RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013889
(434 letters)
>gnl|CDD|215461 PLN02856, PLN02856, fumarylacetoacetase.
Length = 424
Score = 783 bits (2024), Expect = 0.0
Identities = 312/436 (71%), Positives = 350/436 (80%), Gaps = 16/436 (3%)
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 LPMEIGDYTDFFSSMHHAKNCGTIFRGPANAVPANCIFHLQVYRVVPYFRFHLPIAYHGR 180
LP IGDYTDFFSS HA N GT+FRGP NA+ N HLPI YHGR
Sbjct: 123 LPAVIGDYTDFFSSREHATNVGTMFRGPENALNPNW--------------LHLPIGYHGR 168
Query: 181 ASSVVISGTDIVRPRGQFAP-SGNSPPPFGPSQKLDFELEMAAVVGPGNELGKPIDVNEA 239
ASSVV SGTDI RPRGQ P G+S P FGPS KLDFELEMAA VGPGNELGKPI VNEA
Sbjct: 169 ASSVVPSGTDIRRPRGQLHPNDGSSRPYFGPSAKLDFELEMAAFVGPGNELGKPIPVNEA 228
Query: 240 ADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTTLSPWIVTLDALEPFACDSPKQDP 299
DHIFG++LMNDWSARDIQ WEYVPLGPFLGKSF TT+SPWIVTLDALEPF CD+P QDP
Sbjct: 229 KDHIFGLVLMNDWSARDIQKWEYVPLGPFLGKSFATTISPWIVTLDALEPFRCDAPAQDP 288
Query: 300 QPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNFKYLYWTLTQQLAHHTINGCNLR 359
PLPYLAEK K+YDISLEV IKPAG+ + VV RSNFK+LYWTL QQLAHHT+NGCNLR
Sbjct: 289 PPLPYLAEKNRKSYDISLEVAIKPAGQSKASVVCRSNFKHLYWTLAQQLAHHTVNGCNLR 348
Query: 360 SGDLLGTGTISGPEPESLGCLLELTWNGQKPLSL-DGFTRKFLEDGDEVTFTGFCKGNGY 418
GDLLG+GTISGPEP SLGCLLELTW G + +SL G RKFLEDGDEV +G+CKG+GY
Sbjct: 349 PGDLLGSGTISGPEPGSLGCLLELTWAGSREVSLEGGTRRKFLEDGDEVVLSGWCKGDGY 408
Query: 419 TVGFGTCSGKIVPSTP 434
VGFGTCSGK++P+ P
Sbjct: 409 RVGFGTCSGKVLPALP 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 = 570 bits (1471), Expect = 0.0
Identities = 252/430 (58%), Positives = 309/430 (71%), Gaps = 18/430 (4%)
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 EIGDYTDFFSSMHHAKNCGTIFRGPANAVPANCIFHLQVYRVVPYFRFHLPIAYHGRASS 183
+IGDYTDF+SS+ HA N G +FRG NA+ N ++ HLP+ YHGRASS
Sbjct: 119 QIGDYTDFYSSIQHATNVGIMFRGKENALLPN-------WK-------HLPVGYHGRASS 164
Query: 184 VVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMAAVVGPGNELGKPIDVNEAADHI 243
+V+SGT + RP GQ P PP FGP + LD ELEMA VGPGN LG+PI +++A +HI
Sbjct: 165 IVVSGTPLRRPMGQTLPDNAKPPVFGPCKLLDMELEMAFFVGPGNRLGEPIPISKAEEHI 224
Query: 244 FGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTTLSPWIVTLDALEPFACDSPKQDPQPLP 303
FGV+LMNDWSARDIQAWEYVPLGPFL KSFGTT+SPW+V +DALEPF +PKQDP+PLP
Sbjct: 225 FGVVLMNDWSARDIQAWEYVPLGPFLAKSFGTTISPWVVPIDALEPFRVPNPKQDPKPLP 284
Query: 304 YLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNFKYLYWTLTQQLAHHTINGCNLRSGDL 363
YL +DI+LEV +K G + + RSNFK++YWT+ QQLAHH++NGCNLR GDL
Sbjct: 285 YLCHDAPYTFDINLEVSLKGEGMSEPATICRSNFKHMYWTMLQQLAHHSVNGCNLRPGDL 344
Query: 364 LGTGTISGPEPESLGCLLELTWNGQKPLSL-DGFTRKFLEDGDEVTFTGFCKGNGYTVGF 422
LG+GTISG EP S G +LEL+W G+KP+ + G TR FLEDGDEV G C+G GY VGF
Sbjct: 345 LGSGTISGSEPGSFGSMLELSWKGKKPIDVAQGETRTFLEDGDEVILRGHCQGEGYRVGF 404
Query: 423 GTCSGKIVPS 432
G C+GK++P+
Sbjct: 405 GECAGKVLPA 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 (354), Expect = 1e-40
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 = 122 bits (309), Expect = 7e-33
Identities = 68/273 (24%), Positives = 101/273 (36%), Gaps = 83/273 (30%)
Query: 160 LQVYRVVPYFRFHLPIAYHGRASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELE 219
L P + P+ + S++V G IV PRG S++LD+E E
Sbjct: 16 LGSGVEPPDY--GPPVFFLKPPSALVGPGDPIVLPRG--------------SERLDYEAE 59
Query: 220 MAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSF--GTTL 277
+A V+G + + EA D++ G L ND SARD+Q F KSF L
Sbjct: 60 LAVVIGKD---LRAVTPEEALDYVAGYTLANDVSARDLQD--RDYRPWFRAKSFDGFAPL 114
Query: 278 SPWIVTLDALEPFACDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNF 337
PWIVT D L A D+ L +++ G+ +V +
Sbjct: 115 GPWIVTPDELGDPA----------------------DLELRLRV--NGE----LVQDGST 146
Query: 338 KYLYWTLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLDGFT 397
+ ++ + +AH + L GD++ TGT SG P
