RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14666
(256 letters)
>gnl|CDD|238729 cd01452, VWA_26S_proteasome_subunit, 26S proteasome plays a major
role in eukaryotic protein breakdown, especially for
ubiquitin-tagged proteins. It is an ATP-dependent
protease responsible for the bulk of non-lysosomal
proteolysis in eukaryotes, often using covalent
modification of proteins by ubiquitylation. It consists
of a 20S proteolytic core particle (CP) and a 19S
regulatory particle (RP). The CP is an ATP independent
peptidase consisting of hydrolyzing activities. One or
both ends of CP carry the RP that confers both ubiquitin
and ATP dependence to the 26S proteosome. The RP's
proposed functions include recognition of substrates and
translocation of these to CP for proteolysis. The RP can
dissociate into a stable lid and base subcomplexes. The
base is composed of three non-ATPase subunits (Rpn 1, 2
and 10). A single residue in the vWA domain of Rpn10 has
been implicated to be responsible for stabilizing the
lid-base association.
Length = 187
Score = 231 bits (591), Expect = 3e-77
Identities = 95/155 (61%), Positives = 116/155 (74%), Gaps = 3/155 (1%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMA-DSVEVLATLTSDVGRILSK 59
MRNGD+ PTR QAQ DAVNL+C +KTRSNPENNVGL+ MA +S EVL TLT+D G+ILSK
Sbjct: 16 MRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEVLVTLTNDQGKILSK 75
Query: 60 LHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKE 119
LH VQP G NF+TGI+IA LALKHRQ KN K RI+AFVGSP++ +E++L KLAKRLKK
Sbjct: 76 LHDVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKN 135
Query: 120 KVNVDIVSFGEEREGGKGQDEEEEEVQNTDRPNCH 154
V+VDI++FGE + + + V D H
Sbjct: 136 NVSVDIINFGEIDDNTEKLTAFIDAVNGKD--GSH 168
Score = 93.6 bits (233), Expect = 1e-23
Identities = 35/50 (70%), Positives = 43/50 (86%)
Query: 205 TSLNVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMA 254
T + +DNS++MRNGD+ PTR QAQ DAVNL+C +KTRSNPENNVGL+ MA
Sbjct: 6 TMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMA 55
>gnl|CDD|227477 COG5148, RPN10, 26S proteasome regulatory complex, subunit
RPN10/PSMD4 [Posttranslational modification, protein
turnover, chaperones].
Length = 243
Score = 131 bits (330), Expect = 2e-37
Identities = 61/134 (45%), Positives = 85/134 (63%), Gaps = 1/134 (0%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMAD-SVEVLATLTSDVGRILSK 59
+NGD+LPTR +AQ+DAV + K NPEN +GL+ + VL+T T G+IL+
Sbjct: 16 SQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQAQPNVLSTPTKQRGKILTF 75
Query: 60 LHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKE 119
LH ++ +G + M ++IA L LKHR K + RI+AFVGSP+ E EL +LAK+LKK
Sbjct: 76 LHDIRLHGGADIMRCLQIAQLILKHRDNKGQRQRIVAFVGSPIQESEDELIRLAKQLKKN 135
Query: 120 KVNVDIVSFGEERE 133
V +DI+ FGE
Sbjct: 136 NVAIDIIFFGEAAN 149
Score = 58.1 bits (140), Expect = 5e-10
Identities = 23/52 (44%), Positives = 35/52 (67%)
Query: 204 TTSLNVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMAE 255
T + +DNS+ +NGD+LPTR +AQ+DAV + K NPEN +GL+ + +
Sbjct: 5 ATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQ 56
>gnl|CDD|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain. VWA
domains in extracellular eukaryotic proteins mediate
adhesion via metal ion-dependent adhesion sites (MIDAS).
Intracellular VWA domains and homologues in prokaryotes
have recently been identified. The proposed VWA domains
in integrin beta subunits have recently been
substantiated using sequence-based methods.
