RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 012786
(456 letters)
>gnl|CDD|215461 PLN02856, PLN02856, fumarylacetoacetase.
Length = 424
Score = 783 bits (2024), Expect = 0.0
Identities = 313/458 (68%), Positives = 351/458 (76%), Gaps = 38/458 (8%)
Query: 1 MALQSFIEVEPDSHFPIQNLPYGVFKPEPASVARPGVAIGEYVLDLSEISKAGLFNGPIL 60
L+SFI+V PDS FPIQNLPYGVF PE + RPGVAIG+YVLDLS +S+AGLF+GP+L
Sbjct: 3 SPLKSFIDVAPDSDFPIQNLPYGVFSPESGATPRPGVAIGDYVLDLSALSEAGLFDGPLL 62
Query: 61 KDSDCFLQPNLNKFLSLGRPAWKEARDMLQKLLSSNEATLRDNANLRQKSLVPMGKVEML 120
DSDCF QP LNKF+++GRPAWKEAR LQ+LLS++E LRDN+ LR+K+ PM VEML
Sbjct: 63 SDSDCFSQPTLNKFMAMGRPAWKEARSTLQRLLSADEPALRDNSELRKKAFHPMSDVEML 122
Query: 121 LPMEIGDYTDFFSSMHHAKNCGTIFRGPANAVPANWYVILKSTSKQGIVSVLTLVYYSIF 180
LP IGDYTDFFSS HA N GT+FRGP NA+ NW
Sbjct: 123 LPAVIGDYTDFFSSREHATNVGTMFRGPENALNPNW------------------------ 158
Query: 181 HLQVYRVVPYFRFHLPIAYHGRASSVVISGTDIVRPRGQFAP-SGNSPPPFGPSQKLDFE 239
HLPI YHGRASSVV SGTDI RPRGQ P G+S P FGPS KLDFE
Sbjct: 159 ------------LHLPIGYHGRASSVVPSGTDIRRPRGQLHPNDGSSRPYFGPSAKLDFE 206
Query: 240 LEMAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTTL 299
LEMAA VGPGNELGKPI VNEA DHIFG++LMNDWSARDIQ WEYVPLGPFLGKSF TT+
Sbjct: 207 LEMAAFVGPGNELGKPIPVNEAKDHIFGLVLMNDWSARDIQKWEYVPLGPFLGKSFATTI 266
Query: 300 SPWIVTLDALEPFACDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNF 359
SPWIVTLDALEPF CD+P QDP PLPYLAEK K+YDISLEV IKPAG+ + VV RSNF
Sbjct: 267 SPWIVTLDALEPFRCDAPAQDPPPLPYLAEKNRKSYDISLEVAIKPAGQSKASVVCRSNF 326
Query: 360 KYLYWTLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSL-DGF 418
K+LYWTL QQLAHHT+NGCNLR GDLLG+GTISGPEP SLGCLLELTW G + +SL G
Sbjct: 327 KHLYWTLAQQLAHHTVNGCNLRPGDLLGSGTISGPEPGSLGCLLELTWAGSREVSLEGGT 386
Query: 419 TRKFLEDGDEVTFTGFCKGNGYTVGFGTCSGKIVPSTP 456
RKFLEDGDEV +G+CKG+GY VGFGTCSGK++P+ P
Sbjct: 387 RRKFLEDGDEVVLSGWCKGDGYRVGFGTCSGKVLPALP 424
>gnl|CDD|162276 TIGR01266, fum_ac_acetase, fumarylacetoacetase. This enzyme
catalyzes the final step in the breakdown of tyrosine or
phenylalanine to fumarate and acetoacetate [Energy
metabolism, Amino acids and amines].
