RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3828
(365 letters)
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 203 bits (517), Expect = 3e-65
Identities = 87/116 (75%), Positives = 98/116 (84%), Gaps = 3/116 (2%)
Query: 36 MSGRGKGGKAKAKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEY 92
G+GK G KA K +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAV+EY
Sbjct: 1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60
Query: 93 LAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
L AEVLELAGNAA+DNKK RI PRH+QLAIRNDEELNKLL+GVTIA GGVLPNI
Sbjct: 61 LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHK 116
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 198 bits (506), Expect = 6e-64
Identities = 89/106 (83%), Positives = 96/106 (90%)
Query: 42 GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 101
GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAV+EYL AEVLELA
Sbjct: 3 GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62
Query: 102 GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
GNAARDNKK RI PRHLQLA+RNDEELNKLL GVTIA GGVLPNI
Sbjct: 63 GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIH 108
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 194 bits (494), Expect = 6e-62
Identities = 88/115 (76%), Positives = 100/115 (86%), Gaps = 2/115 (1%)
Query: 36 MSGRGK--GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
MSGRGK GG K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAV+EYL
Sbjct: 1 MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYL 60
Query: 94 AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
AAEVLELAGNAARDNKK+RI+PRH+QLA+RNDEEL+KLL GVTIA GGVLPNI +
Sbjct: 61 AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHS 115
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 190 bits (484), Expect = 9e-61
Identities = 87/98 (88%), Positives = 91/98 (92%)
Query: 51 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 110
+RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAV+EYL AEVLELAGNAARDNKK
Sbjct: 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60
Query: 111 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
RI PRHLQLAIRNDEELNKLL GVTIAQGGVLPNI
Sbjct: 61 RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHK 98
>gnl|CDD|197718 smart00427, H2B, Histone H2B.
Length = 97
Score = 178 bits (453), Expect = 3e-56
Identities = 81/97 (83%), Positives = 93/97 (95%)
Query: 267 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 326
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 327 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61 STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 172 bits (438), Expect = 2e-53
Identities = 86/114 (75%), Positives = 98/114 (85%), Gaps = 1/114 (0%)
Query: 35 TMSGRGKGGKAKA-KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
+ + +G GK KA KS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AV+EYL
Sbjct: 4 SGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYL 63
Query: 94 AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
AAEVLELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL VTIA GGVLPNI
Sbjct: 64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIH 117
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 167 bits (424), Expect = 2e-51
Identities = 89/114 (78%), Positives = 98/114 (85%), Gaps = 2/114 (1%)
Query: 38 GRGKGGKAKA--KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
GKGGKA S++RS++AGL FPVGR+ RLL+KGNY R+GAGAPVYLAAV+EYLAA
Sbjct: 3 SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62
Query: 96 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAG 149
E+LELAGNAARDNKK RIIPRHLQLAIRNDEELNKLL VTIAQGGVLPNI G
Sbjct: 63 EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPG 116
>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional.
Length = 116
Score = 166 bits (420), Expect = 4e-51
Identities = 84/121 (69%), Positives = 96/121 (79%), Gaps = 6/121 (4%)
Query: 244 AGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
A S K KKA K K KK + E+Y IYIYKVLKQVHPDTG+SSKAMSIMN
Sbjct: 2 AKTPSKKPAKKAAKGAK------KKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMN 55
Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
SF+NDIFE+IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 56 SFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTS 115
Query: 364 S 364
+
Sbjct: 116 A 116
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 162 bits (411), Expect = 1e-49
Identities = 87/113 (76%), Positives = 98/113 (86%)
Query: 36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
M+GRGKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL A
Sbjct: 1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTA 60
Query: 96 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
EVLELAGNAARDNKK RI+PRH+QLAIRNDEEL KLL VTIA GGVLPNI A
Sbjct: 61 EVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHA 113
>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional.
