RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy634
(139 letters)
>gnl|CDD|238117 cd00195, UBCc, Ubiquitin-conjugating enzyme E2, catalytic (UBCc)
domain. This is part of the ubiquitin-mediated protein
degradation pathway in which a thiol-ester linkage forms
between a conserved cysteine and the C-terminus of
ubiquitin and complexes with ubiquitin protein ligase
enzymes, E3. This pathway regulates many fundamental
cellular processes. There are also other E2s which form
thiol-ester linkages without the use of E3s as well as
several UBC homologs (TSG101, Mms2, Croc-1 and similar
proteins) which lack the active site cysteine essential
for ubiquitination and appear to function in DNA repair
pathways which were omitted from the scope of this CD.
Length = 141
Score = 68.8 bits (169), Expect = 7e-16
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSPANVDASVMYRRWRDSKGCDKEYENIIRKQV 61
W+P +RT+LLS+ SLLNEPN S P N +A+ +Y+ R +E++ R+
Sbjct: 90 HGWSPAYTLRTVLLSLQSLLNEPNPSDPLNAEAAKLYKENR------EEFKKKAREWT 141
>gnl|CDD|215772 pfam00179, UQ_con, Ubiquitin-conjugating enzyme. Proteins destined
for proteasome-mediated degradation may be
ubiquitinated. Ubiquitination follows conjugation of
ubiquitin to a conserved cysteine residue of UBC
homologues. TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 139
Score = 68.4 bits (168), Expect = 1e-15
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 6/58 (10%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSPANVDASVMYRRWRDSKGCDKEYENIIRKQV 61
E W+P + +LLS+ SLL+EPN P N +A+ +YR+ R +E+E +R+ V
Sbjct: 88 ENWSPALTIEQVLLSIQSLLSEPNPEDPLNAEAAKLYRKNR------EEFEKKVREYV 139
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 67.3 bits (165), Expect = 3e-15
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 6/61 (9%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSPANVDASVMYRRWRDSKGCDKEYENIIRKQVSG 63
+RW+P + TILLS+ SLL PN SP N +A+ +YR + +EYE +R+ V
Sbjct: 96 DRWSPVYTLETILLSLQSLLLSPNPDSPLNTEAATLYREDK------EEYEKKVREWVKK 149
Query: 64 G 64
Sbjct: 150 Y 150
>gnl|CDD|214562 smart00212, UBCc, Ubiquitin-conjugating enzyme E2, catalytic domain
homologues. Proteins destined for proteasome-mediated
degradation may be ubiquitinated. Ubiquitination follows
conjugation of ubiquitin to a conserved cysteine residue
of UBC homologues. This pathway functions in regulating
many fundamental processes required for cell
viability.TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 145
Score = 62.7 bits (153), Expect = 2e-13
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 6/59 (10%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSPANVDASVMYRRWRDSKGCDKEYENIIRKQVS 62
E+W+P + T+LLS+ SLL+EPN SP N DA+ +Y++ R +E++ R+
Sbjct: 89 EKWSPALTLETVLLSLQSLLSEPNPDSPLNADAAELYKKNR------EEFKKKAREWTK 141
>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 = 33.4 bits (77), Expect = 0.029
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D Y D + DDDD+E +EE+ E E+ D DD + +
Sbjct: 118 DAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDD 157
Score = 31.1 bits (71), Expect = 0.15
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
++ D DD++ ++E+EE + ++E D DD +
Sbjct: 124 EEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIA 159
Score = 27.3 bits (61), Expect = 3.2
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 92 DTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDD 133
+ + Y D Y ++DD+D+EE EE E + +D
Sbjct: 107 EEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDED 148
Score = 26.1 bits (58), Expect = 7.0
Identities = 8/32 (25%), Positives = 18/32 (56%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
DD + D++D+E + E +E +++ D +
Sbjct: 129 DDEESDEEDEESSKSEDDEDDDDDDDDDDIAT 160
>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 = 32.9 bits (76), Expect = 0.029
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGG 128
D+ DL+DDDD+DE+E+ ++ E + G
Sbjct: 49 DEEDLEDDDDDDEDEDEDDEEEADLG 74
Score = 30.2 bits (69), Expect = 0.21
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDD 133
+ + D +DD+D++E+ +E EEE D G D
Sbjct: 47 ELDEEDLEDDDDDDEDEDEDDEEE-ADLGPD 76
Score = 28.3 bits (64), Expect = 1.1
Identities = 6/28 (21%), Positives = 17/28 (60%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSG 135
+ D+++ E+++ ++ E+E + D G
Sbjct: 47 ELDEEDLEDDDDDDEDEDEDDEEEADLG 74
Score = 26.8 bits (60), Expect = 3.5
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
DD D D+D+DED+EEE + G + E
Sbjct: 55 DDDDDDEDEDEDDEEEADLGPDPE 78
Score = 26.4 bits (59), Expect = 5.0
Identities = 7/32 (21%), Positives = 18/32 (56%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGEL 139
+ + DE++ E+ ++ E+E D +++ G
Sbjct: 45 ESELDEEDLEDDDDDDEDEDEDDEEEADLGPD 76
Score = 26.0 bits (58), Expect = 7.4
Identities = 3/31 (9%), Positives = 16/31 (51%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+ + ++E+ E ++ +E+ + ++ +
Sbjct: 44 IESELDEEDLEDDDDDDEDEDEDDEEEADLG 74
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 33.5 bits (76), Expect = 0.031
Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEEGAEEE 126
+F +DD D D+D+D+D+EE+ EE EEE
Sbjct: 150 NFVIDDDDEDEDEDDDDEEDDEEEEEEE 177
Score = 33.1 bits (75), Expect = 0.040
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 95 MDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGD 129
+ D D + DDDDEDE+E+ ++ ++E +
Sbjct: 140 LAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEE 174
Score = 30.0 bits (67), Expect = 0.48