Length = 415
Score = 568 bits (1465), Expect = 0.0
Identities = 253/452 (55%), Positives = 308/452 (68%), Gaps = 40/452 (8%)
Query: 5 SFIEVEPDSHFPIQNLPYGVFKPEPASVARPGVAIGEYVLDLSEISKAGLFNGPILKD-S 63
SF+ V +S FPIQNLPYGVF + S R GVAIG+ +LDLS I A LF GP L
Sbjct: 1 SFVPVAENSDFPIQNLPYGVFSTQANSSPRIGVAIGDQILDLSVI--AHLFTGPALSKHQ 58
Query: 64 DCFLQPNLNKFLSLGRPAWKEARDMLQKLLSSNEATLRDNANLRQKSLVPMGKVEMLLPM 123
F Q LN F++LGRPAWKEAR LQ LLS+++A LRDNA LRQ++L P + M LP
Sbjct: 59 HVFDQSTLNAFMALGRPAWKEARARLQNLLSASQARLRDNAALRQRALTPQAEATMHLPA 118
Query: 124 EIGDYTDFFSSMHHAKNCGTIFRGPANAVPANWYVILKSTSKQGIVSVLTLVYYSIFHLQ 183
+IGDYTDF+SS+ HA N G +FRG NA+ NW
Sbjct: 119 QIGDYTDFYSSIQHATNVGIMFRGKENALLPNWK-------------------------- 152
Query: 184 VYRVVPYFRFHLPIAYHGRASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMA 243
HLP+ YHGRASS+V+SGT + RP GQ P PP FGP + LD ELEMA
Sbjct: 153 ----------HLPVGYHGRASSIVVSGTPLRRPMGQTLPDNAKPPVFGPCKLLDMELEMA 202
Query: 244 AVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTTLSPWI 303
VGPGN LG+PI +++A +HIFGV+LMNDWSARDIQAWEYVPLGPFL KSFGTT+SPW+
Sbjct: 203 FFVGPGNRLGEPIPISKAEEHIFGVVLMNDWSARDIQAWEYVPLGPFLAKSFGTTISPWV 262
Query: 304 VTLDALEPFACDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNFKYLY 363
V +DALEPF +PKQDP+PLPYL +DI+LEV +K G + + RSNFK++Y
Sbjct: 263 VPIDALEPFRVPNPKQDPKPLPYLCHDAPYTFDINLEVSLKGEGMSEPATICRSNFKHMY 322
Query: 364 WTLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSL-DGFTRKF 422
WT+ QQLAHH++NGCNLR GDLLG+GTISG EP S G +LEL+W G+KP+ + G TR F
Sbjct: 323 WTMLQQLAHHSVNGCNLRPGDLLGSGTISGSEPGSFGSMLELSWKGKKPIDVAQGETRTF 382
Query: 423 LEDGDEVTFTGFCKGNGYTVGFGTCSGKIVPS 454
LEDGDEV G C+G GY VGFG C+GK++P+
Sbjct: 383 LEDGDEVILRGHCQGEGYRVGFGECAGKVLPA 414
>gnl|CDD|220168 pfam09298, DUF1969, Domain of unknown function (DUF1969). The
N-terminal domain of fumarylacetoacetate hydrolase is
functionally uncharacterized, and adopts a structure
consisting of an SH3-like barrel.
