (68), Expect = 0.96
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 2 EEEETKLQNSDKDEDSEED-------DEEGEGEKEEKLEVEPEEQTTLQKAK 46
EE++ + + +++E+ E D D+E E + EE+ E E + + L+K K
Sbjct: 37 EEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKK 88
Score = 27.3 bits (61), Expect = 6.5
Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKF 47
EEEE + +SD D DSE+D+ E + E+E + E++ EE+ +K
Sbjct: 47 EEEEEEEVDSDFD-DSEDDEPESDDEEEGEKELQREERLKKKKRVK 91
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 31.6 bits (72), Expect = 0.33
Identities = 10/37 (27%), Positives = 23/37 (62%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE K + ++++D E ++E E +++E+ E + +E
Sbjct: 280 EELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDE 316
Score = 29.2 bits (66), Expect = 1.9
Identities = 7/36 (19%), Positives = 21/36 (58%)
Query: 4 EETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
E+ + + + D ED++E + ++EE+ + + ++
Sbjct: 284 EKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
Score = 28.9 bits (65), Expect = 2.5
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE+ +L ++E+ E+D E E E EE + E EE
Sbjct: 276 EEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEE 312
Score = 28.5 bits (64), Expect = 3.2
Identities = 10/30 (33%), Positives = 22/30 (73%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEK 31
EEE+ ++ D+DE+ E+++EE + ++ +K
Sbjct: 290 EEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
Score = 28.1 bits (63), Expect = 5.1
Identities = 9/37 (24%), Positives = 20/37 (54%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE + +++ED + E+ + E E++ E E ++
Sbjct: 279 LEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDD 315
>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator. This protein
is found in a wide range of eukaryotes. It is a nuclear
protein and is suggested to be DNA binding. In plants,
this family is essential for correct circadian clock
functioning by acting as a light-quality regulator
coordinating the activities of blue and red light
signalling pathways during plant growth - inhibiting
growth in red light but promoting growth in blue light.
Length = 233
Score = 31.2 bits (71), Expect = 0.35
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 4 EETKLQNS----DKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFY 48
++ K + S D++ E++DE + +K K EP+E K
Sbjct: 2 KKKKKKKSKLSFGDDDEEEDEDEGEDEKKVPKESSEPDEANVNPNKKKI 50
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This
is a family of uncharacterized proteins.
Length = 449
Score = 31.5 bits (71), Expect = 0.39
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQ 43
EE D D+D +ED+++ + + +E E E ++ +TL
Sbjct: 50 MEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLH 90
Score = 27.3 bits (60), Expect = 8.8
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT-----TLQKAKFYVS 50
EE++ + D+D+D ++DDE+ E E ++ + + T +A F S
Sbjct: 57 EEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNETDNEAGFADS 110
>gnl|CDD|204519 pfam10587, EF-1_beta_acid, Eukaryotic elongation factor 1 beta
central acidic region.
Length = 28
Score = 28.0 bits (63), Expect = 0.49
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 16 DSEEDDEEGEGEKEEKLE 33
D EE+DEE E +EE+L
Sbjct: 5 DDEEEDEEAERIREERLA 22
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 31.4 bits (71), Expect = 0.54
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
+E E + +++E+ EE++EE + +EE+ E E EE+
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEE 474
Score = 29.9 bits (67), Expect = 1.4
Identities = 15/45 (33%), Positives = 29/45 (64%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
M +E++ + S ++E+ EE++EE E ++ E+ E E EE+ +A
Sbjct: 434 MASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEA 478
Score = 29.1 bits (65), Expect = 2.8
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
EEEE + + + +E+ ED+EE E E E E E +
Sbjct: 451 EEEEEEEEEQESEEEEGEDEEE-EEEVEADNGSEEEME 487
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 30.4 bits (69), Expect = 0.55
Identities = 10/40 (25%), Positives = 25/40 (62%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
+++ K ++ DKD+ ++ D++ E + E++ E + E+ T
Sbjct: 88 KKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTK 127
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 31.2 bits (71), Expect = 0.56
Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 6 TKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
T + KDE+ E++DEE E E+EE E EPEE
Sbjct: 340 TWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
Score = 30.8 bits (70), Expect = 0.74
Identities = 8/29 (27%), Positives = 19/29 (65%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPE 37
++ +++++ EE++EE E +E + E P
Sbjct: 347 KDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375
Score = 28.9 bits (65), Expect = 2.9
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 12 DKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
+ +D EE+ E+ E E+EE+ EPE +
Sbjct: 344 PEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 30.9 bits (70), Expect = 0.62
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
+E+E + Q SD+ E+ E +D E EG + +
Sbjct: 373 DEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSD 411
Score = 30.5 bits (69), Expect = 0.92
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
++ +L D +E E++DEE E +E E E E + + +
Sbjct: 355 RDKRRARLDPIDFEEVDEDEDEEEEQRSDEH-EEEEGEDSEEEGS 398
Score = 28.5 bits (64), Expect = 3.1
Identities = 8/37 (21%), Positives = 20/37 (54%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
+ ++ ++ E+++EE ++ E+ E E E+ Q
Sbjct: 365 IDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSR 401
>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein)
[Posttranslational modification, protein turnover,
chaperones].