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNG 137
+D D DDDD+ED+EEE EE E +G D D+ G
Sbjct: 158 EDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEG 192
Score = 29.2 bits (65), Expect = 0.71
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
DD D D+DDD++E++E EE EEE D+ E
Sbjct: 156 DDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDE 191
>gnl|CDD|215079 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 32.8 bits (75), Expect = 0.041
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+VD + D +D +++ ++ G ++ GN
Sbjct: 29 WVDGSEDDSEDPASLDDDDDDRDSGGGMLEEEEDGNMR 66
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 32.1 bits (73), Expect = 0.044
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSPANVDASV 38
++W+P +RT+LLS+ +LL+ P P +D SV
Sbjct: 92 DKWSPALQIRTVLLSIQALLSAPEPDDP--LDTSV 124
>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 = 31.9 bits (73), Expect = 0.094
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
+D + DDDD E+EEE+ + EEE + D
Sbjct: 329 GVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSD 364
Score = 31.1 bits (71), Expect = 0.17
Identities = 13/43 (30%), Positives = 15/43 (34%)
Query: 96 DMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D D DD D DDDD D + G D +D
Sbjct: 127 DKDDDVRDDDDFDDDDLGDLASDDRAAHFGGGEDDEEDEEEQP 169
Score = 30.7 bits (70), Expect = 0.21
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 103 DDYDLDDDDD------EDEEEEGEEGAEEEGGDSGDDSGNGE 138
D+++ DDDD+ E++EEE E+G ++E + DD E
Sbjct: 304 DEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEE 345
Score = 30.4 bits (69), Expect = 0.32
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGN 136
D+ + DDDDD +EEEE + ++EE + +DS +
Sbjct: 332 DEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDD 365
Score = 30.4 bits (69), Expect = 0.34
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGEL 139
D D++DD+D+ EE EE + + ++ + +
Sbjct: 329 GVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDD 365
Score = 30.0 bits (68), Expect = 0.36
Identities = 8/34 (23%), Positives = 20/34 (58%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSG 135
++ +DD+D+ED++++ EE E+ ++
Sbjct: 325 EEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDE 358
Score = 30.0 bits (68), Expect = 0.38
Identities = 13/45 (28%), Positives = 18/45 (40%)
Query: 94 SMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
S+ D D D DD DD+D + + G DD + E
Sbjct: 122 SLSEIDKDDDVRDDDDFDDDDLGDLASDDRAAHFGGGEDDEEDEE 166
Score = 29.2 bits (66), Expect = 0.76
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 103 DDYDLDDD---DDEDEEEEGEEGAEEEGGDSGDDSG 135
D+ D DDD ++ED + EE EE+ +D
Sbjct: 334 DEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDE 369
Score = 28.4 bits (64), Expect = 1.2
Identities = 8/36 (22%), Positives = 21/36 (58%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
D ++ D+D D+E++EE+ + E++ + ++
Sbjct: 341 DLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEK 376
Score = 28.0 bits (63), Expect = 2.0
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D D +D++D+D++ E EE + + D+
Sbjct: 328 DGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDS 363
Score = 27.3 bits (61), Expect = 3.2
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
D+ D D DD++DEEEE EE +++ +
Sbjct: 357 DEEDEDSDDEDDEEEEEEEKEKKKKKSAESTR 388
Score = 26.9 bits (60), Expect = 4.4
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
VDD D +DDDD+ EEEE + +E D D+ + E
Sbjct: 330 VDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDE 366
Score = 26.5 bits (59), Expect = 6.3
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
+D D DD+DDE+EEEE +E +++ +S
Sbjct: 359 EDEDSDDEDDEEEEEEEKEKKKKKSAESTRSE 390
>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 = 31.8 bits (72), Expect = 0.11
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 14/65 (21%)
Query: 84 IKAKTRPADTSM-------DMTDFYVDDYDLDD-----DDDEDEEEEGEEGAEEEGGDSG 131
+KA + D D D D D+ D + + E +GE+G E+E D
Sbjct: 632 LKADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQED-- 689
Query: 132 DDSGN 136
D N
Sbjct: 690 DAEAN 694
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 31.5 bits (72), Expect = 0.13
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
DD D DDDD +DE+EE +E E E S DD +
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELE-KLSDDDDFVWD 190
Score = 30.0 bits (68), Expect = 0.43
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
DD D+DD+D+E +E + E ++ D+
Sbjct: 161 DDDDVDDEDEEKKEAKELEKLSDDDDFVWDED 192
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 31.1 bits (70), Expect = 0.14
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 97 MTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
M + D+ D DDDDDEDE+++ ++ E++ + DDS
Sbjct: 50 MEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDS 87
Score = 28.4 bits (63), Expect = 1.4
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 86 AKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGN 136
A D D D +D D DDDDD++++E+ ++ DS D GN
Sbjct: 49 AMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGN 99
Score = 26.5 bits (58), Expect = 5.4
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 96 DMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNG 137
+ D DD D DDDDD+D+E++ +E ++ + +G
Sbjct: 57 EEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDG 98
Score = 26.1 bits (57), Expect = 6.8