Length = 175
Score = 56.3 bits (136), Expect = 7e-10
Identities = 25/129 (19%), Positives = 46/129 (35%), Gaps = 7/129 (5%)
Query: 8 PTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATL--TSDVGRILSKLHQVQP 65
R + ++ V + + VGL+ +D VL L + +L L +
Sbjct: 14 GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDARVLFPLNDSRSKDALLEALASLSY 73
Query: 66 NGNINFMTG--IRIAHLALKHRQGKNHKMR---IIAFVGSPVDLEERELTKLAKRLKKEK 120
G ++ A L + + + +I + ++L K AK LK+
Sbjct: 74 KLGGGTNLGAALQYALENLFSKSAGSRRGAPKVVILITDGESNDGPKDLLKAAKELKRSG 133
Query: 121 VNVDIVSFG 129
V V +V G
Sbjct: 134 VKVFVVGVG 142
>gnl|CDD|222192 pfam13519, VWA_2, von Willebrand factor type A domain.
Length = 172
Score = 53.5 bits (129), Expect = 6e-09
Identities = 32/140 (22%), Positives = 52/140 (37%), Gaps = 13/140 (9%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKL 60
M D P+RL + A+ + P + VGL+A A S ++ LT D + + L
Sbjct: 12 MNATDLKPSRLTRAKAAIADL----LARLPGDRVGLIAFAGSAYLVLPLTDDRAALAAAL 67
Query: 61 HQVQ----PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRL 116
+ P G N + LAL+ G I + + L + A L
Sbjct: 68 PALSPRIMPGGGTNLAAALA---LALRLLAGAGGGSGAIVLITD--GEDTPSLLEAASAL 122
Query: 117 KKEKVNVDIVSFGEEREGGK 136
K+ V V ++ G +
Sbjct: 123 KQAGVRVYVLGVGTDEGAED 142
Score = 31.5 bits (72), Expect = 0.20
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 209 VDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMAE 255
+D S M D P+RL + A+ + P + VGL+A A
Sbjct: 6 LDVSGSMNATDLKPSRLTRAKAAIADL----LARLPGDRVGLIAFAG 48
>gnl|CDD|238119 cd00198, vWFA, Von Willebrand factor type A (vWA) domain was
originally found in the blood coagulation protein von
Willebrand factor (vWF). Typically, the vWA domain is
made up of approximately 200 amino acid residues folded
into a classic a/b para-rossmann type of fold. The vWA
domain, since its discovery, has drawn great interest
because of its widespread occurrence and its involvement
in a wide variety of important cellular functions. These
include basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains.
Length = 161
Score = 51.8 bits (124), Expect = 2e-08
Identities = 28/129 (21%), Positives = 54/129 (41%), Gaps = 6/129 (4%)
Query: 8 PTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLT-----SDVGRILSKLHQ 62
+L ++A+ + S + S P + VGL+ + V+ LT +D+ + L +
Sbjct: 15 GEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDKADLLEAIDALKK 74
Query: 63 VQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVN 122
G N +R+A LK + N + II + L + A+ L+K +
Sbjct: 75 -GLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDGEPNDGPELLAEAARELRKLGIT 133
Query: 123 VDIVSFGEE 131
V + G++
Sbjct: 134 VYTIGIGDD 142
>gnl|CDD|238730 cd01453, vWA_transcription_factor_IIH_type, Transcription factors
IIH type: TFIIH is a multiprotein complex that is one of
the five general transcription factors that binds RNA
polymerase II holoenzyme. Orthologues of these genes are
found in all completed eukaryotic genomes and all these
proteins contain a VWA domain. The p44 subunit of TFIIH
functions as a DNA helicase in RNA polymerase II
transcription initiation and DNA repair, and its
transcriptional activity is dependent on its C-terminal
Zn-binding domains. The function of the vWA domain is
unclear, but may be involved in complex assembly. The
MIDAS motif is not conserved in this sub-group.
Length = 183
Score = 38.5 bits (90), Expect = 0.001
Identities = 29/133 (21%), Positives = 56/133 (42%), Gaps = 3/133 (2%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADS-VEVLATLTSDVGRILSK 59
M D P+RL + L NP + +G++++ + E L LT + + +
Sbjct: 16 MEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQA 75
Query: 60 LHQVQ-PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKK 118
L + +G + G+ +A +LKH + +I F S + + + +LKK
Sbjct: 76 LKTARECSGEPSLQNGLEMALESLKHMPSHGSREVLIIF-SSLSTCDPGNIYETIDKLKK 134
Query: 119 EKVNVDIVSFGEE 131
E + V ++ E
Sbjct: 135 ENIRVSVIGLSAE 147
Score = 28.1 bits (63), Expect = 3.1
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 209 VDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAM 253
+D S M D P+RL + L NP + +G++++
Sbjct: 10 IDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISI 54
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1; Validated.
