RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13485
(152 letters)
>gnl|CDD|239072 cd02257, Peptidase_C19, Peptidase C19 contains ubiquitinyl
hydrolases. They are intracellular peptidases that
remove ubiquitin molecules from polyubiquinated peptides
by cleavage of isopeptide bonds. They hydrolyse bonds
involving the carboxyl group of the C-terminal Gly
residue of ubiquitin The purpose of the
de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 255
Score = 40.2 bits (94), Expect = 1e-04
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 37 LVGVVTYYGK-----HYSTFFFHTKLKVWIYFDDATVREVGPRWEQVRSAFYFFNSEYTL 91
LV VV + G HY + W F+D V EV E+V +S Y L
Sbjct: 195 LVAVVVHSGTSADSGHYVAYVKDPSDGKWYKFNDDKVTEV--SEEEVLEFGSLSSSAYIL 252
Query: 92 Y 92
+
Sbjct: 253 F 253
>gnl|CDD|215922 pfam00443, UCH, Ubiquitin carboxyl-terminal hydrolase.
Length = 313
Score = 38.9 bits (91), Expect = 3e-04
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 36 QLVGVVTYYGK-----HYSTFFFHTKLKVWIYFDDATVREVGPRWEQVRSAFYF 84
+LV VV + G HY + + W+ FDD V V E +RS+ Y
Sbjct: 258 ELVAVVVHSGSSLSGGHYIAYIKKREKNKWVKFDDEKVSVVTE-EEVLRSSAYI 310
>gnl|CDD|239139 cd02674, Peptidase_C19R, A subfamily of peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 230
Score = 35.0 bits (81), Expect = 0.008
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 36 QLVGVVTYYGK----HYSTFFFHTKLKVWIYFDDATVREVGPRWEQVRSA---FY 83
L VV +YG HY+ + + + W FDD+ V +V SA FY
Sbjct: 175 DLYAVVNHYGSLNGGHYTAYCKNNETNDWYKFDDSRVTKVSESSVVSSSAYILFY 229
>gnl|CDD|239122 cd02657, Peptidase_C19A, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyse bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 305
Score = 33.8 bits (78), Expect = 0.019
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 20 DVFHGCDNAAASTPLHQLVGVVTYYGK-----HYSTFFFHTKLKVWIYFDDATVREV 71
D++ C + ++LV V+T+ G+ HY + WI FDD V EV
Sbjct: 230 DLYELCTPSG----YYELVAVITHQGRSADSGHYVAWVRRKNDGKWIKFDDDKVSEV 282
>gnl|CDD|132883 cd07062, Peptidase_S66_mccF_like, Microcin C7 self-immunity protein
determines resistance to exogenous microcin C7.
Microcin C7 self-immunity protein (mccF): MccF, a
homolog of the LD-carboxypeptidase family, mediates
resistance against exogenously added microcin C7
(MccC7), a ribosomally-encoded peptide antibiotic that
contains a phosphoramidate linkage to adenosine
monophosphate at its C-terminus. The plasmid-encoded
mccF gene is transcribed in the opposite direction to
the other five genes (mccA-E) and is required for the
full expression of immunity but not for production. The
catalytic triad residues (Ser, His, Glu) of
LD-carboxypeptidase are also conserved in MccF, strongly
suggesting that MccF shares the hydrolytic activity with
LD-carboxypeptidases. Substrates of MccF have not been
deduced, but could likely be microcin C7 precursors. The
possible role of MccF is to defend producer cells
against exogenous microcin from re-entering after having
been exported. It is suggested that MccF is involved in
microcin degradation or sequestration in the periplasm.
Length = 308
Score = 31.8 bits (73), Expect = 0.11
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 26 DNAAASTPLHQLVGVVTYYGKHYSTFF 52
D A +++ G+VTYYG + FF
Sbjct: 103 DITALHLAIYKKTGLVTYYGPNLLDFF 129
>gnl|CDD|181546 PRK08751, PRK08751, putative long-chain fatty acyl CoA ligase;
Provisional.
Length = 560
Score = 29.5 bits (66), Expect = 0.72
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 66 ATVREVGPRWEQVRSAFYFFNSEYTLYSAAPKASLLPLPLSLYKLELTRPFPSFSGC 122
A R V RW+QV Y L +P A + PL L Y + P PS C
Sbjct: 340 AVQRSVAERWKQVTGLTLV--EAYGLTETSPAACINPLTLKEYNGSIGLPIPSTDAC 394
>gnl|CDD|165398 PHA03126, PHA03126, dUTPase; Provisional.
Length = 326
Score = 28.8 bits (64), Expect = 0.96
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 115 PFPSFSGCGEVQARPLPAAPTPILWGFT 142
PFP++S G +A +P+LW FT
Sbjct: 282 PFPTYSPTGATKA-----PQSPVLWKFT 304
>gnl|CDD|215142 PLN02254, PLN02254, gibberellin 3-beta-dioxygenase.
