RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2747
(557 letters)
>gnl|CDD|237989 cd00022, BIR, Baculoviral inhibition of apoptosis protein repeat
domain; Found in inhibitors of apoptosis proteins (IAPs)
and other proteins. In higher eukaryotes, BIR domains
inhibit apoptosis by acting as direct inhibitors of the
caspase family of protease enzymes. In yeast, BIR
domains are involved in regulating cytokinesis. This
novel fold is stabilized by zinc tetrahedrally
coordinated by one histidine and three cysteine residues
and resembles a classical zinc finger.
Length = 69
Score = 105 bits (265), Expect = 8e-28
Identities = 38/65 (58%), Positives = 47/65 (72%)
Query: 230 RLATFNNWPVSFIVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHKRQSP 289
RL TF NWP+S VTPE LA+ GFYY +GD+VKC +C + + WE GD+ EHKR SP
Sbjct: 3 RLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSP 62
Query: 290 NCPFL 294
NCPF+
Sbjct: 63 NCPFV 67
Score = 101 bits (253), Expect = 3e-26
Identities = 33/69 (47%), Positives = 44/69 (63%)
Query: 397 DSRVLTFTTWPRDSPLGPQSLAVAGFFYDGQGDWVRCFHCDGGLRKWTAMDEPWSEHARW 456
++R+ TF WP + P+ LA AGF+Y G+GD V+CF C L+ W D+PW EH RW
Sbjct: 1 EARLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRW 60
Query: 457 FPECHFVML 465
P C FV+L
Sbjct: 61 SPNCPFVLL 69
Score = 91.2 bits (227), Expect = 1e-22
Identities = 29/67 (43%), Positives = 45/67 (67%)
Query: 7 RLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDP 66
RL+TF++WP + V+ +++A+AGF+YTG EV+CF CG+++ NW D +H+ P
Sbjct: 3 RLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSP 62
Query: 67 GCPFVKN 73
CPFV
Sbjct: 63 NCPFVLL 69
Score = 91.2 bits (227), Expect = 1e-22
Identities = 29/67 (43%), Positives = 45/67 (67%)
Query: 143 RLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDP 202
RL+TF++WP + V+ +++A+AGF+YTG EV+CF CG+++ NW D +H+ P
Sbjct: 3 RLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSP 62
Query: 203 GCPFVKN 209
CPFV
Sbjct: 63 NCPFVLL 69
Score = 50.0 bits (120), Expect = 4e-08
Identities = 20/32 (62%), Positives = 24/32 (75%)
Query: 344 RLATFNNWPVSFIVTPEALAKTGFYYLKQGDK 375
RL TF NWP+S VTPE LA+ GFYY +GD+
Sbjct: 3 RLKTFKNWPISLKVTPEKLAEAGFYYTGRGDE 34
>gnl|CDD|197595 smart00238, BIR, Baculoviral inhibition of apoptosis protein
repeat. Domain found in inhibitor of apoptosis proteins
(IAPs) and other proteins. Acts as a direct inhibitor of
caspase enzymes.
Length = 71
Score = 98.9 bits (247), Expect = 2e-25
Identities = 33/71 (46%), Positives = 43/71 (60%)
Query: 395 TLDSRVLTFTTWPRDSPLGPQSLAVAGFFYDGQGDWVRCFHCDGGLRKWTAMDEPWSEHA 454
+ ++R+ TF WP +S P+ LA AGF+Y G GD V+CF C G L W D+PW EH
Sbjct: 1 SEEARLKTFQNWPYNSKCTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60
Query: 455 RWFPECHFVML 465
+W P C FV
Sbjct: 61 KWSPNCPFVRN 71
Score = 95.8 bits (239), Expect = 3e-24
Identities = 36/69 (52%), Positives = 44/69 (63%)
Query: 226 LESGRLATFNNWPVSFIVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHK 285
E RL TF NWP + TPE LA+ GFYY GD+VKC +C + WE GD+ EHK
Sbjct: 1 SEEARLKTFQNWPYNSKCTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60
Query: 286 RQSPNCPFL 294
+ SPNCPF+
Sbjct: 61 KWSPNCPFV 69
Score = 89.7 bits (223), Expect = 5e-22
Identities = 33/71 (46%), Positives = 48/71 (67%)
Query: 3 FERSRLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHR 62
E +RL+TFQ+WP NS + +++A+AGF+YTG EV+CF CG ++ NW D +H+
Sbjct: 1 SEEARLKTFQNWPYNSKCTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60
Query: 63 AKDPGCPFVKN 73
P CPFV+N
Sbjct: 61 KWSPNCPFVRN 71
Score = 89.7 bits (223), Expect = 5e-22
Identities = 33/71 (46%), Positives = 48/71 (67%)
Query: 139 FERSRLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHR 198
E +RL+TFQ+WP NS + +++A+AGF+YTG EV+CF CG ++ NW D +H+
Sbjct: 1 SEEARLKTFQNWPYNSKCTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60
Query: 199 AKDPGCPFVKN 209
P CPFV+N
Sbjct: 61 KWSPNCPFVRN 71
>gnl|CDD|216045 pfam00653, BIR, Inhibitor of Apoptosis domain. BIR stands for
'Baculovirus Inhibitor of apoptosis protein Repeat'. It
is found repeated in inhibitor of apoptosis proteins
(IAPs), and in fact it is also known as IAP repeat.