Length = 193
Score = 30.4 bits (69), Expect = 0.62
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEE--KLEVEPEEQT 40
EE K + + +E+ E++ E E E++E +LE + EE
Sbjct: 15 ETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELK 56
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 31.2 bits (70), Expect = 0.62
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
EE+ + N D+D E++DE+ + E++++ E E EE+
Sbjct: 142 EEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEE 179
Score = 29.2 bits (65), Expect = 2.4
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFYVSLC 52
E+E+ + + DE+ EE++EE +G +E E E E T +K++ + C
Sbjct: 158 EDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSEVDKTDC 208
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 30.4 bits (69), Expect = 0.73
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 12 DKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+ DSE+++E+ E K+ K + + E
Sbjct: 127 IESSDSEDEEEKDEAAKKAKEDSDEEL 153
Score = 28.1 bits (63), Expect = 4.2
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 1 MEEEETKLQNSDK---DEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
E+EE K + + K D D E +E+ E EE+ +E+ +
Sbjct: 132 SEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEKAS 175
Score = 28.1 bits (63), Expect = 4.6
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEE 30
E E+ + D DE+ E + EE E +E
Sbjct: 87 EAEQGLESDDDDDEEEEWEVEEDEDSDDE 115
Score = 27.3 bits (61), Expect = 8.5
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEE 30
+EEE K + +++ +S++DD+E E + E
Sbjct: 79 KEEERKKKEAEQGLESDDDDDEEEEWEVE 107
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 30.6 bits (69), Expect = 0.75
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKE 29
E EE ++SD +++ ED E+GE + E
Sbjct: 247 ELEENVERDSDDEDEHGEDSEDGETKPE 274
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 30.7 bits (69), Expect = 0.78
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 1 MEEEETKLQNSDKDED---SEEDDEEGEGEKEEKLEVEPEE 38
M ++ D D+D E +E+GEGE E + P+E
Sbjct: 203 MGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQE 243
Score = 28.4 bits (63), Expect = 4.0
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEP 36
E E ++ SD+D+ +E D++ E E P
Sbjct: 251 SESGEEEMVQSDQDDLPDESDDDSETPGEGARPARP 286
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation
termination are recognised and rapidly degraded by
eukaryotic cells through a pathway known as
nonsense-mediated mRNA decay. In Saccharomyces
cerevisiae, three trans-acting factors (Upf1 to Upf3)
are required for nonsense-mediated mRNA decay.
Length = 171
Score = 29.7 bits (67), Expect = 0.84
Identities = 12/39 (30%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGE-KEEKLEVEPEEQ 39
+EEE L + ++DE+S+ ++E+ +EE+++ PE +
Sbjct: 27 DEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVD--PEAE 63
Score = 28.1 bits (63), Expect = 3.0
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
E+EE ++ D + EE+ + + E++E+ + E E+
Sbjct: 11 EEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQ 48
>gnl|CDD|224535 COG1620, LldP, L-lactate permease [Energy production and
conversion].
Length = 522
Score = 30.3 bits (69), Expect = 0.89
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 213 NLRYLILALVVPIVLFFGSLTIL 235
NL L ++PIVLFF L +L
Sbjct: 1 NLWLSALVALLPIVLFFLLLVVL 23
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 30.2 bits (68), Expect = 1.1
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
EE+E L+ +D DED E E+ E E E E E++
Sbjct: 649 EEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQE 688
Score = 28.7 bits (64), Expect = 3.4
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGE-GEKEEKLE 33
+E+E + D + +SE D E+GE E+E+ E
Sbjct: 660 DDEDECE-AIEDSESESESDGEDGEEDEQEDDAE 692
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The
CAF-1 or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression
in addition to DNA-based checkpoints.
