RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780333|ref|YP_003064746.1| alanine racemase [Candidatus
Liberibacter asiaticus str. psy62]
(370 letters)
>gnl|CDD|31130 COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer
membrane].
Length = 360
Score = 330 bits (847), Expect = 4e-91
Identities = 151/364 (41%), Positives = 209/364 (57%), Gaps = 13/364 (3%)
Query: 8 RLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEE 67
+IDL AL++N ++ L+G A+ AVVK NAYG G ++A AL +AG F V S+EE
Sbjct: 6 TAEIDLGALRHNLRALRELAGPAKLMAVVKANAYGHGAVRVAKALLDAGADGFGVASLEE 65
Query: 68 GVKLRLYTPQ-ARIFVLYGIHPGQE-KIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYA 125
++LR A I VL G P +E ++ NL PV++S+ QL
Sbjct: 66 AIELREAGITGAPILVLEGFFPAEELELAAAYNLTPVVNSLEQLEALKNAALKNKPLKVH 125
Query: 126 LQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTL 185
L++DTG NRLGL +EA+ + K L I SH ACAD+P QLERF
Sbjct: 126 LKIDTGMNRLGLRPEEAVALAIDLIALKNLDLEGIFSHFACADEPEDPYTLKQLERFNLA 185
Query: 186 ISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILI 245
G + LA+S+G+LLGP+YHF + RPGI+LYG + + ++ V+T +ARII +
Sbjct: 186 KQGLPGELSHLANSAGLLLGPDYHFDMVRPGIALYGLSPSGGLDNGLKPVMTLKARIIQV 245
Query: 246 RKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGY 305
R AGE V YG RD+ IAV AIGYADGYP LS G I G
Sbjct: 246 RTVPAGETVGYGATFTAERDTRIAVVAIGYADGYPRALSN-----------GTPVLINGK 294
Query: 306 MVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRY 365
VPI+G+++MDM M D+TD ++VGD +++FG +I +D+VA A+GT NY+LL +G+R
Sbjct: 295 RVPIVGRVSMDMIMVDLTDLPQVKVGDEVELFGEEITVDEVAEAAGTINYELLTLLGSRV 354
Query: 366 AKFY 369
+ Y
Sbjct: 355 PRVY 358
>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Alanine Racemase. This family
includes predominantly bacterial alanine racemases (AR),
some serine racemases (SerRac), and putative
bifunctional enzymes containing N-terminal
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase (murF) and C-terminal AR domains. These proteins
are fold type III PLP-dependent enzymes that play
essential roles in peptidoglycan biosynthesis. AR
catalyzes the interconversion between L- and D-alanine,
which is an essential component of the peptidoglycan
layer of bacterial cell walls. SerRac converts L-serine
into its D-enantiomer (D-serine) for peptidoglycan
synthesis. murF catalyzes the addition of D-Ala-D-Ala to
UDPMurNAc-tripeptide, the final step in the synthesis of
the cytoplasmic precursor of bacterial cell wall
peptidoglycan. Members of this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain. They exist as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. AR and other
members of this family require dimer formation and the
presence of the PLP cofactor for catalytic activity.
Fungal ARs and eukaryotic serine racemases, which are
fold types I and II PLP-dependent enzymes respectively,
are excluded from this family.