These domains characteristically have a number of
invariant residues, including 3 conserved cysteines and
one conserved histidine that coordinate a zinc ion. They
are usually made up of 4-5 alpha helices and a
three-stranded beta-sheet. BIR is also found in other
proteins known as BIR-domain-containing proteins
(BIRPs), such as Survivin.
Length = 69
Score = 98.1 bits (245), Expect = 4e-25
Identities = 35/68 (51%), Positives = 45/68 (66%), Gaps = 3/68 (4%)
Query: 230 RLATFNNWPVSFI---VTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHKR 286
RLATF NWP++ +PE LA+ GFYY GD+V+C YC + + WE D+ EHKR
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTGDRVRCFYCGLELDNWEPDDDPWEEHKR 60
Query: 287 QSPNCPFL 294
SPNCPF+
Sbjct: 61 WSPNCPFV 68
Score = 90.4 bits (225), Expect = 2e-22
Identities = 33/68 (48%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 399 RVLTFTTWPRDSPLG---PQSLAVAGFFYDGQGDWVRCFHCDGGLRKWTAMDEPWSEHAR 455
R+ TF WP P+ LA AGF+Y G GD VRCF+C L W D+PW EH R
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTGDRVRCFYCGLELDNWEPDDDPWEEHKR 60
Query: 456 WFPECHFV 463
W P C FV
Sbjct: 61 WSPNCPFV 68
Score = 87.0 bits (216), Expect = 3e-21
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 7 RLRTFQSWPS---NSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRA 63
RL TF++WP + S +++A+AGF+YTG V+CF CG+++ NW +D +H+
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTGDRVRCFYCGLELDNWEPDDDPWEEHKR 60
Query: 64 KDPGCPFVK 72
P CPFV
Sbjct: 61 WSPNCPFVL 69
Score = 87.0 bits (216), Expect = 3e-21
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 143 RLRTFQSWPS---NSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRA 199
RL TF++WP + S +++A+AGF+YTG V+CF CG+++ NW +D +H+
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTGDRVRCFYCGLELDNWEPDDDPWEEHKR 60
Query: 200 KDPGCPFVK 208
P CPFV
Sbjct: 61 WSPNCPFVL 69
Score = 45.7 bits (109), Expect = 1e-06
Identities = 18/35 (51%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 344 RLATFNNWPVSFI---VTPEALAKTGFYYLKQGDK 375
RLATF NWP++ +PE LA+ GFYY GD+
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTGDR 35
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 67.4 bits (165), Expect = 2e-14
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSL---PRCPVCRENIKAT 551
E LC IC+++ VV LPCGHL C CA L +CP+CR+ I++
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSKKKCPICRQPIESV 49
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 44.0 bits (104), Expect = 3e-06
Identities = 19/46 (41%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 506 EARLCKICMDKEVG-VVLLPCGHLVTCVLCASSL----PRCPVCRE 546
E C IC+D VVL PCGH V C C +CP+CR
Sbjct: 1 EELECPICLDLLRDPVVLTPCGH-VFCRECILRYLKKKSKCPICRT 45
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 41.3 bits (97), Expect = 2e-05
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 510 CKICMDK-EVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENI 548
C IC+++ VVLLPCGH V C C CP+CR I
Sbjct: 2 CPICLEEFREPVVLLPCGH-VFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 36.6 bits (85), Expect = 0.001
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 510 CKICMDKEVG---VVLLPCGHLVTCVLCASSL----PRCPVCR 545
C IC+D+ VV+LPCGH+ C CP+CR
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVF-HKECLDKWLRSSNTCPLCR 44
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 35.9 bits (83), Expect = 0.002
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 7/41 (17%)
Query: 510 CKICMDK-EVGVVLLPCGHLVTCVLCASSL-----PRCPVC 544
C IC+++ V+LPCGH C C CP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTF-CRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 33.9 bits (77), Expect = 0.22
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 489 TPKFFVKSLEEEVRRLREARLCKICMDKEVGVVLLPCGHLVTCVLCA----SSLPRCPVC 544
P + ++ ++ L C+IC + CGH C LC + P CPVC
Sbjct: 7 DPSDWNQTKIPSLKGLDSMLRCRICDCRISIPCETTCGHTF-CSLCIRRHLGTQPFCPVC 65
Query: 545 RE 546
RE
Sbjct: 66 RE 67
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 29.4 bits (66), Expect = 0.38
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 510 CKICMDK-EVGVVLLPCGHLVTCVLCASSL-----PRCPVC 544
C IC+++ + V +LPCGHL C C S CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLF-CSKCILSWLESGNVTCPLC 40
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 33.1 bits (75), Expect = 0.39
Identities = 19/55 (34%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSL------PRCPVCRENIKATVRT 554
E C+IC PCGH C CA L CP+CR +A V T
Sbjct: 60 ENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTETEAVVFT 113
>gnl|CDD|131471 TIGR02418, acolac_catab, acetolactate synthase, catabolic.