Sbjct: 147 ADMIFSPAELIAHLS-RFLTLEPGDIILTGTPSGRAP----------------------- 182
Query: 398 RKFLEDGDEVTFTGFCKGNGYTVGFGTCSGKIV 430
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 (303), Expect = 2e-31
Identities = 65/261 (24%), Positives = 97/261 (37%), Gaps = 83/261 (31%)
Query: 174 PIAYHGRASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMAAVVGPGNELGKP 233
P+ + ++V+ I P G S+ LD+E E+A V+G GK
Sbjct: 86 PVFFLKPPTAVIGPNDPIPLPPG--------------SKGLDYEGELAVVIGKR---GKD 128
Query: 234 IDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGTT--LSPWIVTLDALEPFA 291
+ V +A D+I G + ND +ARD+Q E K F T + PWIVT D +
Sbjct: 129 VSVEDALDYIAGYTIGNDVTARDLQMEEKGRPW-TRAKGFDTFAPVGPWIVTKDEIS--- 184
Query: 292 CDSPKQDPQPLPYLAEKISKNYDISLEVQIKPAGKEDSCVVTRSNFKYLYWTLTQQLAHH 351
DPQ LP +SL V G+ V R N + +++ + +A+
Sbjct: 185 ------DPQNLP-----------LSLRVN----GE----VRQRGNTSDMIFSIPELIAYL 219
Query: 352 TINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLDGFTRKFLEDGDEVTFTG 411
+ L GD++ TGT SG FL+ GD V
Sbjct: 220 S-RFMTLEPGDVILTGTPSGVG--------------------------FLKPGDVVE--- 249
Query: 412 FCKGNGYTVGFGTCSGKIVPS 432
+ 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 = 0.006
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 216 FELEMAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSFGT 275
+E E+A VVG + K + +A D++ G + ND++ RD Y P + T
Sbjct: 95 YECELAVVVG---KTAKNVKREDAMDYVLGYTIANDYAIRDYLENYYRPNLRVKNRDTFT 151
Query: 276 TLSPWIVTLDALEPFACDSPKQDPQPL 302
+ 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 = 0.38
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 343 TLTQQLAHHTINGCNLRSGDLLGTGTISGPEPESLGCLLELTWNGQKPLSLD 394
+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 = 0.56
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 = 31.6 bits (72), Expect = 0.79
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 29/101 (28%)
Query: 181 ASSVVISGTDIVRPRGQFAPSGNSPPPFGPSQKLDFELEMAAVVGPGNELGKPIDVNEAA 240
+SS+ +SG + RP G ++ L FE E+A V+G + + +A
Sbjct: 52 SSSLALSGGTVERPAG--------------TELLAFEGEIALVIG---RPARRVSPEDAW 94
Query: 241 DHIFGVMLMNDWSARDIQAWE------------YVPLGPFL 269
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 = 30.0 bits (67), Expect = 2.3
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 214 LDFELEMAAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQAWEYVPLGPFLGKSF 273
+ +E E+ V+G + + + +A D++ G + ND++ RD Y P +
Sbjct: 273 MHYEAELVVVIG---KQARKVSEADAMDYVAGYTVCNDYAIRDYLENYYRPNLRVKSRDG 329
Query: 274 GTTLSPWIVTLDAL 287
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 = 3.7
Identities = 8/32 (25%), Positives = 11/32 (34%), Gaps = 3/32 (9%)
Query: 276 TLSPWIVTLDALEPFACDSPKQDPQPLPYLAE 307
+ 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 = 4.1
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 395 GFTRKFLEDGDEVTFTGFCKGNG 417
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 = 4.1
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 397 TRKFLEDGDEVTFTGFCKGNG 417
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 = 8.3
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 221 AAVVGPGNELGKPIDVNEAADHIFGVMLMNDWSARDIQ 258
+ 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 = 8.6
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 358 LRSGDLLGTGTISGPEPESLGCLLELTWNGQ 388
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 0.432
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: 22,557,061
Number of extensions: 2190247
Number of successful extensions: 1577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1563
Number of HSP's successfully gapped: 19
Length of query: 434
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 334
Effective length of database: 6,502,202
Effective search space: 2171735468
Effective search space used: 2171735468
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: 60 (26.9 bits)