Length = 76
Score = 28.0 bits (63), Expect = 1.1
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEG 26
EEE L++ D++++ E+DD++ +G
Sbjct: 51 EEEGEDLESEDEEDEEEDDDDDMDG 75
>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family.
This family includes the HABP4 family of
hyaluronan-binding proteins, and the PAI-1 mRNA-binding
protein, PAI-RBP1. HABP4 has been observed to bind
hyaluronan (a glucosaminoglycan), but it is not known
whether this is its primary role in vivo. It has also
been observed to bind RNA, but with a lower affinity
than that for hyaluronan. PAI-1 mRNA-binding protein
specifically binds the mRNA of type-1 plasminogen
activator inhibitor (PAI-1), and is thought to be
involved in regulation of mRNA stability. However, in
both cases, the sequence motifs predicted to be
important for ligand binding are not conserved
throughout the family, so it is not known whether
members of this family share a common function.
Length = 106
Score = 28.5 bits (64), Expect = 1.2
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
EEEE +++ + E++ EG EE+ E E++
Sbjct: 43 EEEEKNEV---EEKQAVEEEANKEGVVEEEEVEEEEDK 77
Score = 28.1 bits (63), Expect = 1.5
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
EEE K + +K EE ++EG E+EE E E +E T
Sbjct: 43 EEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMT 80
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 29.6 bits (67), Expect = 1.2
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 2 EEEETKLQNS-----DKDEDSEEDDEEGEG-EKEEKLEVEPEEQTTLQKAK 46
EE E + DK +D +EDD+ + ++EE E E E+ KAK
Sbjct: 7 EEFEPPAPPAKAVVKDKWDDEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAK 57
Score = 27.3 bits (61), Expect = 6.4
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
E+E+ + KD EE+DEE E EK + + + + L+
Sbjct: 27 EDED----DDVKDSWDEEEDEEKEEEKAKV-AAKAKAKKALKAK 65
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 30.1 bits (67), Expect = 1.2
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFYVSLCSGV 55
++EE + + K+E + +E EKEE E E E+ T A L G+
Sbjct: 297 QQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHTELLADELNELEKGI 350
>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT. This family
consists of several bacterial cobalamin biosynthesis
(CobT) proteins. CobT is involved in the transformation
of precorrin-3 into cobyrinic acid.
Length = 282
Score = 29.8 bits (67), Expect = 1.2
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
E +++ + D +EDD++GE E+ + E+
Sbjct: 217 ESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSED 253
Score = 29.0 bits (65), Expect = 2.4
Identities = 8/39 (20%), Positives = 13/39 (33%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
+ E D ED ++D E E E + +
Sbjct: 219 ADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDAS 257
Score = 27.9 bits (62), Expect = 4.6
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
M EE S ED+E++D+ E E +++ E E
Sbjct: 208 MAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGS 246
Score = 27.9 bits (62), Expect = 5.0
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
E N D+D+ E++D++ E+E E
Sbjct: 216 PESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSED 253
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 30.0 bits (68), Expect = 1.2
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
E+++ + D D++ EE E E EK + +
Sbjct: 154 EDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWD 190
Score = 28.8 bits (65), Expect = 3.1
Identities = 11/40 (27%), Positives = 26/40 (65%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
++++ + D+D+D ++DD++ + E EEK E + E+ +
Sbjct: 143 DDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLS 182
Score = 27.3 bits (61), Expect = 8.8
Identities = 10/37 (27%), Positives = 24/37 (64%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+ ++ + + D DED +EDD++ + + E++ + E +E
Sbjct: 141 DLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKE 177
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 1.2
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 12 DKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
DKD +ED+EE + E++P+ Q +
Sbjct: 3947 DKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQ 3979
>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein
(DUF2052). This entry is of sequences of two conserved
domains separated by a region of low complexity,
spanning some 200 residues. The function is unknown.
Length = 178
Score = 29.3 bits (66), Expect = 1.3
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
++ EE +L+ ++ E+ E +EE E +EE E E E Q
Sbjct: 64 LDREEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQ 102
>gnl|CDD|184540 PRK14153, PRK14153, heat shock protein GrpE; Provisional.
