RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025777
(248 letters)
>gnl|CDD|177701 PLN00072, PLN00072, 3-isopropylmalate isomerase/dehydratase small
subunit; Provisional.
Length = 246
Score = 358 bits (920), Expect = e-126
Identities = 160/244 (65%), Positives = 174/244 (71%), Gaps = 1/244 (0%)
Query: 4 ASSISFGANTTFTSSPIP-KTKPLFIPHSLKFTTGNGRAAVTFQRAVSVIPKATSADSRA 62
A+S T S K+ P + S + + A
Sbjct: 2 AASQQSANPTLAPSLASTNKSSSSATPRPFLRFSSTSSIFPFKPLTTSSGTSSPTISDSA 61
Query: 63 TKEPTATFHGLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFI 122
+ TFHGLC+VVGDNIDTDQIIPAEYLTLVPS PDEYEKLGSYALIGLPA Y TRF+
Sbjct: 62 ESTSSTTFHGLCFVVGDNIDTDQIIPAEYLTLVPSKPDEYEKLGSYALIGLPAFYKTRFV 121
Query: 123 DENETKTKYKIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYP 182
+ E KTKY III G NFGCGSSREHAPVALGAAG AVVAESYARIFFRNSVATGE+YP
Sbjct: 122 EPGEMKTKYSIIIGGENFGCGSSREHAPVALGAAGAKAVVAESYARIFFRNSVATGEVYP 181
Query: 183 LDSEARLCEECSTGDVVTIEIAESRLINHTTGKEYKLKPIGDLGPVIDAGGIFAYARKTG 242
L+SE R+CEEC TGDVVT+E+ S LINHTTGKEYKLKPIGD GPVIDAGGIFAYARKTG
Sbjct: 182 LESEVRICEECKTGDVVTVELGNSVLINHTTGKEYKLKPIGDAGPVIDAGGIFAYARKTG 241
Query: 243 MIAS 246
MI S
Sbjct: 242 MIPS 245
>gnl|CDD|234762 PRK00439, leuD, 3-isopropylmalate dehydratase small subunit;
Reviewed.
Length = 163
Score = 156 bits (398), Expect = 2e-48
Identities = 72/173 (41%), Positives = 100/173 (57%), Gaps = 15/173 (8%)
Query: 71 HGLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTK 130
G + GDNIDTD IIPA YL S+P E L + + L + +
Sbjct: 1 KGRVWKFGDNIDTDVIIPARYLNT--SDPQE---LAKHCMEDLDPEFAKKV-------KP 48
Query: 131 YKIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARLC 190
II+AG NFGCGSSREHAP+AL AAG SAV+A+S+ARIF+RN++ G P+
Sbjct: 49 GDIIVAGKNFGCGSSREHAPIALKAAGVSAVIAKSFARIFYRNAINIG--LPVLECDEAV 106
Query: 191 EECSTGDVVTIEIAESRLINHTTGKEYKLKPIGD-LGPVIDAGGIFAYARKTG 242
++ GD V +++ + N TTG+EYK KPI + + ++ AGG+ Y +K G
Sbjct: 107 DKIEDGDEVEVDLETGVITNLTTGEEYKFKPIPEFMLEILKAGGLIEYLKKKG 159
>gnl|CDD|131139 TIGR02084, leud, 3-isopropylmalate dehydratase, small subunit.
Homoaconitase, aconitase, and 3-isopropylmalate
dehydratase have similar overall structures. All are
dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur
cluster. 3-isopropylmalate dehydratase is split into
large (leuC) and small (leuD) chains in eubacteria.
Several pairs of archaeal proteins resemble the leuC and
leuD pair in length and sequence but even more closely
resemble the respective domains of homoaconitase, and
their identity is uncertain. The members of the seed for
this model are those sequences which are gene clustered
with other genes involved in leucine biosynthesis and
include some archaea [Amino acid biosynthesis, Pyruvate
family].
Length = 156
Score = 127 bits (321), Expect = 5e-37
Identities = 67/173 (38%), Positives = 98/173 (56%), Gaps = 21/173 (12%)
Query: 72 GLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKY 131
G + GDN+DTD IIPA YL N + ++L + + L + + K
Sbjct: 1 GKVHKYGDNVDTDVIIPARYL-----NTSDPKELAKHCMEDL----------DKDFVKKV 45
Query: 132 K---IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEAR 188
K II+AG NFGCGSSREHAP+A+ A+G S V+A+S+ARIF+RN++ G P+
Sbjct: 46 KEGDIIVAGENFGCGSSREHAPIAIKASGISCVIAKSFARIFYRNAINIG--LPIVESEE 103
Query: 189 LCEECSTGDVVTIEIAESRLINHTTGKEYKLKPIGD-LGPVIDAGGIFAYARK 240
+E GD V +++ + + N T GKEYK P + L ++ AGG+ Y +K
Sbjct: 104 AVDEIEEGDEVEVDLEKGIIKNLTKGKEYKATPFPEFLQKIMKAGGLLNYVKK 156
>gnl|CDD|223144 COG0066, LeuD, 3-isopropylmalate dehydratase small subunit [Amino
acid transport and metabolism].