Length = 108
Score = 35.0 bits (81), Expect = 0.008
Identities = 29/82 (35%), Positives = 39/82 (47%), Gaps = 15/82 (18%)
Query: 39 MADSVEVLATLTSDVGRILS-KLHQVQPNGNINFMTGI-RIAHLALKHRQGKNHKMRIIA 96
M+DS L T D GRI K +P G+ GI RI RQ K + +
Sbjct: 1 MSDSNSRLVYST-DTGRIDEEKAKPERPKGD-----GIVRI------QRQTSGRKGKGVC 48
Query: 97 FVGSPVDLEERELTKLAKRLKK 118
+ + +DL++ EL KLA LKK
Sbjct: 49 LI-TGLDLDDAELKKLAAELKK 69
>gnl|CDD|190848 pfam04056, Ssl1, Ssl1-like. Ssl1-like proteins are 40kDa subunits
of the Transcription factor II H complex.
Length = 193
Score = 35.9 bits (83), Expect = 0.010
Identities = 28/135 (20%), Positives = 50/135 (37%), Gaps = 5/135 (3%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRI---- 56
M D P+R + NP + +GL+ D T + R+
Sbjct: 8 MEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKA 67
Query: 57 LSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRL 116
L L + + G+ + + +A +LKH + +I F GS + ++ L
Sbjct: 68 LKSLREAECGGDPSLQNALELARASLKHVPSHGSREVLIIF-GSLSTCDPGDIYSTIDTL 126
Query: 117 KKEKVNVDIVSFGEE 131
KKEK+ ++ E
Sbjct: 127 KKEKIRCSVIGLSAE 141
>gnl|CDD|238742 cd01465, vWA_subgroup, VWA subgroup: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Not much is known about the function of the VWA
domain in these proteins. The members do have a
conserved MIDAS motif. The biochemical function however
is not known.
Length = 170
Score = 34.6 bits (80), Expect = 0.022
Identities = 24/138 (17%), Positives = 54/138 (39%), Gaps = 18/138 (13%)
Query: 3 NGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVL--ATLTSDVGRILSKL 60
+G LP A + V+ + P++ + ++ + E + AT D IL+ +
Sbjct: 14 DGPKLPLVKSALKLLVD-------QLRPDDRLAIVTYDGAAETVLPATPVRDKAAILAAI 66
Query: 61 HQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRII------AFVGSPVDLEERELTKLAK 114
++ G+ GI++ + + RI+ VG + EL +L
Sbjct: 67 DRLTAGGSTAGGAGIQLGYQEAQKHFVPGGVNRILLATDGDFNVGET---DPDELARLVA 123
Query: 115 RLKKEKVNVDIVSFGEER 132
+ ++ + + + FG+
Sbjct: 124 QKRESGITLSTLGFGDNY 141
>gnl|CDD|153226 cd03132, GATase1_catalase, Type 1 glutamine amidotransferase
(GATase1)-like domain found in at the C-terminal of
several large catalases. Type 1 glutamine
amidotransferase (GATase1)-like domain found in at the
C-terminal of several large catalases. Catalase
catalyzes the dismutation of hydrogen peroxide (H2O2) to
water and oxygen. This group includes the large
catalases: Neurospora crassa Catalase-1 and Catalase-3
and, Escherichia coli HP-II. This GATase1-like domain
has an essential role in HP-II catalase activity.
However, it lacks enzymatic activity and the catalytic
triad typical of GATase1 domains. Catalase-1 and -3 are
homotetrameric, HP-II is homohexameric. It has been
proposed that this domain may facilitate the folding and
oligomerization process. The interface between this
GATase1-like domain of HP-II and the core of the subunit
forms part of a channel which provides access to the
deeply buried catalase active sites of HPII. Catalase-1
is associated with non-growing cells; Catalase-3 is
associated with growing conditions. HP-II is produced in
stationary phase. Catalase-1 is induced by ethanol and
heat shock. Catalase-3 is induced under stress
conditions such a hydrogen peroxide, paraquat, cadmium,
heat shock, uric acid and nitrate treatment.