Length = 194
Score = 29.0 bits (65), Expect = 1.5
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 7 KLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQT 40
K DK E+SE + E+ E+L+ EPE+ T
Sbjct: 4 KEVGKDKAENSEARNSGSSAEEAEELKEEPEDST 37
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 28.9 bits (65), Expect = 1.6
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
++ + + S E+S +++EEGE +K+E+ E+
Sbjct: 105 KGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 29.6 bits (66), Expect = 1.7
Identities = 10/43 (23%), Positives = 22/43 (51%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
E + S ++ S+++ E+ E +K E+ E E+++ Q
Sbjct: 137 EADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQA 179
Score = 29.6 bits (66), Expect = 1.9
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
E + + D+ ED EE E E EEK VE +
Sbjct: 144 SESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQATR 181
>gnl|CDD|216546 pfam01516, Orbi_VP6, Orbivirus helicase VP6. The VP6 protein a
minor protein in the core of the virion is probably the
viral helicase.
Length = 322
Score = 29.3 bits (65), Expect = 1.7
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 1 MEEEETKLQNSDKDED-SEEDDEEGEGEKEEKLEVEPEEQTT 41
E E+K + KDED E+ +GEGE+++K E ++ T
Sbjct: 28 FESGESK-EKEPKDEDGQEQRISDGEGEQKQKGGKEESDKET 68
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 29.4 bits (67), Expect = 1.8
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
++L+ D DED EE+++E + PE+
Sbjct: 182 PAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEK 219
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 28.9 bits (64), Expect = 1.8
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEK---EEKLEVEPEEQTTLQKAK 46
EE + + + ++ E E+ E K EE+ + E EEQ +QK K
Sbjct: 65 AEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQK 112
Score = 28.1 bits (62), Expect = 3.3
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
EEE + +K + E++E+ E E++E+++ + EE
Sbjct: 79 EEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEA 117
>gnl|CDD|225743 COG3202, COG3202, ATP/ADP translocase [Energy production and
conversion].
Length = 509
Score = 29.6 bits (67), Expect = 1.9
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 198 VFPTLHVVAKYNWDDNLRYLILALVVPIVLFFGSLTILG 236
+FP +++ + W AL+ P+V+ + G
Sbjct: 339 LFPGSNLIRRVGW------FTGALITPLVMLITGVLFFG 371
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus.
This family represents the C-terminus (approximately
500 residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have
been proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 29.1 bits (65), Expect = 2.3
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 11 SDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
D +E E DEEG + E+ L + PE +A
Sbjct: 62 LDDEEGPEGGDEEGGWDVEDDLVLPPELDVPKDQA 96
>gnl|CDD|217638 pfam03611, EIIC-GAT, PTS system sugar-specific permease component.
This family includes bacterial transmembrane proteins
with a putative sugar-specific permease function,
including and analogous to the IIC component of the PTS
system. It has been suggested that this permease may
form part of an L-ascorbate utilisation pathway, with
proposed specificity for 3-keto-L-gulonate (formed by
hydrolysis of L-ascorbate). This family includes the IIC
component of the galactitol specific GAT family PTS
system.
Length = 406
Score = 29.0 bits (66), Expect = 2.3
Identities = 7/23 (30%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 217 LILALVVP--IVLFFGSLTILGY 237
+LA+++P + LFFG +
Sbjct: 334 ALLAVILPGNVPLFFGGAAAGVF 356
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 28.6 bits (64), Expect = 2.9
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 11/50 (22%)
Query: 2 EEEETKLQNSDKDED-----------SEEDDEEGEGEKEEKLEVEPEEQT 40
+ + K D+DED EE+ EE E K E E EE T
Sbjct: 294 KRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVT 343
>gnl|CDD|236733 PRK10672, PRK10672, rare lipoprotein A; Provisional.