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 95 MDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
M+ D +D D DDD+DED++++ ++ +E+ D +
Sbjct: 50 MEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDS 93
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 30.5 bits (68), Expect = 0.15
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 4 ERWNPTQNVRTILLSVISLLNEPNTSSP 31
++W+P V +LLS+ SLL +PN P
Sbjct: 91 DQWSPALTVSKVLLSISSLLTDPNPDDP 118
>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 = 31.1 bits (70), Expect = 0.15
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 88 TRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
R SM++ + DD + +D++D D+++ E EE+G G+
Sbjct: 190 VREMLRSMELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQ 236
>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 = 30.8 bits (70), Expect = 0.17
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEE 126
D D DD +D++ E + EE E+E
Sbjct: 52 EEVDSDFDDSEDDEPESDDEEEGEKE 77
Score = 26.2 bits (58), Expect = 5.8
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 99 DFYVDDYDLDDDDDE--DEEEEGEEGAEEE 126
+ D+D +DD+ D+EEEGE+ + E
Sbjct: 52 EEVDSDFDDSEDDEPESDDEEEGEKELQRE 81
Score = 26.2 bits (58), Expect = 5.9
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEG 127
++ ++D D D+ E++E E EEEG
Sbjct: 50 EEEEVDSDFDDSEDDEPESDDEEEG 74
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 31.0 bits (70), Expect = 0.18
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 16/64 (25%)
Query: 88 TRPADTSMDMTDFYVDDYDLDDDDDED----------------EEEEGEEGAEEEGGDSG 131
R SMDM + DD +D D+ED EE EG + +EE+ ++
Sbjct: 209 VRDMLGSMDMAEETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEAT 268
Query: 132 DDSG 135
D G
Sbjct: 269 DGEG 272
>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase 19
kDa subunit. This family contains several DNA-directed
RNA polymerase 19 kDa polypeptides. The Poxvirus
DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes
DNA-template-directed extension of the 3'-end of an RNA
strand by one nucleotide at a time.
Length = 167
Score = 30.4 bits (69), Expect = 0.19
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 92 DTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
+ S D+ D+ DD DD ++ +EEEE EE AE
Sbjct: 2 EDSDDIIDYESDD---DDSEEYEEEEEDEEDAESLESSDVSSL 41
>gnl|CDD|219232 pfam06934, CTI, Fatty acid cis/trans isomerase (CTI). This
family consists of several fatty acid cis/trans
isomerase proteins which appear to be found exclusively
in bacteria of the orders Vibrionales and
Pseudomonadales. Cis/trans isomerase (CTI) catalyzes
the cis-trans isomerisation of esterified fatty acids
in phospholipids, mainly cis-oleic acid (C(16:1,9)) and
cis-vaccenic acid (C(18:1,11)), in response to
solvents. The CTI protein has been shown to be involved
in solvent resistance in Pseudomonas putida.
Length = 688
Score = 30.3 bits (69), Expect = 0.32
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 21 SLLNEPNTSSPANVDASVMYR 41
+LNE + AN+ AS+M R
Sbjct: 24 PVLNEREQTPEANLQASLMAR 44
>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 = 30.1 bits (68), Expect = 0.35
Identities = 14/32 (43%), Positives = 23/32 (71%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
D ++D+D+DE+EE+ +E EEEG DS ++
Sbjct: 366 DFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEG 397
Score = 27.8 bits (62), Expect = 2.2
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSG 135
VD+ + ++++ +E E EEG + E S
Sbjct: 369 EVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSRED 403
Score = 26.6 bits (59), Expect = 4.5
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+ +D+D+E+E+ E EE + S + E
Sbjct: 367 FEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSRE 402
>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 = 29.8 bits (67), Expect = 0.38
Identities = 22/59 (37%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 84 IKAKTRPADTSMDMTDFYVDDYDLDDDDDEDEE--------EEGEEGAEEEGG-DSGDD 133
K AD ++ D + +D DL D+D E EEG EG +EEGG D DD
Sbjct: 24 GGDKAAAADFAVMGGDDWGEDADLGLDEDGYLEGEDGLLDDEEGPEGGDEEGGWDVEDD 82
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 30.0 bits (67), Expect = 0.42
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
D D +++++E+EEEE EE EEE
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEEE 882
Score = 30.0 bits (67), Expect = 0.45
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D +++E+EEEE EE EEE + ++ N E
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 30.0 bits (67), Expect = 0.48
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
D + +++++E+EEEE EE EEE
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEE 885
Score = 29.6 bits (66), Expect = 0.66
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 111 DDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+++ E ++ E+G + GG G DS E
Sbjct: 840 ENQGEAKQDEKGVDGGGGSDGGDSEEEE 867
Score = 28.4 bits (63), Expect = 1.4
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
++ + +++++E+EEEE EE EEE
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEE 888
Score = 28.4 bits (63), Expect = 1.5
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
++ + +++++E+EEEE EE EEE
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEE 887
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 29.7 bits (67), Expect = 0.46
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 85 KAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEE----GEEGAEEEGGDSGDDSGN 136