Length = 358
Score = 27.4 bits (61), Expect = 3.3
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 2 SGFLHVCPASGGIFENLSDVFHGCDNAAASTPLHQLV 38
G++ V P G + N+ D+ H N + LH+ V
Sbjct: 256 VGWVTVPPVPGSLVVNVGDLLHILSNGRFPSVLHRAV 292
>gnl|CDD|185297 PRK15399, PRK15399, lysine decarboxylase LdcC; Provisional.
Length = 713
Score = 27.0 bits (60), Expect = 4.6
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 26 DNAAASTPLHQLVGVVTYYGKHYSTFFFHTKLKV-WIYFDDATV 68
A P+H ++ TY G Y+T + L V I+FD A V
Sbjct: 291 ATTQAQWPVHAVITNSTYDGLLYNTDWIKQTLDVPSIHFDSAWV 334
>gnl|CDD|239128 cd02663, Peptidase_C19G, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 300
Score = 26.5 bits (59), Expect = 6.0
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 21 VFHGCDNAAASTPLHQLVGVVTYYGK-----HYSTFFFHTKLKVWIYFDDATVREVGPRW 75
+F+ D+A L++LV VV + G HY + W+ FDD TV ++
Sbjct: 223 LFNTTDDAENPDRLYELVAVVVHIGGGPNHGHYVSIVKSHGG--WLLFDDETVEKIDE-- 278
Query: 76 EQVRSAFYFFNSEYTLY 92
V F ++ T Y
Sbjct: 279 NAVEEFFGDSPNQATAY 295
>gnl|CDD|227847 COG5560, UBP12, Ubiquitin C-terminal hydrolase [Posttranslational
modification, protein turnover, chaperones].
Length = 823
Score = 26.4 bits (58), Expect = 7.5
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 45 GKHYSTFFFHTKLKVWIYFDDATVREVGPRWEQVRSAFYFF 85
G HY+ + + W FDD+ + EV P SA+ F
Sbjct: 778 GGHYTAYARNFANNGWYLFDDSRITEVDPEDSVTSSAYVLF 818
>gnl|CDD|239125 cd02660, Peptidase_C19D, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 328
Score = 26.2 bits (58), Expect = 8.3
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 36 QLVGVVTYYGK----HYSTFFFHTKLKVWIYFDDATVREV 71
L VV + G HY+ + W FDDA + V
Sbjct: 274 DLFAVVVHKGTLDTGHYTAYCRQGD-GQWFKFDDAMITRV 312
>gnl|CDD|239138 cd02673, Peptidase_C19Q, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 245
Score = 26.0 bits (57), Expect = 8.4
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 6/45 (13%)
Query: 33 PLHQLVGVVTYYGK-----HYSTFFFH-TKLKVWIYFDDATVREV 71
+ LV V+ + G+ HY + W+Y D +R V
Sbjct: 182 AKYSLVAVICHLGESPYDGHYIAYTKELYNGSSWLYCSDDEIRPV 226
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. 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 numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, 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. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, 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.
Length = 242
Score = 26.1 bits (58), Expect = 8.5
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 15/65 (23%)
Query: 28 AAASTPLHQLVGVVTYYGKHYSTFFFHTKLKVWI-YFD-----DATVREVGPRWEQVRSA 81
AA + V +S+ KL + + +FD + +R G +R A
Sbjct: 93 AAKRAGVQHFV---------FSSVPDVEKLTLAVPHFDSKAEVEEYIRASGLPATILRPA 143
Query: 82 FYFFN 86
F+ N
Sbjct: 144 FFMEN 148
>gnl|CDD|185298 PRK15400, PRK15400, lysine decarboxylase CadA; Provisional.
Length = 714
Score = 26.3 bits (58), Expect = 8.5
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 30 ASTPLHQLVGVVTYYGKHYSTFFFHTKLKV-WIYFDDATV 68
A+ P+H ++ TY G Y+T F L V I+FD A V
Sbjct: 295 ATWPVHAVITNSTYDGLLYNTDFIKKTLDVKSIHFDSAWV 334
>gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I,
proteobacterial subset. This enzyme resembles some
other chorismate-binding enzymes, including
para-aminobenzoate synthase (pabB) and isochorismate
synthase. There is a fairly deep split between two sets,
seen in the pattern of gaps as well as in amino acid
sequence differences. This group includes proteobacteria
such as E. coli and Helicobacter pylori but also the
gram-positive organism Corynebacterium glutamicum. The
second group includes eukaryotes, archaea, and most
other bacterial lineages; sequences from the second
group may resemble pabB more closely than other trpE
from this group [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 498
Score = 26.0 bits (57), Expect = 9.7
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 82 FYFFNSEYTLYSAAPKASLLPLPLS----LYKLELTRP 115
FY ++++ L+ A+P+++L LS +Y + TRP
Sbjct: 277 FYMQDNDFILFGASPESALKYDALSRQIEIYPIAGTRP 314
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
0.324 0.140 0.459
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,955,725
Number of extensions: 691888
Number of successful extensions: 672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 671
Number of HSP's successfully gapped: 25
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.0 bits)