Length = 367
Score = 317 bits (814), Expect = 4e-87
Identities = 126/375 (33%), Positives = 190/375 (50%), Gaps = 24/375 (6%)
Query: 8 RLKIDLTALKNNWHSMNALSG-NARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVE 66
+IDL AL++N + L G + AVVK +AYG G ++A AL AG F V ++E
Sbjct: 3 WAEIDLDALRHNLRVIRRLLGPGTKIMAVVKADAYGHGAVEVAKALEEAGADYFAVATLE 62
Query: 67 EGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKL-MSCGVSHPYA 125
E ++LR A I VL G P + + + +L P +SS+ Q S G +
Sbjct: 63 EALELREAGITAPILVLGGTPPEEAEEAIEYDLTPTVSSLEQAEALSAAAARLGKTLKVH 122
Query: 126 LQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTL 185
L++DTG RLG +EA + +L + +H A AD+P QLERF
Sbjct: 123 LKIDTGMGRLGFRPEEAEELLEALKALPGLELEGVFTHFATADEPDKAYTRRQLERFLEA 182
Query: 186 ISH-----YKGIEASLASSSGILLGPNYHFQLTRPGISLYG--GTDKINKSHPMQTVVTA 238
++ LA+S+ IL P HF + RPGI+LYG + ++ ++ V++
Sbjct: 183 LAELEEAGIPPPLKHLANSAAILRFPEAHFDMVRPGIALYGLYPSPEVKSPLGLKPVMSL 242
Query: 239 EARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGG 298
+AR++ ++ AGE VSYG R + IA +GYADGYP LS G
Sbjct: 243 KARVVQVKTVPAGEGVSYGRTYTAPRPTRIATLPVGYADGYPRALSN-----------KG 291
Query: 299 KGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPD----IKLDDVALASGTTN 354
+ I+G PI+G++ MD TM D+TD ++VGD + +FG I +++A +GT N
Sbjct: 292 EVLIRGKRAPIVGRVCMDQTMVDVTDIPDVKVGDEVVLFGRQGDEEITAEELAELAGTIN 351
Query: 355 YDLLVRIGTRYAKFY 369
Y++L RI R + Y
Sbjct: 352 YEILCRISKRVPRIY 366
>gnl|CDD|143500 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Proteobacterial Alanine
Racemases. This subfamily is composed mainly of
proteobacterial alanine racemases (EC 5.1.1.1), fold
type III PLP-dependent enzymes that catalyze the
interconversion between L- and D-alanine, which is an
essential component of the peptidoglycan layer of
bacterial cell walls. hese proteins are similar to other
bacterial ARs and are fold type III PLP-dependent
enzymes containing contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
They exist as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Homodimer formation and the presence of the PLP
cofactor are required for catalytic activity.
Length = 354
Score = 234 bits (600), Expect = 3e-62
Identities = 128/365 (35%), Positives = 185/365 (50%), Gaps = 25/365 (6%)
Query: 7 LRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVE 66
R IDL AL++N + L+ N++ AVVK NAYG G ++A AL A F V +E
Sbjct: 2 ARATIDLAALRHNLRLVRELAPNSKILAVVKANAYGHGLVRVAKAL--ADADGFAVACIE 59
Query: 67 EGVKLRLYTPQARIFVLYGIHPGQE-KIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYA 125
E + LR I +L G E + + NL V+ S QL + L +S P
Sbjct: 60 EALALREAGITKPILLLEGFFSADELPLAAEYNLWTVVHSEEQLEW---LEQAALSKPLN 116
Query: 126 --LQVDTGFNRLGLSLQEALDFTHN-SFNKKLGQLSLIISHLACADDPSSHVNSVQLERF 182
L++D+G +RLG S +E + + + L+ +H ACAD+P S + QL F
Sbjct: 117 VWLKLDSGMHRLGFSPEEYAAAYQRLKASPNVASIVLM-THFACADEPDSPGTAKQLAIF 175
Query: 183 RTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGT---DKINKSHPMQTVVTAE 239
+ G SLA+S+ IL P H RPGI LYG + DK ++ V+T
Sbjct: 176 EQATAGLPG-PRSLANSAAILAWPEAHGDWVRPGIMLYGASPFADKSGADLGLKPVMTLS 234
Query: 240 ARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGK 299
+ II +R+ AGE V YG R I V AIGY DGYP H+PS G
Sbjct: 235 SEIIAVRELKAGESVGYGATWTAPRPMRIGVVAIGYGDGYP--------RHAPS---GTP 283
Query: 300 GFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLV 359
+ G P++G+++MDM D+TD +VGD ++++G + +D+VA A+GT Y+LL
Sbjct: 284 VLVNGQRTPLVGRVSMDMLTVDLTDLPEAKVGDPVELWGKGLPVDEVAAAAGTIGYELLC 343
Query: 360 RIGTR 364
R+ R
Sbjct: 344 RLTPR 348
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 188 bits (479), Expect = 3e-48
Identities = 124/378 (32%), Positives = 183/378 (48%), Gaps = 31/378 (8%)