K+ R +D D + DDDDDED E ++ +E G+ D+ N
Sbjct: 234 KSSKRRTIAQIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTDN 289
>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 = 28.8 bits (65), Expect = 0.54
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
+D DD++DE+EE++ E+ E+E
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDE 134
Score = 28.1 bits (63), Expect = 1.1
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 97 MTDFYVDDYDLDDDDDEDEEEEGEEGAEEEG 127
+ DD D +D+++ED+EE+ +E EE
Sbjct: 109 SEEDESDD-DEEDEEEEDDEEDDDEDESEEE 138
Score = 28.1 bits (63), Expect = 1.2
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 96 DMTDFYVDDYDLDDDDDEDEEEEGEEGA 123
D +D +D + +DD+++D+E+E EE
Sbjct: 112 DESDDDEEDEEEEDDEEDDDEDESEEEE 139
Score = 28.1 bits (63), Expect = 1.2
Identities = 8/24 (33%), Positives = 19/24 (79%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEE 126
DD + ++++D++E+++ +E EEE
Sbjct: 116 DDEEDEEEEDDEEDDDEDESEEEE 139
Score = 27.7 bits (62), Expect = 1.5
Identities = 9/26 (34%), Positives = 19/26 (73%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEE 126
++ + DDD++++EEE+ EE +E+
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDED 133
>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 = 29.6 bits (67), Expect = 0.57
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 106 DLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+LDD DDE+EE + +++ D D + E
Sbjct: 221 ELDDIDDEEEERVLADEDDDDEDDMFDMDDDDE 253
>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 = 29.4 bits (66), Expect = 0.62
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
D D +D+DD E+E+ ++G EEE G S S
Sbjct: 220 DSEDNEDEDDPKEDEDDDQGEEEESGSSDSLS 251
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 29.5 bits (66), Expect = 0.64
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 87 KTRPADTSMDMTDFYVDDYDLDD---DDDEDEEEEGEEGAEEEGGDSGDDS 134
+T P TS D D + D D +D+D++ + E+ EE G S D+
Sbjct: 277 RTFPERTSDDDEDAIETEEDDVDESAIEDDDDDSDWEDSVEESGRSSVDEK 327
>gnl|CDD|146444 pfam03805, CLAG, Cytoadherence-linked asexual protein. Clag
(cytoadherence linked asexual gene) is a malaria surface
protein which has been shown to be involved in the
binding of Plasmodium falciparum infected erythrocytes to
host endothelial cells, a process termed cytoadherence.
The cytoadherence phenomenon is associated with the
sequestration of infected erythrocytes in the blood
vessels of the brain, cerebral malaria. Clag is a
multi-gene family in Plasmodium falciparum with at least
9 members identified to date. Orthologous proteins in the
rodent malaria species Plasmodium chabaudi (Lawson D
Unpubl. obs.) suggest that the gene family is found in
other malaria species and may play a more generic role in
cytoadherence.
Length = 1282
Score = 29.3 bits (66), Expect = 0.74
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 13/84 (15%)
Query: 38 VMYRRWRDSKGCDKEYENIIRKQVSG-----GRIEADKDGVKIPMTLEDYCIKAKTRPAD 92
+ + ++K + YE I+ ++S IE ++ +P L Y ++ +
Sbjct: 1202 YESKAYDNTKK-EGYYEEAIKARLSSKDYIKNYIEGERSTDIMPN-LRRYDMENLQK--- 1256
Query: 93 TSMDMTDFYVDDYDLDDDDDEDEE 116
+ YVDD L DD D++E+
Sbjct: 1257 --NSYS-TYVDDNILFDDLDKNEQ 1277
>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 = 28.1 bits (63), Expect = 1.4
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGEL 139
D+YV + +L + ++E+EEEE E EE+ G+ ++ E+
Sbjct: 159 DYYVAEVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEV 199
Score = 26.6 bits (59), Expect = 6.0
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEE 126
+V+ D+++++++EEE EE E E
Sbjct: 341 WVNPEQKDEEEEQEDEEEEEEEEEPE 366
>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 = 28.2 bits (63), Expect = 1.5
Identities = 21/80 (26%), Positives = 29/80 (36%), Gaps = 3/80 (3%)
Query: 41 RRWRDSKGCDKEYENIIRKQVSGGRIEADKDGVKIPMTLEDYCIKAKTRP--ADTSMDMT 98
R + K E+ + E D+D + + I+ R AD S +
Sbjct: 68 RAHKSKKENKLAIEDADKSTNLDASNEGDEDDDEEDEI-KRKRIEEDARNSDADDSDSSS 126
Query: 99 DFYVDDYDLDDDDDEDEEEE 118
D D D DDDD EDE
Sbjct: 127 DSDSSDDDSDDDDSEDETAA 146
>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 = 28.1 bits (63), Expect = 1.5
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 107 LDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
L++ DD+ EEE +E A E +
Sbjct: 242 LEESDDDGEEESDDESAWEGFESEYEPI 269
Score = 26.2 bits (58), Expect = 7.5
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 106 DLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
L ++ D+D EEE ++ + EG +S + N
Sbjct: 240 GLLEESDDDGEEESDDESAWEGFESEYEPINKP 272
>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 = 28.1 bits (63), Expect = 1.5
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 85 KAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+ +D D + + + D +D DDE E + E E E DS D+ E
Sbjct: 88 AEQGLESDDDDDEEEEWEVEED-EDSDDEGEWIDVESDKEIESSDSEDEEEKDE 140
Score = 25.8 bits (57), Expect = 9.2
Identities = 8/36 (22%), Positives = 19/36 (52%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+ + D +DE+E++E + A+E+ + + E
Sbjct: 125 KEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEE 160
>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 = 26.8 bits (60), Expect = 1.7
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 94 SMDMTDFYVDDYDLDDDDDEDEEEEGEE---GAEEEGGDSGDDSGNG 137
S D+ DYD D D + +EEEEGE+ EE+ + DD +G
Sbjct: 32 SQDLPGL---DYDYDSDAEWEEEEEGEDLESEDEEDEEEDDDDDMDG 75
>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional.