Acetolactate synthase (EC 2.2.1.6) combines two
molecules of pyruvate to yield 2-acetolactate with the
release of CO2. This reaction may be involved in either
valine biosynthesis (biosynthetic) or conversion of
pyruvate to acetoin and possibly to 2,3-butanediol
(catabolic). The biosynthetic type, described by
TIGR00118, is also capable of forming
acetohydroxybutyrate from pyruvate and 2-oxobutyrate for
isoleucine biosynthesis. The family described here, part
of the same larger family of thiamine
pyrophosphate-dependent enzymes (pfam00205, pfam02776)
is the catabolic form, generally found associated with
in species with acetolactate decarboxylase and usually
found in the same operon. The model may not encompass
all catabolic acetolactate synthases, but rather one
particular clade in the larger TPP-dependent enzyme
family [Energy metabolism, Fermentation].
Length = 539
Score = 33.2 bits (76), Expect = 0.44
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 279 NAESEHKRQSPNCPFLARDNQATQANMINLRALDAKDPGCPFVKNPEASGNVSIENEEVY 338
+ +E + + L ++ +R L K P V+ + +G VS E E+ +
Sbjct: 186 DEVAEAIQNAKLPVLLLGLRASSPETTEAVRRLLKKTQ-LPVVETFQGAGAVSRELEDHF 244
Query: 339 KLESGRLATFNNWP 352
GR+ F N P
Sbjct: 245 ---FGRVGLFRNQP 255
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 31.8 bits (72), Expect = 0.71
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 508 RLCKICMDKEVGVVLLPCGHLVTC-----VLCASSLPRCPVCR 545
C +C+++ PCGHL CP+CR
Sbjct: 216 YKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCR 258
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 31.9 bits (72), Expect = 0.86
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 510 CKICMDKEVGVVLLPCGHLVTCVLCA----SSLPRCPVCR 545
C IC D VL C H C LC S+ P+CP+CR
Sbjct: 29 CHICKDFFDVPVLTSCSHTF-CSLCIRRCLSNQPKCPLCR 67
>gnl|CDD|173121 PRK14658, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 115
Score = 29.2 bits (65), Expect = 2.1
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 321 VKNPEASGNVSIENEEVYKLESGRLATFNNWPVSFIVTPEALAKTGFYYLKQGDKDMRDL 380
+ NP + + I+NE Y + + S EA+ K LK G D+ L
Sbjct: 17 LNNPLFAKRILIDNELEYYFQLNSSREKKRYLASVFACKEAVMKA--LKLKYGYGDILIL 74
Query: 381 GVQNHR 386
+N R
Sbjct: 75 KTENQR 80
>gnl|CDD|150214 pfam09463, Opy2, Opy2 protein. Opy2p acts as a membrane anchor in
the HOG signalling pathway.
Length = 35
Score = 27.0 bits (60), Expect = 2.5
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 531 CVLCASSLPRCPVCREN 547
CV+C S+ P CP C
Sbjct: 1 CVVCPSTPPSCPSCASG 17
>gnl|CDD|227261 COG4924, COG4924, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 386
Score = 30.3 bits (68), Expect = 2.7
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 379 DLGVQNHRVPKHPNLSTLDSRVLTFTTWPRDSPLGPQSLAVAGFFYDGQGDWVR 432
+ Q HR + +LT WP PL P S A A ++VR
Sbjct: 6 FIDDQLHRS-WKYFHAHRSELLLTEFCWPLSLPLHPPSAAKAAADIQAVREFVR 58
>gnl|CDD|237216 PRK12821, PRK12821, aspartyl/glutamyl-tRNA amidotransferase subunit
C-like protein; Provisional.