Query: 9 LKIDLTALKNNWHSMN-ALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEE 67
L+IDL+AL++N + L + AVVK NAYG G ++A L G+ F V +++E
Sbjct: 4 LEIDLSALEHNVKEIKRLLPSTCKLMAVVKANAYGHGDVEVARVLEQIGIDFFAVATIDE 63
Query: 68 GVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQ 127
G++LR + I +L P + K + +L + S + +L V+ L+
Sbjct: 64 GIRLREAGIKGEILILGYTPPVRAKELKKYSLTQTLIS---EAYAEELSKYAVNIKVHLK 120
Query: 128 VDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACAD--DPSSHV-NSVQLERFRT 184
VDTG +RLG S E +D + K ++S I SHL +D D Q+ F
Sbjct: 121 VDTGMHRLGES-PEDIDSILAIYRLKNLKVSGIFSHLCVSDSLDEDDIAFTKHQIACFDQ 179
Query: 185 LISHYK--GIE---ASLASSSGILLGPNYHFQLTRPGISLYGGT----DKINKSHPMQTV 235
+++ K GIE + SS GIL P+ + RPGI LYG D ++ V
Sbjct: 180 VLADLKARGIEVGKIHIQSSYGILNYPDLKYDYVRPGILLYGVLSDPNDPTKLGLDLRPV 239
Query: 236 VTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVF 295
++ +A++IL+RK GE V YG +R + IA +IGYADGYP +LS
Sbjct: 240 LSLKAKVILVRKVAKGEAVGYGRLFVASRTTRIATVSIGYADGYPRSLSN---------- 289
Query: 296 LGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPD----IKLDDVALASG 351
I G PI+G I MD M D+TD ++ GD + G D + D+VA +
Sbjct: 290 QKAYVLINGKRAPIIGNICMDQLMVDVTDIPEVKEGDTATLIGQDGDEELSADEVARNAH 349
Query: 352 TTNYDLLVRIGTRYAKFY 369
T +LL RIG R + Y
Sbjct: 350 TITNELLSRIGERVKRIY 367
>gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 216
Score = 162 bits (412), Expect = 2e-40
Identities = 76/219 (34%), Positives = 111/219 (50%), Gaps = 8/219 (3%)
Query: 11 IDLTALKNNWHSMNALSG-NARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGV 69
IDL AL++N ++ +G + AVVK NAYG G ++A AL AG F V +++E +
Sbjct: 1 IDLDALRHNIRALRERAGRPVKLMAVVKANAYGHGAVRVARALA-AGADGFGVATLQEAL 59
Query: 70 KLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLM-SCGVSHPYALQV 128
+LR A I VL P + + + +LIP + S+ Q S G L+V
Sbjct: 60 ELREAGITAPILVLGFFPPEELALAAEYDLIPTVDSLEQAEALSAAAAKLGRPLRVHLKV 119
Query: 129 DTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISH 188
DTG RLG + +E L +L +++H ACAD+P + N QL RFR L
Sbjct: 120 DTGMGRLGFTPEELPALAEALALPGL-RLEGLMTHFACADEPDA-TNRAQLARFRELADA 177
Query: 189 YKG--IEASLASSSGILLGPNYH-FQLTRPGISLYGGTD 224
+ SL +S+ +LL P + F + RPGI+LYG
Sbjct: 178 LEAAGPVLSLGNSAALLLAPLHEGFDMVRPGIALYGARP 216
>gnl|CDD|144438 pfam00842, Ala_racemase_C, Alanine racemase, C-terminal domain.
Length = 125
Score = 144 bits (365), Expect = 5e-35
Identities = 58/135 (42%), Positives = 79/135 (58%), Gaps = 11/135 (8%)
Query: 235 VVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSV 294
V++ +AR++ +R AGE V YGG RD+ IA IGYADGYP LS
Sbjct: 1 VMSLKARVLQVRTLPAGEGVGYGGTFTAERDTRIATVPIGYADGYPRALSN--------- 51
Query: 295 FLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTN 354
G I G PI+G+++MD TM D+TD ++VGD + +FGP I D+VA A+GT
Sbjct: 52 --RGYVLINGKRAPIVGRVSMDQTMVDVTDIPDVKVGDEVTLFGPQITADEVAEAAGTIP 109
Query: 355 YDLLVRIGTRYAKFY 369
Y+LL R+G R + Y
Sbjct: 110 YELLTRLGPRVPRIY 124
>gnl|CDD|143499 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme, Alanine Racemase 2. This
subfamily is composed of bacterial alanine racemases (EC
5.1.1.1) with similarity to Yersinia pestis and Vibrio
cholerae alanine racemase (AR) 2. ARs catalyze the
interconversion between L- and D-alanine, an essential
component of the peptidoglycan layer of bacterial cell
walls. These proteins are similar to other bacterial ARs
and are fold type III PLP-dependent enzymes containing
contains an N-terminal PLP-binding TIM-barrel domain and
a C-terminal beta-sandwich domain. They exist as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Homodimer
formation and the presence of the PLP cofactor are
required for catalytic activity.