Length = 413
Score = 28.0 bits (62), Expect = 1.8
Identities = 5/31 (16%), Positives = 7/31 (22%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
EE + E S +S
Sbjct: 104 TPSPSGSAEELASGLSPENTSGSSPESPASH 134
>gnl|CDD|235038 PRK02436, xerD, site-specific tyrosine recombinase XerD-like
protein; Reviewed.
Length = 245
Score = 27.6 bits (62), Expect = 2.2
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 54 ENIIRKQVSGGR--IE-ADKDGVKIPMTLEDY 82
E I KQ G+ E A G+K P+TLE Y
Sbjct: 212 EQFILKQKEAGKSIYELARLLGLKSPVTLEKY 243
>gnl|CDD|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute
binding domain. Human SGLT1 (hSGLT1) is a
high-affinity/low-capacity glucose transporter, which
can also transport galactose. In the transport
mechanism, two Na+ ions first bind to the extracellular
side of the transporter and induce a conformational
change in the glucose binding site. This results in an
increased affinity for glucose. A second conformational
change in the transporter follows, bringing the Na+ and
glucose binding sites to the inner surface of the
membrane. Glucose is then released, followed by the Na+
ions. In the process, hSGLT1 is also able to transport
water and urea and may be a major pathway for transport
of these across the intestinal brush-border membrane.
hSGLT1 is encoded by the SLC5A1 gene and expressed
mostly in the intestine, but also in the trachea,
kidney, heart, brain, testis, and prostate. The
WHO/UNICEF oral rehydration solution (ORS) for the
treatment of secretory diarrhea contains salt and
glucose. The glucose, along with sodium ions, is
transported by hSGLT1 and water is either co-transported
along with these or follows by osmosis. Mutations in
SGLT1 are associated with intestinal glucose galactose
malabsorption (GGM). Up-regulation of intestinal SGLT1
may protect against enteric infections. SGLT1 is
expressed in colorectal, head and neck, and prostate
tumors. Epidermal growth factor receptor (EGFR)
functions in cell survival by stabilizing SGLT1, and
thereby maintaining intracellular glucose levels. SGLT1
is predicted to have 14 membrane-spanning regions. This
subgroup belongs to the solute carrier 5
(SLC5)transporter family.