Length = 361
Score = 28.9 bits (65), Expect = 3.0
Identities = 14/36 (38%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 164 PGTNCTNFVKQ-YGLPESP------SQKSSPPKPFP 192
PGT T KQ Y LP P S P P P
Sbjct: 180 PGTAGTTVAKQSYALPARPDLSGGMGTPSVQPAPAP 215
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 28.6 bits (64), Expect = 3.0
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 9 QNSDKDEDSEEDDEEGEGE--KEEKLEVEPEE 38
+ SD +ED ++D + E + KE++ E E EE
Sbjct: 245 KKSDDEEDDDQDGDYVEEKELKEDEEEEETEE 276
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 28.5 bits (64), Expect = 3.1
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 13/50 (26%)
Query: 10 NSDKDEDSEEDDEEGEGE-------------KEEKLEVEPEEQTTLQKAK 46
+ D+DS++DD E E EEK E E+ +KA+
Sbjct: 128 SDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAR 177
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 28.9 bits (65), Expect = 3.1
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
E + D++E+ EED++EG ++ E E+ +
Sbjct: 385 NTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKY 427
>gnl|CDD|219645 pfam07923, N1221, N1221-like protein. The sequences featured in
this family are similar to a hypothetical protein
product of ORF N1221 in the CPT1-SPC98 intergenic region
of the yeast genome. This encodes an acidic polypeptide
with several possible transmembrane regions.
Length = 293
Score = 28.4 bits (64), Expect = 3.3
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 202 LHVVAKYNWDDN----LRYLILALVVPIVLFFGSLTIL 235
+ + WD +R +IL L ++L FG + L
Sbjct: 197 TKYIERLRWDSALSMPIRKIILLLWKVLLLQFGGSSHL 234
>gnl|CDD|221706 pfam12679, ABC2_membrane_2, ABC-2 family transporter protein. This
family is related to the ABC-2 membrane transporter
family.
Length = 263
Score = 28.4 bits (64), Expect = 3.7
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 199 FPTLHVVAKYNWDDNLRYLILALVVPIVLFFGSLTIL 235
T + + D L ++ ++++ + L F SL +L
Sbjct: 131 AVTAALGDSLSLGDLLLLVLASVLLLLALLFLSLGLL 167
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 28.4 bits (64), Expect = 3.7
Identities = 8/36 (22%), Positives = 19/36 (52%)
Query: 4 EETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
+ + + D +E EED+E + E +E + + ++
Sbjct: 121 RDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDD 156
>gnl|CDD|183731 PRK12766, PRK12766, 50S ribosomal protein L32e; Provisional.
Length = 232
Score = 27.9 bits (62), Expect = 4.2
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 12 DKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
++ ++E +DE GE E+EE +VE E +
Sbjct: 62 SEETEAEVEDEGGEEEEEEDADVETELR 89
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 28.4 bits (63), Expect = 4.2
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
E K + + ++ E+ EE + E+E L + ++ L+ K
Sbjct: 306 PEIPAKPE--IEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKK 348
Score = 27.2 bits (60), Expect = 9.0
Identities = 16/45 (35%), Positives = 20/45 (44%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
EE E KL + E DE+ E +EEK E E +K K
Sbjct: 298 EEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLK 342
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 28.4 bits (63), Expect = 4.2
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+E + DE+SE++ E E EE E+E E
Sbjct: 338 QEGDVVTEESTDEESEDEVEIDESVIEEVAEMELLE 373
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 27.6 bits (62), Expect = 4.5
Identities = 11/43 (25%), Positives = 24/43 (55%)
Query: 4 EETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
+ L +K+E+ EE+ E E ++EE+++ E++ K +
Sbjct: 92 KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKRE 134
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 28.1 bits (62), Expect = 4.9
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 10 NSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
NSD +S E+DE E EKEE+ E + +K +
Sbjct: 763 NSDSFAESSEEDESSEEEKEEEENKEVSAKRAKKKQR 799
>gnl|CDD|217940 pfam04177, TAP42, TAP42-like family. The TOR signalling pathway
activates a cell-growth program in response to
nutrients. TIP41 (pfam04176) interacts with TAP42 and
negatively regulates the TOR signaling pathway.
Length = 335
Score = 28.0 bits (63), Expect = 4.9
Identities = 6/33 (18%), Positives = 17/33 (51%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLE 33
+ +++++ED E+D+E+ + E +
Sbjct: 294 PQGGGEAAASAEEEEDDEDDEEDDDEETLKARA 326
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 27.7 bits (62), Expect = 4.9
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQ 39
+EEE + + + ED E++ E + E L+ E + +
Sbjct: 8 VEEEVEETEVEEAVEDEVEEETVEEESEAELLD-EEQAK 45
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 28.1 bits (62), Expect = 5.6
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKF 47
E+EE+ + D ED E+D E + E+ E+E + + K
Sbjct: 954 EDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAYDSRPGKR 999
>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890). This
family is conserved in dsDNA adenoviruses of
vertebrates. The function is not known.