Length = 117
Score = 140 bits (353), Expect = 3e-41
Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)
Query: 253 KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 310
KK KA+K D KK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 311 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
E+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64 EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 131 bits (331), Expect = 1e-37
Identities = 72/114 (63%), Positives = 84/114 (73%), Gaps = 2/114 (1%)
Query: 35 TMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYL 93
T + K K K K +RSSRAGLQFPVGRIHR L++ A RVGA A VY AA++EYL
Sbjct: 14 TTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYL 73
Query: 94 AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
AEVLELAGNA++D K RI PRHLQLAIR DEEL+ L+ G TIA GGV+P+I
Sbjct: 74 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIH 126
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 104 bits (261), Expect = 2e-27
Identities = 54/110 (49%), Positives = 75/110 (68%), Gaps = 2/110 (1%)
Query: 44 KAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN 103
KA RS++AGL FPVGR+ LLR+G YA R+GA VY+AAV+EYL AE+LEL+
Sbjct: 10 KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69
Query: 104 AARDN--KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA 151
AA K R+ PR + LA+R+D++L LL VT+++GGV+P++ A
Sbjct: 70 AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALA 119
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 92.2 bits (230), Expect = 2e-23
Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 52 RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 110
S L+ P R+ R L++G YAE R+ + APV L +E L E+LE AG AR K+
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 111 TRIIPRHLQLAIRND 125
I PR +QLA+R D
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 90.3 bits (225), Expect = 9e-23
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 271 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 326
R + +V++++ +SSKA + + D+ E I ++ LA + KR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 327 STITSREIQTAVRLL 341
TIT R+IQ AVRL
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|165723 PLN00155, PLN00155, histone H2A; Provisional.
Length = 58
Score = 79.4 bits (195), Expect = 5e-19
Identities = 41/58 (70%), Positives = 50/58 (86%)
Query: 36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
M+GRGKG + K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL
Sbjct: 1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 42.3 bits (99), Expect = 4e-05
Identities = 18/82 (21%), Positives = 37/82 (45%)
Query: 59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 118
+FP+ R+ ++++ +VG PV + +E E++ L+ AR R+ L
Sbjct: 23 RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFL 82
Query: 119 QLAIRNDEELNKLLSGVTIAQG 140
+ A +DE+ + L +
Sbjct: 83 KRATESDEKFDFLKNMEQFKNR 104
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 35.3 bits (82), Expect = 0.003
Identities = 14/63 (22%), Positives = 28/63 (44%)
Query: 60 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 119
P+ R+ R+++ A R+ A +A +E + A + K+ I H++
Sbjct: 3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62
Query: 120 LAI 122
LA+
Sbjct: 63 LAV 65
Score = 30.7 bits (70), Expect = 0.14
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 338
+ +++K +S A ++ V + E IA+E++ + KR TI + I+ AV
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 30.8 bits (70), Expect = 0.23
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 294 VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 344
VSS A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 31.2 bits (71), Expect = 0.82
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 246 KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIY----IYKVLKQVHPDTGVSSKAMSI 301
++ +V K+I + + + +E + + L + D S K ++
Sbjct: 98 EAKATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNL 157
Query: 302 M---NSFVNDIFERIAAESSRLAHYNKR 326
S + E + S +LA
Sbjct: 158 KDDLESLIASAKEELDQLSKKLAELKAE 185
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are not universally
involved for transcription as are GTFs. In yeast and
human cells, TAFs have been found as components of other
complexes besides TFIID. Several TAFs interact via
histone-fold (HFD) motifs; the HFD is the interaction
motif involved in heterodimerization of the core
histones and their assembly into nucleosome octamers.
The minimal HFD contains three alpha-helices linked by
two loops and is found in core histones, TAFs and many
other transcription factors. TFIID has a histone
octamer-like substructure. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 27.6 bits (62), Expect = 2.2
Identities = 10/51 (19%), Positives = 25/51 (49%)
Query: 285 LKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 335
LK++ P + ++ +D + + ++ RLA + K T+ +++Q
Sbjct: 11 LKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQ 61
>gnl|CDD|220258 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
(CRISPR_cse1). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry, represented by
CT1972 from Chlorobaculum tepidum, is found in the
CRISPR/Cas subtype Ecoli regions of many bacteria (most
of which are mesophiles), and not in Archaea. It is
designated Cse1.
Length = 475
Score = 30.0 bits (68), Expect = 2.3
Identities = 17/99 (17%), Positives = 31/99 (31%), Gaps = 16/99 (16%)
Query: 210 TDGGLGDSLDVVTEYFPVP--------LGASFSESLSSLTTAAGKSSGKAVKKAGKAQKN 261
D + + P+P L A E++ A ++ A+K+A A
Sbjct: 356 MDNMQAKWYEWRMDLLPLPAALLSDEDLRAQIKEAVD-AAEEAARALRSALKEAWFALGK 414
Query: 262 IAKSDKKKKHRRKESYAIY-------IYKVLKQVHPDTG 293
AK DK + + ++L + D
Sbjct: 415 DAKGDKSFVDLAGRAEERFWQRLESAFRRLLADLEEDDD 453
>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID
subunit A.