Length = 191
Score = 125 bits (315), Expect = 1e-35
Identities = 56/155 (36%), Positives = 80/155 (51%), Gaps = 20/155 (12%)
Query: 78 GDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDEN--ETKTKYK--- 132
DN+DTDQIIP +L + LG + R++D + Y+
Sbjct: 16 RDNVDTDQIIPKRFLKTI--TRTG---LGKHLFEDW------RYLDPDFVLNVPPYQGGD 64
Query: 133 IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARLCE- 191
I++AG NFGCGSSREHAP AL G AV+A S+A IF+RN++ G + + +E + E
Sbjct: 65 ILVAGENFGCGSSREHAPWALKDYGIRAVIAPSFADIFYRNAINNGLLPIVLAEEDVTEL 124
Query: 192 -ECSTGDVVTIEIAESRLINHTTGKEYKLKPIGDL 225
E GD VT+++ + N T G+E I D
Sbjct: 125 FEDVPGDEVTVDLETGEVTNPTGGEEP--FEIDDF 157
>gnl|CDD|233716 TIGR02087, LEUD_arch, 3-isopropylmalate dehydratase, small subunit.
This subfamily is most closely related to the
3-isopropylmalate dehydratase, small subunits which form
TIGR00171. This subfamily includes the members of
TIGR02084 which are gene clustered with other genes of
leucine biosynthesis. The rest of the subfamily includes
mainly archaeal species which exhibit two hits to this
model. In these cases it is possible that one or the
other of the hits does not have a 3-isopropylmalate
dehydratase activity but rather one of the other related
aconitase-like activities.
Length = 154
Score = 122 bits (307), Expect = 5e-35
Identities = 65/173 (37%), Positives = 98/173 (56%), Gaps = 22/173 (12%)
Query: 72 GLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKY 131
G + GD+IDTD+IIP YL +PDE L S+A+ G ID K
Sbjct: 1 GRVWKFGDDIDTDEIIPGRYLRTT--DPDE---LASHAMEG---------IDPEFAKKVR 46
Query: 132 K--IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARL 189
+I+AG NFGCGSSRE A +AL AAG +AV+AES+ARIF+RN++ G + ++++
Sbjct: 47 PGDVIVAGKNFGCGSSREQAALALKAAGIAAVIAESFARIFYRNAINIG-LPLIEAKTEG 105
Query: 190 CEECSTGDVVTIEIAESRLINHTTGKEYKLKPIGDLG-PVIDAGGIFAYARKT 241
++ GD VT+++ + +EYK +P+ D ++ GG+ Y +K
Sbjct: 106 IKD---GDEVTVDLETGEIRV-NGNEEYKGEPLPDFLLEILREGGLLEYLKKR 154
>gnl|CDD|238809 cd01577, IPMI_Swivel, Aconatase-like swivel domain of
3-isopropylmalate dehydratase and related
uncharacterized proteins. 3-isopropylmalate dehydratase
catalyzes the isomerization between 2-isopropylmalate
and 3-isopropylmalate, via the formation of
2-isopropylmaleate 3-isopropylmalate. IPMI is involved
in fungal and bacterial leucine biosynthesis and is also
found in eukaryotes. This is the aconitase-like swivel
domain, which is believed to undergo swivelling
conformational change in the enzyme mechanism.
Length = 91
Score = 116 bits (293), Expect = 1e-33
Identities = 50/128 (39%), Positives = 61/128 (47%), Gaps = 39/128 (30%)
Query: 76 VVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKIII 135
+ GDNIDTDQIIPA +L II+
Sbjct: 1 LFGDNIDTDQIIPARFL--------------------------------------GDIIV 22
Query: 136 AGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARLCEECST 195
AG NFGCGSSREHAP AL AG AV+AES+ARIFFRN++ G + P+ EE
Sbjct: 23 AGKNFGCGSSREHAPWALKDAGIRAVIAESFARIFFRNAINNG-LLPVTLADEDVEEVEA 81
Query: 196 GDVVTIEI 203
+E+
Sbjct: 82 KPGDEVEV 89
>gnl|CDD|179314 PRK01641, leuD, isopropylmalate isomerase small subunit;
Provisional.