Length = 477
Score = 29.9 bits (67), Expect = 3.9
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 112 LAKTGFYYLKQGDKKYFLISFRSITMNFER-SRLRTFQSWPSNSPV--SSKRIAKAGFFY 168
LA+ + L + + + F+ IT +F++ ++ T P +P S + K
Sbjct: 397 LARLVMFDLDDAELEKLQVEFKDITSSFKQVEKIDTTNVKPMYAPFSNSPTPLRKDKDVV 456
Query: 169 TGHQHEVQCFACGVK 183
HQ +
Sbjct: 457 QKHQKILLKNCKETL 471
>gnl|CDD|183965 PRK13308, ureC, urease subunit alpha; Reviewed.
Length = 569
Score = 29.7 bits (67), Expect = 4.3
Identities = 24/99 (24%), Positives = 34/99 (34%), Gaps = 22/99 (22%)
Query: 220 NEEVYKLESGRLATFNNW-PVSFIVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGD 278
++ + LE G+LA W P F + PE + K GF GD
Sbjct: 420 DDHIGSLEPGKLADIVLWRPAFFGIKPELVIKGGF-----------------PAWAAMGD 462
Query: 279 NAES----EHKRQSPNCPFLARDNQATQANMINLRALDA 313
S E Q P R QA ++ A++A
Sbjct: 463 ANGSLMTCEPMLQRPQWGAFGRAKQALSVCFVSPLAIEA 501
Score = 28.9 bits (65), Expect = 7.6
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 84 NEEVYKLESGRLATFNNW-PVSFIVTPEALAKTGF 117
++ + LE G+LA W P F + PE + K GF
Sbjct: 420 DDHIGSLEPGKLADIVLWRPAFFGIKPELVIKGGF 454
Score = 28.9 bits (65), Expect = 7.6
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 334 NEEVYKLESGRLATFNNW-PVSFIVTPEALAKTGF 367
++ + LE G+LA W P F + PE + K GF
Sbjct: 420 DDHIGSLEPGKLADIVLWRPAFFGIKPELVIKGGF 454
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 29.3 bits (67), Expect = 4.6
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 67 GCPFVKNPEASGNVSIENEEVYKLESGRLAT 97
GCPF P A+GNV+ E + VY LE + T
Sbjct: 231 GCPFA--PGATGNVATE-DLVYMLEGMGIET 258
Score = 29.3 bits (67), Expect = 4.6
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 203 GCPFVKNPEASGNVSIENEEVYKLESGRLAT 233
GCPF P A+GNV+ E + VY LE + T
Sbjct: 231 GCPFA--PGATGNVATE-DLVYMLEGMGIET 258
Score = 29.3 bits (67), Expect = 4.6
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 317 GCPFVKNPEASGNVSIENEEVYKLESGRLAT 347
GCPF P A+GNV+ E + VY LE + T
Sbjct: 231 GCPFA--PGATGNVATE-DLVYMLEGMGIET 258
>gnl|CDD|236397 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated.
Length = 294
Score = 29.2 bits (66), Expect = 5.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 25 IAKAGFFYTGHQHEVQCFA 43
+AGFF+ GH+ C A
Sbjct: 171 AGQAGFFHEGHRAVDDCQA 189
Score = 29.2 bits (66), Expect = 5.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 161 IAKAGFFYTGHQHEVQCFA 179
+AGFF+ GH+ C A
Sbjct: 171 AGQAGFFHEGHRAVDDCQA 189
>gnl|CDD|215276 PLN02500, PLN02500, cytochrome P450 90B1.
Length = 490
Score = 29.1 bits (65), Expect = 7.0
Identities = 26/88 (29%), Positives = 34/88 (38%), Gaps = 39/88 (44%)
Query: 133 RSITMNF-ERSRLRT-------------FQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCF 178
RSI++NF +RLRT SW NS S+ Q E + F
Sbjct: 137 RSISLNFLSHARLRTHLLKEVERHTLLVLDSWKENSTFSA-------------QDEAKKF 183
Query: 179 ACGVKISNWTYNDSVMAKH-RAKDPGCP 205
T+N +MAKH + DPG
Sbjct: 184 ---------TFN--LMAKHIMSMDPGEE 200
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
0.320 0.135 0.433
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,528,667
Number of extensions: 2752702
Number of successful extensions: 2164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2148
Number of HSP's successfully gapped: 53
Length of query: 557
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 455
Effective length of database: 6,413,494
Effective search space: 2918139770
Effective search space used: 2918139770
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: 62 (27.7 bits)