Length = 172
Score = 27.2 bits (60), Expect = 5.6
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 2 EEEETKLQNSD---KDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKA 45
+EEE ++ +DE+ ED E+ E++E+ E EE KA
Sbjct: 19 DEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKA 65
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 27.0 bits (60), Expect = 5.7
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 9 QNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
+ S D++ EE +EE E E++ E + ++ +K +
Sbjct: 90 ELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKR 127
>gnl|CDD|218336 pfam04935, SURF6, Surfeit locus protein 6. The surfeit locus
protein SURF-6 is shown to be a component of the
nucleolar matrix and has a strong binding capacity for
nucleic acids.
Length = 206
Score = 27.3 bits (61), Expect = 6.0
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 3 EEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKF 47
+E K +++ K E E +EE + +K+ E K +F
Sbjct: 27 KEAKKKEDAQKSEAEEVKNEENKSKKKAAPIENAEGNIVFSKVEF 71
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 27.8 bits (62), Expect = 6.1
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
EE+E +L+ + S+ DD+E E E++ E + EE
Sbjct: 12 EEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEE 48
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 28.1 bits (63), Expect = 6.1
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 4 EETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
EE + + + E + E + E E ++E E E E + ++
Sbjct: 533 EEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVA 575
>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional.
Length = 374
Score = 27.7 bits (61), Expect = 6.2
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPE 37
+EE E + D DEDSE+DDE+ + ++ E+ E
Sbjct: 121 VEEVEVVEEEYDDDEDSEKDDEKESDAEGDENELAGE 157
>gnl|CDD|217046 pfam02453, Reticulon, Reticulon. Reticulon, also know as
neuroendocrine-specific protein (NSP), is a protein of
unknown function which associates with the endoplasmic
reticulum. This family represents the C-terminal domain
of the three reticulon isoforms and their homologues.
Length = 164
Score = 27.2 bits (61), Expect = 6.4
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 7/40 (17%)
Query: 49 VSLCSGVTACLSAFAFLFLIPFI-------IEPAIKTIMA 81
SL SG+T F +P + I+ ++ A
Sbjct: 121 GSLFSGLTLLYIGVILAFTVPLLYEKYQDEIDAYVEKAKA 160
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP),
alpha subunit. The alpha-subunit of the TRAP complex
(TRAP alpha) is a single-spanning membrane protein of
the endoplasmic reticulum (ER) which is found in
proximity of nascent polypeptide chains translocating
across the membrane.
Length = 281
Score = 27.4 bits (61), Expect = 6.5
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTT 41
E+EE ++ D E++++E E++E E EE
Sbjct: 36 EDEE-----AEDDVVDEDEEDEAVVEEDENELTEEEEDEE 70
>gnl|CDD|237626 PRK14154, PRK14154, heat shock protein GrpE; Provisional.
Length = 208
Score = 27.5 bits (60), Expect = 6.9
Identities = 13/32 (40%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 3 EEETKLQNS-DKDEDSEEDDEEGEGEKEEKLE 33
E ETK +N +K ++EE+ EEG G+ +++E
Sbjct: 12 ESETKAKNKWEKVMEAEEEQEEGGGDGSQEME 43
>gnl|CDD|181395 PRK08341, PRK08341, amidophosphoribosyltransferase; Provisional.
Length = 442
Score = 27.5 bits (61), Expect = 7.5
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 165 GTNCTNFVK---QYGLPESPSQKSSPPKPFPCYYSKVFPTLH 203
GT VK G E + +SPP +PCY PT H
Sbjct: 347 GTTMKRIVKMLRDAGAREVHVRIASPPIRYPCYMGIDIPTRH 388
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 27.6 bits (62), Expect = 7.9
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 1 MEEEETKLQNSDKDEDSEED--DEEGEGEKEEKLEVEP 36
E E ++ K + E +E+ +EEK E +P
Sbjct: 469 PEFEGKPFKSITKGDLDLELLEEEDEADSEEEKKEFKP 506
>gnl|CDD|219780 pfam08286, Spc24, Spc24 subunit of Ndc80. Spc24 is a component
of the evolutionarily conserved kinetochore-associated
Ndc80 complex and is involved in chromosome
segregation.