Length = 635
Score = 27.5 bits (61), Expect = 2.3
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 106 DLDDDDDEDEEEEGEEGAEEEGGDSG 131
DLD DD ++E+E E +EE G
Sbjct: 546 DLDADDWTEDEDENEMETDEERKKPG 571
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 27.3 bits (61), Expect = 2.5
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGD 129
DDY +D+DE++E+E EE ++EG
Sbjct: 293 DDYSESEDEDEEDEDEEEEEDDDEGDK 319
Score = 26.9 bits (60), Expect = 3.5
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDD 133
++ + D + EDE+EE E+ EEE D GD
Sbjct: 288 EEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
Score = 26.5 bits (59), Expect = 5.1
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGN 136
+++DD E E+ +E E+E + DD G+
Sbjct: 290 EEEDDYSESEDEDEEDEDEEEEEDDDEGD 318
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 27.5 bits (62), Expect = 2.5
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAE 124
+ + DDD D+D +E+ +EG E
Sbjct: 363 EVEEEDDDDWDDDWDEDDDEGVE 385
>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 = 27.6 bits (61), Expect = 2.6
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+D++E+EE E + G+EEE S + G+GE
Sbjct: 467 GEDEEEEEEVEADNGSEEEMEGSSEGDGDGE 497
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 26.5 bits (59), Expect = 2.7
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 108 DDDDDEDEEEEGEEGAEEEGG 128
+++++E+EEEE EE +EEE
Sbjct: 77 EEEEEEEEEEEEEEESEEEAM 97
Score = 25.0 bits (55), Expect = 8.2
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 109 DDDDEDEEEEGEEGAEEEGGDSG 131
++++E+EEEE EE EE +G
Sbjct: 77 EEEEEEEEEEEEEEESEEEAMAG 99
>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 = 27.0 bits (60), Expect = 3.1
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
+ D+D++D++DEEEE EE E+E D DD
Sbjct: 164 EAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDD 195
Score = 26.6 bits (59), Expect = 4.3
Identities = 12/56 (21%), Positives = 25/56 (44%)
Query: 77 MTLEDYCIKAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGD 132
ED K + ++ + D++++E+EEEE E+ +++ D D
Sbjct: 144 EEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDDD 199
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 27.3 bits (60), Expect = 3.8
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 90 PADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGN 136
+D D ++ V +Y+ DD+ DE +E EE E S D+S N
Sbjct: 926 GSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESEN 972
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 26.8 bits (59), Expect = 3.9
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 91 ADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D + DD + +D DEEE+G++ E+ D+ + G+ +
Sbjct: 262 GDFKGVNYGYESDDDEGSSSNDYDEEEDGDDDDNEDNDDTNTNHGDED 309
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 26.8 bits (60), Expect = 4.0
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 110 DDDEDEEEEGEEGAEEEGGDSG 131
+++E+EEEE EE EE +G
Sbjct: 303 EEEEEEEEEEEEEPSEEEAAAG 324
Score = 26.4 bits (59), Expect = 6.2
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 109 DDDDEDEEEEGEEGAEEEGGDS 130
++++E+EEEE EE +EEE
Sbjct: 303 EEEEEEEEEEEEEPSEEEAAAG 324
>gnl|CDD|234064 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of
this family are homodimeric ferredoxins from nitrogen
fixation regions of many nitrogen-fixing bacteria. As
characterized in Rhodobacter capsulatus, these proteins
are homodimeric, with two 4Fe-4S clusters bound per
monomer. Although nif-specific, this protein family is
not usiveral, as other nitrogenase systems may
substitute flavodoxins, or different types of ferredoxin
[Central intermediary metabolism, Nitrogen fixation].
Length = 91
Score = 25.8 bits (57), Expect = 4.0
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 83 CIKAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEE 117
C K R + + + + DDD+DE E
Sbjct: 29 CYKVCGRDV---LTLKGINEEGELVASDDDDDEIE 60
>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 = 26.5 bits (59), Expect = 4.3
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGN 136
DDD+E++E+EGE+ + S D N
Sbjct: 14 GDDDEEEDEDEGEDEKKVPKESSEPDEAN 42
>gnl|CDD|240226 PTZ00007, PTZ00007, (NAP-L) nucleosome assembly protein -L;
Provisional.
Length = 337
Score = 26.7 bits (59), Expect = 4.5
Identities = 14/63 (22%), Positives = 24/63 (38%)
Query: 75 IPMTLEDYCIKAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDS 134
IP + + +A +D S D D D YD D D + + E++ G+ +
Sbjct: 268 IPYAVYWFLGEAIDEDSDYSSDEDDDDYDSYDSSDSASSDSNSDVDTNEEDDRGEKESNG 327
Query: 135 GNG 137
Sbjct: 328 AKS 330
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved in
conjugation with cellular fusion (mating) and invasive
growth. A high throughput localisation study has
localised RXT2 to the nucleus.
Length = 141
Score = 26.2 bits (58), Expect = 4.7
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 101 YVDDYDLDDDDDEDEEEEGEEGAEEE 126
+D DDDDED+E++ E AE++
Sbjct: 47 IDEDGGDIDDDDEDDEDDEEADAEDD 72
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 25.8 bits (57), Expect = 5.0
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 109 DDDDEDEEEEGEEGAEEEGGDSG 131
+ DE EEEE EE AEEE D
Sbjct: 81 AEADEAEEEEKEEEAEEESDDDM 103
Score = 25.1 bits (55), Expect = 8.2
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSG 131
+ D+ +EEE+ EE EE D
Sbjct: 81 AEADEAEEEEKEEEAEEESDDDML 104
>gnl|CDD|216652 pfam01698, FLO_LFY, Floricaula / Leafy protein. This family
consists of various plant development proteins which are
homologues of floricaula (FLO) and Leafy (LFY) proteins
which are floral meristem identity proteins. Mutations
in the sequences of these proteins affect flower and
leaf development.
Length = 382
Score = 26.5 bits (59), Expect = 5.1
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGD 129
+DDDD+++E++ EG E G +
Sbjct: 200 EDDDDDEDEDDDGEGGGEGGEE 221
Score = 25.7 bits (57), Expect = 9.5
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAE 124
+D D D+D+D+D E GE G E
Sbjct: 199 REDDDDDEDEDDDGEGGGEGGEE 221
>gnl|CDD|221753 pfam12753, Nro1, Nuclear pore complex subunit Nro1. In fission
yeast, this protein is a positive regulator of the
stability of Sre1N, the sterol regulatory
element-binding protein which is an ER membrane-bound
transcription factor that controls adaptation to low
oxygen-growth. In addition, the fission yeast Nro1 is a
direct inhibitor of a protein that inhibits SreN1
degradation, Ofd1 (an oxoglutamate deoxygenase). The
outcome of this reactivity is that Ofd1 acts as an
oxygen sensor that regulates the binding of Nro1 to Ofd1
to control the stability of Sre1N. Solution of the
structure of Nro1 reveals it to be made up of a number
of TPR coils.