Length = 142
Score = 33.8 bits (78), Expect = 0.029
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 5/57 (8%)
Query: 93 RIIA-FVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEREGGKGQDEEEEEVQNT 148
R + V VD E L+ L LK NV +V G D + EV T
Sbjct: 2 RKVGILVADGVDAAE--LSALKAALKAAGANVKVV--APTLGGVVDSDGKTLEVDQT 54
>gnl|CDD|203195 pfam05189, RTC_insert, RNA 3'-terminal phosphate cyclase (RTC),
insert domain. RNA cyclases are a family of
RNA-modifying enzymes that are conserved in all cellular
organisms. They catalyze the ATP-dependent conversion of
the 3'-phosphate to the 2',3'-cyclic phosphodiester at
the end of RNA, in a reaction involving formation of the
covalent AMP-cyclase intermediate. The structure of RTC
demonstrates that RTCs are comprised two domain. The
larger domain contains an insert domain of approximately
100 amino acids.
Length = 101
Score = 31.4 bits (72), Expect = 0.10
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 86 QGKNHKMRIIAFVGS-PVDLEERELTKLAKRLKKEKVNVDIVSFGEEREGGKG 137
+G+ ++R +A+V P + ER L K +V I + R+ GK
Sbjct: 3 RGRIKRIRGVAYVARVPPHVAERMADAARGVLNKPLPDVYIETDKRGRDSGKS 55
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 33.4 bits (76), Expect = 0.11
Identities = 26/137 (18%), Positives = 50/137 (36%), Gaps = 11/137 (8%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDV-GRILSK 59
M DFLPTR NP + + ++++ D A TS + G +
Sbjct: 100 MDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRD---GCAKYTSSMDGNPQAH 156
Query: 60 LHQV----QPNGNINFMTGIRIAHLALKHRQGKNHKMR-IIAFVGSPVDLEERELTKLAK 114
+ Q+ +GN + + +A + L H R ++ GS + ++ +
Sbjct: 157 IGQLKSKRDCSGNFSLQNALEMARIELMKN--TMHGTREVLIIFGSTSTRDPGDIAETID 214
Query: 115 RLKKEKVNVDIVSFGEE 131
+L + V + E
Sbjct: 215 KLVAYNIRVHFIGLCAE 231
>gnl|CDD|184242 PRK13685, PRK13685, hypothetical protein; Provisional.
Length = 326
Score = 32.0 bits (73), Expect = 0.24
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSD 52
MR D P RL A Q+A T P N+GL+A A + VL + T++
Sbjct: 101 MRATDVEPNRLAAAQEAAKQFADELT---PGINLGLIAFAGTATVLVSPTTN 149
Score = 31.2 bits (71), Expect = 0.47
Identities = 24/67 (35%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 188 TSLVRCPHVSHVVAMITTSLNVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENN 247
T VR P VV ++ +D S MR D P RL A Q+A T P N
Sbjct: 79 THDVRIPRNRAVVMLV-----IDVSQSMRATDVEPNRLAAAQEAAKQFADELT---PGIN 130
Query: 248 VGLLAMA 254
+GL+A A
Sbjct: 131 LGLIAFA 137
>gnl|CDD|217511 pfam03358, FMN_red, NADPH-dependent FMN reductase.
Length = 151
Score = 29.9 bits (68), Expect = 0.79
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 12/60 (20%)
Query: 92 MRIIAFVGSPVDLEERE-------LTKLAKRLKKEKVNVDIVSFGEEREGGKGQDEEEEE 144
M+I+ GSP R+ A+ L++ V+++ + +D E
Sbjct: 1 MKILVISGSP-----RKGSNTRKLAEWAAELLEEAGAEVELIDLADLPLPLYDEDLEACG 55
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 29.5 bits (67), Expect = 1.2
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 68 NINFMTGIRIAHLALKHRQGKNHKMRIIAFVGS 100
++N+ + +AH L K + I FV S
Sbjct: 111 DVNYFGSLNVAHAVLPL--MKEQRPGHIVFVSS 141
>gnl|CDD|143398 cd07079, ALDH_F18-19_ProA-GPR, Gamma-glutamyl phosphate reductase
(GPR), aldehyde dehydrogenase families 18 and 19.
Gamma-glutamyl phosphate reductase (GPR), a L-proline
biosynthetic pathway (PBP) enzyme that catalyzes the
NADPH dependent reduction of L-gamma-glutamyl
5-phosphate into L-glutamate 5-semialdehyde and
phosphate. The glutamate route of the PBP involves two
enzymatic steps catalyzed by gamma-glutamyl kinase (GK,
EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are
fused into the bifunctional enzyme, ProA or
delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in
plants and animals, whereas they are separate enzymes in
bacteria and yeast. In humans, the P5CS (ALDH18A1), an
inner mitochondrial membrane enzyme, is essential to the
de novo synthesis of the amino acids proline and
arginine. Tomato (Lycopersicon esculentum) has both the
prokaryotic-like polycistronic operons encoding GK and
GPR (PRO1, ALDH19) and the full-length, bifunctional
P5CS (PRO2, ALDH18B1).