Length = 101
Score = 140 bits (356), Expect = 8e-41
Identities = 53/105 (50%), Positives = 65/105 (61%), Gaps = 4/105 (3%)
Query: 18 QNLPYGVFKPEPASVARPGVAIGEYVLDLSEISKAGLFNGPILKDSDCFLQPNLNKFLSL 77
QNLP+GVF R GVAIG+ VLDL+ + AGLF+G L + F QP LN F++L
Sbjct: 1 QNLPFGVFSTAAGPAPRIGVAIGDQVLDLAALEAAGLFDGA-LGAAGVFAQPTLNAFMAL 59
Query: 78 GRPAWKEARDMLQKLLSSNEATLRDNANLRQKSLVPMGKVEMLLP 122
GRPAW R LQ+LLS L DN LR+ +LVP VE+ LP
Sbjct: 60 GRPAWSAVRARLQELLSR---ELSDNQALREPALVPQADVELHLP 101
>gnl|CDD|216570 pfam01557, FAA_hydrolase, Fumarylacetoacetate (FAA) hydrolase
family. This family consists of fumarylacetoacetate
(FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH)
and it also includes HHDD isomerase/OPET decarboxylase
from E. coli strain W. FAA is the last enzyme in the
tyrosine catabolic pathway, it hydrolyses
fumarylacetoacetate into fumarate and acetoacetate which
then join the citric acid cycle. Mutations in FAA cause
type I tyrosinemia in humans this is an inherited
disorder mainly affecting the liver leading to liver
cirrhosis, hepatocellular carcinoma, renal tubular
damages and neurologic crises amongst other symptoms.
The enzymatic defect causes the toxic accumulation of
phenylalanine/tyrosine catabolites. The E. coli W enzyme
HHDD isomerase/OPET decarboxylase contains two copies of
this domain and functions in fourth and fifth steps of
the homoprotocatechuate pathway; here it decarboxylates
OPET to HHDD and isomerises this to OHED. The final
products of this pathway are pyruvic acid and succinic
semialdehyde. This family also includes various
hydratases and 4-oxalocrotonate decarboxylases which are
involved in the bacterial meta-cleavage pathways for
degradation of aromatic compounds. 2-hydroxypentadienoic
acid hydratase, encoded by mhpD in E. coli, is involved
in the phenylpropionic acid pathway of E. coli and
catalyzes the conversion of 2-hydroxy pentadienoate to
4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor.
OHED hydratase encoded by hpcG in E. coli is involved in
the homoprotocatechuic acid (HPC) catabolism. XylI in P.
putida is a 4-Oxalocrotonate decarboxylase.
Length = 207
Score = 123 bits (310), Expect = 7e-33
Identities = 68/273 (24%), Positives = 101/273 (36%), Gaps = 83/273 (30%)
Query: 182 LQVYRVVPYFRFHLPIAYHGRASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELE 241
L P + P+ + S++V G IV PRG S++LD+E E
Sbjct: 16 LGSGVEPPDY--GPPVFFLKPPSALVGPGDPIVLPRG--------------SERLDYEAE 59
Query: 242 MAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSF--GTTL 299
+A V+G + + EA D++ G L ND SARD+Q F KSF L
Sbjct: 60 LAVVIGKD---LRAVTPEEALDYVAGYTLANDVSARDLQD--RDYRPWFRAKSFDGFAPL 114
Query: 300 SPWIVTLDALEPFACDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNF 359
PWIVT D L A D+ L +++ G+ +V +
Sbjct: 115 GPWIVTPDELGDPA----------------------DLELRLRV--NGE----LVQDGST 146
Query: 360 KYLYWTLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLDGFT 419
+ ++ + +AH + L GD++ TGT SG P
Sbjct: 147 ADMIFSPAELIAHLS-RFLTLEPGDIILTGTPSGRAP----------------------- 182
Query: 420 RKFLEDGDEVTFTGFCKGNGYTVGFGTCSGKIV 452
FL+ GD V G GT ++V
Sbjct: 183 ALFLQPGDVVE--------VEIEGLGTLENRVV 207
>gnl|CDD|223257 COG0179, MhpD, 2-keto-4-pentenoate
hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
(catechol pathway) [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 266
Score = 120 bits (304), Expect = 2e-31
Identities = 65/261 (24%), Positives = 97/261 (37%), Gaps = 83/261 (31%)