Length = 67
Score = 27.3 bits (61), Expect = 2.6
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 335
+ +++Q+ +T + ++ +D E + + +LA + K + R+IQ
Sbjct: 5 LQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQ 59
>gnl|CDD|132835 cd00147, cPLA2_like, Cytosolic phospholipase A2, catalytic domain;
hydrolyses arachidonyl phospholipids. Catalytic domain
of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4)
hydrolyzes the sn-2-acyl ester bond of phospholipids to
release arachidonic acid. At the active site, cPLA2
contains a serine nucleophile through which the
catalytic mechanism is initiated. The active site is
partially covered by a solvent-accessible flexible lid.
cPLA2 displays interfacial activation as it exists in
both "closed lid" and "open lid" forms. Movement of the
cPLA2 lid possibly exposes a greater hydrophobic surface
and the active site. cPLA2 belongs to the alpha-beta
hydrolase family which is identified by a characteristic
nucleophile elbow with a consensus sequence of
Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu =
nucleophile). Calcium is required for cPLA2 to bind with
membranes or phospholipids. Group IV cPLA2 includes six
intercellular enzymes: cPLA2alpha, cPLA2beta,
cPLA2gamma, cPLA2delta, cPLA2epsilon, and cPLA2zeta.
Length = 438
Score = 29.5 bits (67), Expect = 3.4
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 7 LFCKRNDSSITQSRSFSIPGAVPIPQIYTMSGR 39
L + DSS++ R F G P+P IYT
Sbjct: 157 LLKELTDSSLSDQREFVQNGQNPLP-IYTALNV 188
>gnl|CDD|237406 PRK13515, PRK13515, carboxylate-amine ligase; Provisional.
Length = 371
Score = 28.8 bits (65), Expect = 4.9
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 62 VGRIHRLLRKGNYAER---VGAGAPVYLAAVMEYLAAEVLE 99
V +L +G A+R V A L AV+++L E LE
Sbjct: 326 VEYARTILEEGTSADRQLRVYAETGGALRAVVDWLIEETLE 366
>gnl|CDD|233866 TIGR02435, CobG, precorrin-3B synthase. An iron-sulfur protein. An
oxygen atom from dioxygen is incorporated into the
macrocycle at C-20. In the aerobic cobalamin biosythesis
pathway, four enzymes are involved in the conversion of
precorrin-3A to precorrin-6A. The first of the four
steps is carried out by EC 1.14.13.83, precorrin-3B
synthase (CobG), yielding precorrin-3B as the product.
This is followed by three methylation reactions, which
introduce a methyl group at C-17 (CobJ; EC 2.1.1.131),
C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152)
of the macrocycle, giving rise to precorrin-4,
precorrin-5 and precorrin-6A, respectively [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 390
Score = 27.8 bits (62), Expect = 8.9
Identities = 32/133 (24%), Positives = 51/133 (38%), Gaps = 10/133 (7%)
Query: 53 SSRAGLQF-PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKT 111
++R LQ + H L + A +GA A + EV LAG + T
Sbjct: 52 TARGNLQLRGLTADHDALSQALLAAGLGAAGA----AADDIRNIEVSPLAGIDPGEIADT 107
Query: 112 RIIPRHLQLAIRNDEELNKLLS--GVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLG 169
R + L+ A+ N+ L +L V I GG L + A + + + G G++
Sbjct: 108 RPLAAELRAALENERALLELPPKFSVAIDGGGRLVLLGDTADVRLQALTT---GAGVAWV 164
Query: 170 VLGVGDGVADHVL 182
V G + L
Sbjct: 165 VSLAGISTSARSL 177
>gnl|CDD|177669 PLN00035, PLN00035, histone H4; Provisional.
Length = 103
Score = 26.3 bits (58), Expect = 9.8
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 36 MSGRGKGG----KAKAKSKTRSSRAGLQ-FPVGRIHRLLRKG 72
MSGRGKGG K AK + R +Q I RL R+G
Sbjct: 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRG 42
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
0.313 0.130 0.356
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,156,596
Number of extensions: 1789799
Number of successful extensions: 1493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1479
Number of HSP's successfully gapped: 45
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (27.1 bits)