Length = 117
Score = 26.5 bits (59), Expect = 7.9
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAKFYVSL 51
++ E +L+ +E E++ E E +++E P + + + K K Y SL
Sbjct: 25 LQSELEELKER-LEELEEQEVEGDEVDEDE----TPVDDSNVLKLKLYRSL 70
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 26.5 bits (58), Expect = 8.0
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEE 38
+ + + + DE +E +E + E EE E E EE
Sbjct: 92 DAADEADEEEETDEAVDETADEADAEAEEADEEEDEE 128
>gnl|CDD|177102 MTH00016, CYTB, cytochrome b; Validated.
Length = 378
Score = 27.3 bits (61), Expect = 8.0
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 54 GVTACLSAFAFLFLIPFIIEPAIKT 78
GV A ++ LF +PFI + +
Sbjct: 291 GVVAMFASILILFFLPFIFKQKFRG 315
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 27.6 bits (62), Expect = 8.1
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQKAK 46
EEE+ + + +E++EE E EK+E+ + E EE+ +K +
Sbjct: 424 EEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEE 468
>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional.
Length = 196
Score = 26.8 bits (59), Expect = 8.7
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 3/43 (6%)
Query: 1 MEEEETKL-QNSDKDEDSEEDDEEGEG--EKEEKLEVEPEEQT 40
MEE E ++ + +KD ++ +E+ EG E E+ + +P++QT
Sbjct: 1 MEEVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQT 43
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 27.3 bits (61), Expect = 8.7
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 14/61 (22%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGE------------KEEKLE--VEPEEQTTLQKAK 46
+E + ++ D+D DSEE+DE+ + + K KL+ + EE + L K
Sbjct: 318 IEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSGLLSMK 377
Query: 47 F 47
F
Sbjct: 378 F 378
>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of
pre-ribosomes [Translation, ribosomal structure and
biogenesis / Intracellular trafficking and secretion].
Length = 657
Score = 27.3 bits (60), Expect = 8.9
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 5 ETKLQNSD-KDEDSEEDDEEGEGEKEEK----LEVEPEEQTTLQKAKFYVSLCSGV 55
E L S+ + + D + E +K + P +Q + + S+C+ +
Sbjct: 92 EEFLSESESEASLEIDSDIKDEKQKSLEEQKIAPEIPVKQQIDSEKERIASICTKI 147
>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region. The precise
function of this eukaryotic protein family is unknown.
The yeast orthologues have been implicated in cell
cycle progression and biogenesis of 60S ribosomal
subunits. The Schistosoma mansoni Mak16 has been shown
to target protein transport to the nucleolus.
Length = 97
Score = 26.0 bits (57), Expect = 9.6
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTLQK 44
EE E N +++E+ EE+++EGE E E EE L+
Sbjct: 58 EESEE---NDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLED 97
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.1 bits (60), Expect = 9.6
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 1 MEEEETKLQNSDKDEDSEEDDEEGEGEKEEK----LEVEPEEQTTLQKAK 46
++ +D E++E +E + ++EE E E++ QK +
Sbjct: 382 TKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDE 431
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 27.3 bits (61), Expect = 9.7
Identities = 11/41 (26%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEPEEQTTL 42
+EEE ++ DED +++D+ + + +++ E +PE + T
Sbjct: 227 DEEEERVLA---DEDDDDEDDMFDMDDDDEEESDPEVERTS 264
>gnl|CDD|227499 COG5171, YRB1, Ran GTPase-activating protein (Ran-binding
protein) [Intracellular trafficking and secretion].
Length = 211
Score = 26.9 bits (59), Expect = 9.8
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 2 EEEETKLQNSDKDEDSEEDDEEGEGEKEEKLEVEP 36
EE K+Q S E++ + +EG+G + + EP
Sbjct: 39 GGEEKKVQQSPFLENAVPEGDEGKGPESPNIHFEP 73
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 27.1 bits (60), Expect = 10.0
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 1 MEEEETKLQNSDKDEDSEED-DEEGEGEKEEKLEVEPEEQ 39
+EEE L ++ E ++D D E +EEK ++E EE
Sbjct: 76 KKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEEL 115
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
0.319 0.137 0.433
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,709,337
Number of extensions: 1171927
Number of successful extensions: 3526
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3058
Number of HSP's successfully gapped: 226
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
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 (21.7 bits)
S2: 58 (25.9 bits)