Query: 196 PIAYHGRASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMAAVVGPGNELGKP 255
P+ + ++V+ I P G S+ LD+E E+A V+G GK
Sbjct: 86 PVFFLKPPTAVIGPNDPIPLPPG--------------SKGLDYEGELAVVIGKR---GKD 128
Query: 256 IDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTT--LSPWIVTLDALEPFA 313
+ V +A D+I G + ND +ARD+Q E K F T + PWIVT D +
Sbjct: 129 VSVEDALDYIAGYTIGNDVTARDLQMEEKGRPW-TRAKGFDTFAPVGPWIVTKDEIS--- 184
Query: 314 CDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNFKYLYWTLTQQLAHH 373
DPQ LP +SL V G+ V R N + +++ + +A+
Sbjct: 185 ------DPQNLP-----------LSLRVN----GE----VRQRGNTSDMIFSIPELIAYL 219
Query: 374 TINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLDGFTRKFLEDGDEVTFTG 433
+ L GD++ TGT SG FL+ GD V
Sbjct: 220 S-RFMTLEPGDVILTGTPSGVG--------------------------FLKPGDVVE--- 249
Query: 434 FCKGNGYTVGFGTCSGKIVPS 454
+ G G +V
Sbjct: 250 -VEIE----GIGELENTVVKE 265
>gnl|CDD|131356 TIGR02303, HpaG-C-term, 4-hydroxyphenylacetate degradation
bifunctional isomerase/decarboxylase, C-terminal
subunit. This model represents one of two
subunits/domains of the bifunctional
isomerase/decarboxylase involved in
4-hydroxyphenylacetate degradation. In E. coli and some
other species this enzyme is encoded by a single
polypeptide containing both this domain and the closely
related N-terminal domain (TIGR02305). In other species
such as Pasteurella multocida these domains are found as
two separate proteins (usually as tandem genes).
Together, these domains carry out the decarboxylation of
5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Length = 245
Score = 37.9 bits (88), Expect = 0.007
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 238 FELEMAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGT 297
+E E+A VVG + K + +A D++ G + ND++ RD Y P + T
Sbjct: 95 YECELAVVVG---KTAKNVKREDAMDYVLGYTIANDYAIRDYLENYYRPNLRVKNRDTFT 151
Query: 298 TLSPWIVTLDALEPFACDSPKQDPQPL 324
+ PWIV + +E DP L
Sbjct: 152 PIGPWIVDKEDVE---------DPMNL 169
>gnl|CDD|235891 PRK06933, PRK06933, type III secretion system protein; Validated.
Length = 308
Score = 32.4 bits (74), Expect = 0.40
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 365 TLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLD 416
+L Q+L+H+ + + + T+S P P SL C+L+L W GQ +L
Sbjct: 15 SLRQRLSHYQ---QHFLWEEGKLSLTVSQP-PSSLDCILQLQWKGQ-TFTLY 61
>gnl|CDD|200525 cd11264, Sema_5B, The Sema domain, a protein interacting module, of
semaphorin 5B (Sema5B). Sema5B is expressed in regions
of the basal telencephalon in rat. Sema5B is an
inhibitory cue for corticofugal axons and acts as a
source of repulsion for the appropriate guidance of
cortical axons away from structures such as the
ventricular zone as they navigate toward and within
subcortical regions. In addition to its role as a
guidance cue, Sema5B regulates the development and
maintenance of synapse size and number in hippocampal
neurons. In addition, the sema domain of Sema5B can be
cleaved of the whole protein and exerts its function in
regulation of synapse morphology. Sema5B belongs to the
class 5 semaphorin family of proteins, which are
transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 437
Score = 32.3 bits (73), Expect = 0.58
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 8 EVEPDSHFPIQNLPYGVFKPEPASVARPGVAIGEYVLDLSEISKAGLFNGP 58
E++ + P Q+L YGVF S+A V +LS I++A FNGP
Sbjct: 241 ELQSTFYLPEQDLIYGVFTTNVNSIAASAVC----AFNLSAITQA--FNGP 285
>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional.