Length = 365
Score = 118 bits (299), Expect = 2e-27
Identities = 100/378 (26%), Positives = 159/378 (42%), Gaps = 34/378 (8%)
Query: 9 LKIDLTALKNNWHSMNA-LSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEE 67
L+I A +NN + L GN + AV+K +AYG G + P++ + +TS EE
Sbjct: 4 LEISTGAFENNIKLLKKLLGGNTKLCAVMKADAYGHGIALVMPSIIAQNIPCVGITSNEE 63
Query: 68 GVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLM-SCGVSHPYAL 126
+R +I + P + + N+ +I S+ Q L G + P L
Sbjct: 64 ARVVREAGFTGKILRVRTATPSEIEDALAYNIEELIGSLDQAEQIDSLAKRHGKTLPVHL 123
Query: 127 QVDT-GFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQ--LERFR 183
+++ G +R GL L + +L I + P + V+ L RF
Sbjct: 124 ALNSGGMSRNGLEL--STAQGKEDAVAIATLPNLKIVGI-MTHFPVEDEDDVRAKLARFN 180
Query: 184 T----LISHYK----GIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTV 235
LIS+ K I A+S L P H + RPG LYG D S + +
Sbjct: 181 EDTAWLISNAKLKREKITLHAANSFATLNVPEAHLDMVRPGGILYG--DTPP-SPEYKRI 237
Query: 236 VTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVF 295
++ ++R+ + G V Y LTRDSL+A +GY+DGY + S
Sbjct: 238 MSFKSRVASLNTYPKGSTVGYDRTFTLTRDSLLANIPVGYSDGYRRSFSN---------- 287
Query: 296 LGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFG----PDIKLDDVALASG 351
I G VP++GK++M+ M D+TD ++ GD + +FG +I ++ SG
Sbjct: 288 -KAHVLINGQRVPVVGKVSMNTVMVDVTDIPGVKAGDEVVLFGKQGGAEITAAEIEEGSG 346
Query: 352 TTNYDLLVRIGTRYAKFY 369
T +L G + Y
Sbjct: 347 TILAELYTLWGQTNPRVY 364
>gnl|CDD|144985 pfam01601, Corona_S2, Coronavirus S2 glycoprotein. The coronavirus
spike glycoprotein forms the characteristic 'corona'
after which the group is named. The Spike glycoprotein
is translated as a large polypeptide that is
subsequently cleaved to S1 pfam01600 and S2.
Length = 609
Score = 27.6 bits (62), Expect = 5.1
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 123 PYALQVDTGFNRLGLS---LQEALDFTHNSFNKKLGQLSL 159
P+A QV N +GL+ LQE NSFNK LG +
Sbjct: 227 PFATQVQARLNYVGLTTDVLQENQKLIANSFNKALGNIQD 266
>gnl|CDD|143490 cd06815, PLPDE_III_AR_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Alanine Racemase-like 1. This
subfamily is composed of uncharacterized bacterial
proteins with similarity to bacterial alanine racemases
(AR), which are fold type III PLP-dependent enzymes
containing an N-terminal PLP-binding TIM-barrel domain
and a C-terminal beta-sandwich domain. AR exists as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. It catalyzes
the interconversion between L- and D-alanine, which is
an essential component of the peptidoglycan layer of
bacterial cell walls. Members of this subfamily may act
as PLP-dependent enzymes.
Length = 353
Score = 27.5 bits (62), Expect = 5.9
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 8 RLKIDLTALKNNWHSMNAL--SGNARTAAVVKDNAYGLGCEKIAPALYNAGVQ 58
RL+I+L+ +++N + L S V K G +IA AL G+
Sbjct: 3 RLEINLSKIRHNAKVLVELCKSRGIEVTGVTK---VVCGDPEIAEALLEGGIT 52
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist as homodimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 27.5 bits (62), Expect = 6.5
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 53 YNAGVQDFFVTSVEEGVKLRLYTPQARIFV 82
GV+ F S +E K+ + P A++ +
Sbjct: 88 AELGVRLFTFDSEDELEKIAKHAPGAKLLL 117
>gnl|CDD|48459 cd03761, proteasome_beta_type_5, proteasome beta type-5 subunit.
The 20S proteasome, multisubunit proteolytic complex, is
the central enzyme of nonlysosomal protein degradation
in both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each..
Length = 188
Score = 27.1 bits (60), Expect = 7.8
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 114 KLMSCGVSHPYALQV-DTGFNRLGLSLQEALDFTHNS 149
L S G YA V D+G+ R LS++EA D +
Sbjct: 124 DLFSVGSGSTYAYGVLDSGY-RYDLSVEEAYDLARRA 159
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.137 0.397
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,335,992
Number of extensions: 229515
Number of successful extensions: 540
Number of sequences better than 10.0: 1
Number of HSP's gapped: 509
Number of HSP's successfully gapped: 13
Length of query: 370
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 275
Effective length of database: 4,210,882
Effective search space: 1157992550
Effective search space used: 1157992550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)