Length = 406
Score = 29.7 bits (68), Expect = 1.4
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 36 LLAMADSVEVLATLTSDVGRILSKLHQVQPNG 67
+ AMA+ + +A L VG +L PNG
Sbjct: 71 IEAMAEGLRQVAALPDPVGEVLRG--WTLPNG 100
>gnl|CDD|234685 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
Length = 417
Score = 29.7 bits (68), Expect = 1.7
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 36 LLAMADSVEVLATLTSDVGRILSKLHQVQPNG 67
+ +A+ + +A L VG +L PNG
Sbjct: 77 IEGIAEGLRQVAALPDPVGEVLD--GWTLPNG 106
>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 = 29.0 bits (65), Expect = 2.0
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 81 ALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEREGGKGQDE 140
A K K ++ F D++E+ K + E +VD EE E + ++E
Sbjct: 126 AGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVD-----EEDEKDEEEEE 180
Query: 141 EEEEV 145
EEEE
Sbjct: 181 EEEEE 185
>gnl|CDD|187769 cd09638, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas2 is present in majority of CRISPR/Cas systems along
with Cas1; RNAse specific to U-rich regions; Possesses
an RRM/ferredoxin fold.
Length = 90
Score = 27.3 bits (61), Expect = 3.0
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 92 MRIIAFVGSPVDLEERELTKLAKRLKKE 119
M ++ P D E + KL K L+K
Sbjct: 1 MLVLVVYDIPEDTERKRRRKLRKLLEKY 28
>gnl|CDD|223784 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial
oligomycin sensitivity protein) [Energy production and
conversion].
Length = 178
Score = 28.0 bits (63), Expect = 3.9
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 90 HKMRIIAFVGSPVDLEERELTKLAKRLKKE-----KVNVDI 125
+ + A V S +L + +LTKL +L+K+ K+N I
Sbjct: 105 SRGIVEAEVTSAFELSDEQLTKLEAKLEKKFGKKVKLNNKI 145
>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional.
Length = 667
Score = 28.3 bits (64), Expect = 4.7
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 86 QGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNV-DIVSF 128
GK K RI+ + LE+R + K + EKV V DI F
Sbjct: 320 AGKGTKTRIVTLTRDKIRLEDRAVKMSVKTVGGEKVGVLDIPGF 363
>gnl|CDD|234956 PRK01490, tig, trigger factor; Provisional.
Length = 435
Score = 28.2 bits (64), Expect = 5.0
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 14/53 (26%)
Query: 100 SPVDLEERELTKLAKRLK----KE-------KVNVDIVSF--GEEREGGKGQD 139
+ D++E EL +L K+ E +V +D V GEE EGGK +D
Sbjct: 133 TDEDVDE-ELERLRKQFATLVPVERPAENGDRVTIDFVGSIDGEEFEGGKAED 184
>gnl|CDD|218615 pfam05504, Spore_GerAC, Spore germination B3/ GerAC like,
C-terminal. The GerAC protein of the Bacillus subtilis
spore is required for the germination response to
L-alanine. Members of this family are thought to be
located in the inner spore membrane. Although the
function of this family is unclear, they are likely to
encode the components of the germination apparatus that
respond directly to this germinant, mediating the
spore's response.
Length = 171
Score = 27.5 bits (62), Expect = 5.4
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 106 ERELTKLAKRLKKEKVNVDIVSFGEE 131
++E+ KL K+L+KE VDI FGE
Sbjct: 107 KKEIEKLIKKLQKEY-KVDIFGFGEY 131
>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 = 6.1
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 99 GSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEREGGKGQDEEEEEVQNTDRPNCH 154
GS +E L ++ E+ N D SF E E + +EE+EE +N +
Sbjct: 740 GSQESDQEEGLDEIFYSFDGEQDNSD--SFAESSEEDESSEEEKEEEENKEVSAKR 793
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 27.6 bits (62), Expect = 6.9
Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 13/67 (19%)
Query: 95 IAFVGSPVDLEERELT----KLAKRLKKEKVNVDIVSFGEER---------EGGKGQDEE 141
+ +VG V+ R+L KL + K EKV EER + GQ E
Sbjct: 89 VGYVGRDVESIIRDLVEIAVKLVREEKIEKVKDKAEELAEERILDALVPPAKNFWGQSEN 148
Query: 142 EEEVQNT 148
++E T
Sbjct: 149 KQESSAT 155
>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011).