Length = 500
Score = 32.0 bits (73), Expect = 0.75
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 29/101 (28%)
Query: 203 ASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMAAVVGPGNELGKPIDVNEAA 262
+SS+ +SG + RP G ++ L FE E+A V+G + + +A
Sbjct: 52 SSSLALSGGTVERPAG--------------TELLAFEGEIALVIG---RPARRVSPEDAW 94
Query: 263 DHIFGVMLMNDWSARDIQAWE------------YVPLGPFL 291
H+ V ND D++ + + P+GP L
Sbjct: 95 SHVAAVTAANDLGVYDLRYADKGSNLRSKGGDGFTPIGPAL 135
>gnl|CDD|185125 PRK15203, PRK15203, 4-hydroxyphenylacetate degradation bifunctional
isomerase/decarboxylase; Provisional.
Length = 429
Score = 30.4 bits (68), Expect = 2.3
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 236 LDFELEMAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSF 295
+ +E E+ V+G + + + +A D++ G + ND++ RD Y P +
Sbjct: 273 MHYEAELVVVIG---KQARKVSEADAMDYVAGYTVCNDYAIRDYLENYYRPNLRVKSRDG 329
Query: 296 GTTLSPWIVTLDAL 309
T + IV +A+
Sbjct: 330 LTPILSTIVPKEAI 343
>gnl|CDD|221378 pfam12013, DUF3505, Protein of unknown function (DUF3505). This
family of proteins is functionally uncharacterized. This
protein is found in eukaryotes. Proteins in this family
are typically between 247 to 1018 amino acids in length.
This region contains two segments that are likely to be
C2H2 zinc binding domains.
Length = 108
Score = 28.1 bits (63), Expect = 3.3
Identities = 8/32 (25%), Positives = 11/32 (34%), Gaps = 3/32 (9%)
Query: 298 TLSPWIVTLDALEPFACDSPKQDPQPLPYLAE 329
+ W D +P A P P+P L
Sbjct: 48 AIRQWD---DLRDPEAVQWPSALSPPIPGLPV 76
>gnl|CDD|235441 PRK05388, argJ, bifunctional ornithine
acetyltransferase/N-acetylglutamate synthase protein;
Validated.
Length = 395
Score = 29.3 bits (67), Expect = 4.3
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 417 GFTRKFLEDGDEVTFTGFCKGNG 439
R+ DG VT G KG G
Sbjct: 151 QAAREVEIDGKTVTIGGIAKGAG 173
>gnl|CDD|216811 pfam01960, ArgJ, ArgJ family. Members of the ArgJ family catalyze
the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in
arginine biosynthesis.
Length = 380
Score = 29.3 bits (67), Expect = 4.4
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 419 TRKFLEDGDEVTFTGFCKGNG 439
R+ G VT G KG+G
Sbjct: 146 AREVEIGGKTVTIGGIAKGSG 166
>gnl|CDD|176682 cd07261, Glo_EDI_BRP_like_11, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 114
Score = 27.2 bits (61), Expect = 8.5
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 243 AAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQ 280
+ G G+EL +D A D ++ +W A+ ++
Sbjct: 54 SDATGGGSELAFMVDDGAAVDALY-----AEWQAKGVK 86
>gnl|CDD|182650 PRK10691, PRK10691, hypothetical protein; Provisional.
Length = 219
Score = 28.1 bits (63), Expect = 8.8
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 380 LRSGDLLGTGTISGPEPESLGCLLELTWNGQ 410
LR+GD++ TGT G P G L +T+NG
Sbjct: 182 LRAGDVVLTGTPEGVGPLQSGDELTVTFNGH 212
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
0.319 0.138 0.428
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,616,897
Number of extensions: 2299344
Number of successful extensions: 1664
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1652
Number of HSP's successfully gapped: 19
Length of query: 456
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 356
Effective length of database: 6,502,202
Effective search space: 2314783912
Effective search space used: 2314783912
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 (21.7 bits)
S2: 61 (27.3 bits)