Length = 401
Score = 26.4 bits (58), Expect = 5.4
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 89 RPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEE 121
+ D +D+ + + + ++D+ D DEEEE EE
Sbjct: 206 QALDDLLDIVENFGKENEIDEGLDSDEEEEEEE 238
>gnl|CDD|224086 COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and
metabolism].
Length = 598
Score = 26.5 bits (59), Expect = 5.5
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 96 DMTDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDD 133
D++D Y D + + E+ +E + E S +D
Sbjct: 14 DLSDLYPGDELWEAEFLEESKELLKALEFYELILSAED 51
>gnl|CDD|233005 TIGR00516, acpS, holo-[acyl-carrier-protein] synthase. Formerly
dpj. This enzyme adds the prosthetic group,
phosphopantethiene, to the acyl carrier protein (ACP)
apo-enzyme to generate the holo-enzyme. Related
phosphopantethiene--protein transferases also exist.
There is an orthologous domain in eukaryotic proteins
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 121
Score = 26.1 bits (57), Expect = 5.6
Identities = 14/51 (27%), Positives = 20/51 (39%)
Query: 49 CDKEYENIIRKQVSGGRIEADKDGVKIPMTLEDYCIKAKTRPADTSMDMTD 99
K + I +Q+S IE KD P+ Y I K A + +T
Sbjct: 58 FSKAFGTGIGRQLSFQDIEIRKDQNGKPLITLSYIICTKLSIAAVHVSITH 108
>gnl|CDD|233149 TIGR00845, caca, sodium/calcium exchanger 1. The Ca2+:Cation
Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA
family are found ubiquitously, having been identified in
animals, plants, yeast, archaea and widely divergent
bacteria.All of the characterized animal proteins
catalyze Ca2+:Na+ exchange although some also transport
K+. The NCX1 plasma membrane protein exchanges 3 Na+ for
1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+
antiport but may also catalyze Na+:H+ antiport. All
remaining well-characterized members of the family
catalyze Ca2+:H+ exchange.This model is specific for the
eukaryotic sodium ion/calcium ion exchangers of the Caca
family [Transport and binding proteins, Other].
Length = 928
Score = 26.7 bits (59), Expect = 5.7
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 108 DDDDDEDEEEE 118
DDDDDED EE+
Sbjct: 714 DDDDDEDGEEK 724
>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 = 26.2 bits (58), Expect = 5.7
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
+D +L ++D++DE + EE + + E
Sbjct: 12 EDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEE 47
>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family.
This family contains a number of defence peptides
secreted from the skin of amphibians, including the
opiate-like dermorphins and deltorphins, and the
antimicrobial dermoseptins and temporins. The alignment
for this family includes the signal peptide.
Length = 46
Score = 24.6 bits (54), Expect = 6.0
Identities = 8/19 (42%), Positives = 16/19 (84%)
Query: 108 DDDDDEDEEEEGEEGAEEE 126
+D+++ ++EEEGEE +E +
Sbjct: 27 EDEEENEDEEEGEEQSEVK 45
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 26.1 bits (58), Expect = 6.6
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 91 ADTSMDMTDFYVDDYDLDDDDDEDEEEEGEE 121
A+ D T D++LDD+D + E
Sbjct: 6 AEMRADGTWADESDWELDDEDLAELEAAEGG 36
>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2. This family consists
of several Barren protein homologues from several
eukaryotic organisms. In Drosophila Barren (barr) is
required for sister-chromatid segregation in mitosis.
barr encodes a novel protein that is present in
proliferating cells and has homologues in yeast and
human. Mitotic defects in barr embryos become apparent
during cycle 16, resulting in a loss of PNS and CNS
neurons. Centromeres move apart at the
metaphase-anaphase transition and Cyclin B is degraded,
but sister chromatids remain connected, resulting in
chromatin bridging. Barren protein localises to
chromatin throughout mitosis. Colocalisation and
biochemical experiments indicate that Barren associates
with Topoisomerase II throughout mitosis and alters the
activity of Topoisomerase II. It has been suggested that
this association is required for proper chromosomal
segregation by facilitating the decatenation of
chromatids at anaphase. This family forms one of the
three non-structural maintenance of chromosomes (SMC)
subunits of the mitotic condensation complex along with
Cnd1 and Cnd3.