This is a family of fungal proteins whose function is
unknown.
Length = 130
Score = 26.9 bits (60), Expect = 7.0
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 83 KHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKV 121
+ R GK K RI + E E K ++ +++K
Sbjct: 85 RKRPGK--KRRIALRLRRERTKERAEKEKRTRKNREKKF 121
>gnl|CDD|236324 PRK08652, PRK08652, acetylornithine deacetylase; Provisional.
Length = 347
Score = 27.4 bits (61), Expect = 7.5
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 113 AKRLKK--EKVNVDIVSFGEEREGGKG 137
+ L K E +NV I +E EGG+G
Sbjct: 99 LEELGKEFEDLNVGIAFVSDEEEGGRG 125
>gnl|CDD|185090 PRK15136, PRK15136, multidrug efflux system protein EmrA;
Provisional.
Length = 390
Score = 27.4 bits (61), Expect = 8.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 205 TSLNVDNSDFMRNGDFLPT--RLQAQQ 229
T + DN+DF++ GD L T A+Q
Sbjct: 73 TKVWADNTDFVKEGDVLVTLDPTDAEQ 99
>gnl|CDD|216322 pfam01137, RTC, RNA 3'-terminal phosphate cyclase. RNA cyclases
are a family of RNA-modifying enzymes that are conserved
in all cellular organisms. They catalyze the
ATP-dependent conversion of the 3'-phosphate to the
2',3'-cyclic phosphodiester at the end of RNA, in a
reaction involving formation of the covalent AMP-cyclase
intermediate. The structure of RTC demonstrates that
RTCs are comprised two domain. The larger domain
contains an insert domain of approximately 100 amino
acids.
Length = 330
Score = 27.2 bits (61), Expect = 8.7
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 86 QGKNHKMRIIAFV-GSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEREGGKGQ 138
+GK K+R IA+ P + ERE RL K +V IV+ + G
Sbjct: 179 RGKVKKIRGIAYSTRVPPHVAEREADAAKARLNKLLPDVYIVTDVRRGDTGGSG 232
>gnl|CDD|236250 PRK08373, PRK08373, aspartate kinase; Validated.
Length = 341
Score = 27.3 bits (61), Expect = 9.0
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 91 KMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVS 127
KM ++ F GS V + E +L K L +E V +VS
Sbjct: 4 KMIVVKFGGSSVRYDFEEALELVKYLSEENEVVVVVS 40
>gnl|CDD|215793 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D
subunit from E. coli is the same as the OSCP subunit
which is this family. The ATP D subunit from metazoa are
found in family pfam00401.
Length = 171
Score = 26.7 bits (60), Expect = 9.3
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 90 HKMRIIAFVGSPVDLEERELTKLAKRLKKE---KVNVDIV 126
H+ + A V S V L E +L L L+K+ KV ++
Sbjct: 99 HRGIVEATVTSAVPLSEEQLKALKAALEKKTGKKVKLETK 138
>gnl|CDD|241245 cd01209, PTB_Shc, Shc-like phosphotyrosine-binding (PTB) domain.
Shc is a substrate for receptor tyrosine kinases, which
can interact with phosphoproteins at NPXY motifs. Shc
contains an PTB domain followed by an SH2 domain. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Shc-like subgroup.
Length = 170
Score = 26.8 bits (60), Expect = 9.9
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 1 MRNGDFLPTRLQAQQDAVNLVC 22
MR+ DF TR Q ++A+N VC
Sbjct: 31 MRSLDF-NTRTQVTREAINRVC 51
Score = 26.8 bits (60), Expect = 9.9
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 215 MRNGDFLPTRLQAQQDAVNLVC 236
MR+ DF TR Q ++A+N VC
Sbjct: 31 MRSLDF-NTRTQVTREAINRVC 51
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
0.314 0.130 0.367
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,541,755
Number of extensions: 1159648
Number of successful extensions: 963
Number of sequences better than 10.0: 1
Number of HSP's gapped: 954
Number of HSP's successfully gapped: 47
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.3 bits)