Length = 719
Score = 26.3 bits (58), Expect = 6.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 104 DYDLDDDDDEDEEEEGEEGAEEEGG 128
+ + DD ED++EEG +G E+
Sbjct: 159 ETGREGDDGEDDDEEGSDGEEDGAK 183
>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 = 25.5 bits (55), Expect = 7.2
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDD 133
+D D D D++ED+++E EE +E+ + D+
Sbjct: 10 EDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 26.3 bits (59), Expect = 7.3
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 104 DYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNG 137
D +D + +ED G E E + + ++ +
Sbjct: 171 DGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDE 204
>gnl|CDD|221532 pfam12328, Rpp20, Rpp20 subunit of nuclear RNase MRP and P. The
nuclear RNase P of Saccharomyces cerevisiae is made up
of at least nine protein subunits; Pop1, Pop3, Pop4,
Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these
subunits seem to be present also in the RNase MRP, with
the exception of Rpr2 (Rpp21) which is unique to RNase
P. Human nuclear RNase P and MRP appear to contain at
least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25,
Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although
there is recent evidence that not all of these subunits
are shared between P and MRP. Archaeal RNase P has at
least four protein subunits homologous to eukaryotic
RNase P/MRP proteins. In the yeast RNase P, Pop6 and
Pop7 (the Rpp20 homologue) interact with each other and
they are both interaction partners of Pop4; in the human
MRP Rpp25 and Rpp20 interact with each other and Rpp25
binds to Rpp29 (Pop4).
Length = 108
Score = 25.3 bits (56), Expect = 7.6
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 102 VDDYDLDDDDDEDEEEE 118
VD+ D+DDD+DEE E
Sbjct: 80 VDEIVEDEDDDDDEEPE 96
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 26.2 bits (57), Expect = 7.7
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 95 MDMTDFYVDDY-DLDDDDDED-EEEEGEEGAEEEGGDSGDDSGNGE 138
D +D DD LD DDED + E +E +EEG D S +GE
Sbjct: 715 DDFSDSTSDDEPKLDAIDDEDAKSEGSQESDQEEGLDEIFYSFDGE 760
Score = 26.2 bits (57), Expect = 8.4
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 92 DTSMDMTDFYVDDYDLDDDDDEDEEEE 118
D D +D + + + D+ +E++EEE
Sbjct: 758 DGEQDNSDSFAESSEEDESSEEEKEEE 784
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 26.3 bits (58), Expect = 7.7
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 103 DDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
++ ++E++EEE E A G DS DD E
Sbjct: 2 EEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAE 37
Score = 25.9 bits (57), Expect = 9.7
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 108 DDDDDEDEEEEGEEGAEEEGGDSGDDSGNGEL 139
D D+DE +E +EE + + E+
Sbjct: 26 GSDSDDDEVPAEDEDEDEEDDEEAESPAKAEI 57
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 25.3 bits (56), Expect = 7.8
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 110 DDDEDEEEEGEEGAEEEGGDSGDDSGNG 137
EE++ EE EEE +S +++ G
Sbjct: 73 AAAAAEEKKEEEEEEEEKEESEEEAAAG 100
>gnl|CDD|222440 pfam13897, GOLD_2, Golgi-dynamics membrane-trafficking. Sec14-like
Golgi-trafficking domain The GOLD domain is always found
combined with lipid- or membrane-association domains.
Length = 136
Score = 25.4 bits (56), Expect = 7.9
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 102 VDDYDLDDDDDEDEEEEGEEGAEEEG 127
V + +++++E EEEE E G E G
Sbjct: 51 VSESSDEEEEEEAEEEEAETGDVEAG 76
>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 = 25.9 bits (57), Expect = 7.9
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 83 CIKAKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGE---EGAEEEGGDSGD 132
P ++ D+T+ + D+ D+D+EDE E E EEE + G+
Sbjct: 20 TFGNGKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 26.0 bits (57), Expect = 8.5
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 32 ANVDASVMYRRWRDSKGCD--KEYENIIRKQVSGGRIEADKD 71
A VD+S+ R W D+ G D K+Y I R Q AD +
Sbjct: 1548 AAVDSSLFTRAWVDTAGSDGIKDYHAIERWQSQA--AAADSE 1587
>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain
[Transcription].
Length = 293
Score = 25.8 bits (56), Expect = 8.8
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 86 AKTRPADTSMDMTDFYVDDYDLDDDDDEDEEEEGEEGAE 124
A T+ D F D D D D D E EG +G+
Sbjct: 212 AFKGKPTTAKDEGMF--SDLDDSDVDSGDSEIEGTKGST 248
>gnl|CDD|206527 pfam14359, DUF4406, Domain of unknown function (DUF4406). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
viruses. Proteins in this family are typically between
98 and 145 amino acids in length.
Length = 91
Score = 24.8 bits (55), Expect = 8.9
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 35 DASVMYRRWRDSKGCDKEYE 54
DA M W DSKG E+
Sbjct: 60 DAIYMLPGWEDSKGARLEHA 79
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 26.2 bits (57), Expect = 8.9
Identities = 7/23 (30%), Positives = 17/23 (73%)
Query: 99 DFYVDDYDLDDDDDEDEEEEGEE 121
D +VD+ + +DD++ ++E G++
Sbjct: 209 DTWVDEDEYEDDEEYEDENHGKQ 231
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 25.6 bits (56), Expect = 9.8
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 98 TDFYVDDYDLDDDDDEDEEEEGEEGAEEEGGDSGDDSGNGE 138
D Y + +DD+ E E EEE + G++ E
Sbjct: 54 DDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEE 94
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
0.308 0.132 0.386
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,183,343
Number of extensions: 643438
Number of successful extensions: 3266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2299
Number of HSP's successfully gapped: 464
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 54 (24.6 bits)