Length = 200
Score = 96.0 bits (240), Expect = 2e-24
Identities = 44/140 (31%), Positives = 64/140 (45%), Gaps = 26/140 (18%)
Query: 78 GDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENET-------KTK 130
N+DTDQIIP ++L + G R++D+ + + +
Sbjct: 16 RANVDTDQIIPKQFLKRI-----TRTGFGKGLF------DDWRYLDDGQPNPDFVLNQPR 64
Query: 131 YK---IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYP--LDS 185
Y+ I++AG NFGCGSSREHAP AL G AV+A S+A IF+ N G + P L
Sbjct: 65 YQGASILLAGDNFGCGSSREHAPWALADYGFRAVIAPSFADIFYNNCFKNG-LLPIVLPE 123
Query: 186 E--ARLCEECSTGDVVTIEI 203
E L + + +
Sbjct: 124 EDVDELFKLVEANPGAELTV 143
>gnl|CDD|184460 PRK14023, PRK14023, homoaconitate hydratase small subunit;
Provisional.
Length = 166
Score = 91.8 bits (228), Expect = 3e-23
Identities = 58/166 (34%), Positives = 87/166 (52%), Gaps = 16/166 (9%)
Query: 78 GDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKIIIAG 137
GDNI+TD I+P +Y + ++ +YA L + + + I++AG
Sbjct: 8 GDNINTDDILPGKYAPFMVGE----DRFHNYAFAHLRPEFASTVRPGD-------ILVAG 56
Query: 138 GNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARLCEECSTGD 197
NFG GSSRE+AP AL G A++A+SYARIF+RN V G I P +SE + + GD
Sbjct: 57 RNFGLGSSREYAPEALKMLGIGAIIAKSYARIFYRNLVNLG-IPPFESE-EVVDALEDGD 114
Query: 198 VVTIEIAESRLINHTTGKEYKLKPIGD-LGPVIDAGGIFAYARKTG 242
V +++ L G+ ++L+P + L + G I Y RK G
Sbjct: 115 EVELDLETGVLT--RGGETFQLRPPPEFLLEALKEGSILEYYRKHG 158
>gnl|CDD|129275 TIGR00171, leuD, 3-isopropylmalate dehydratase, small subunit.
Homoaconitase, aconitase, and 3-isopropylmalate
dehydratase have similar overall structures. All are
dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur
cluster. 3-isopropylmalate dehydratase is split into
large (leuC) and small (leuD) chains in eubacteria.
Several pairs of archaeal proteins resemble the leuC and
leuD pair in length and sequence but even more closely
resemble the respective domains of homoaconitase, and
their identity is uncertain. The candidate archaeal leuD
proteins are not included in the seed alignment for this
model and score below the trusted cutoff [Amino acid
biosynthesis, Pyruvate family].
Length = 188
Score = 77.9 bits (192), Expect = 9e-18
Identities = 40/111 (36%), Positives = 55/111 (49%), Gaps = 23/111 (20%)
Query: 80 NIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTK--------- 130
N+DTD IIP ++L + + G G + RF+D N +
Sbjct: 18 NVDTDAIIPKQFLKRI-------TRTG----FGKHLFFDWRFLDANGKEPNPDFVLNQPQ 66
Query: 131 YK---IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATG 178
Y+ I++A NFGCGSSREHAP AL G ++A S+A IF+ NS G
Sbjct: 67 YQGASILLARENFGCGSSREHAPWALDDYGFKVIIAPSFADIFYNNSFKNG 117
>gnl|CDD|201399 pfam00694, Aconitase_C, Aconitase C-terminal domain. Members of
this family usually also match to pfam00330. This domain
undergoes conformational change in the enzyme mechanism.
Length = 131
Score = 73.1 bits (180), Expect = 2e-16
Identities = 40/116 (34%), Positives = 57/116 (49%), Gaps = 17/116 (14%)
Query: 79 DNIDTDQIIPAEYL-----TLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYK- 132
N+DTD IIP ++L + + + + LP F+D E +YK
Sbjct: 17 SNVDTDLIIPKQFLGTIANIGLGNILFDGWRANKT--THLPTGENPDFVDAAE---RYKQ 71
Query: 133 -----IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPL 183
++I G N+GCGSSREHA A G AV+A+S+ARI N + G + PL
Sbjct: 72 HGAPILVIGGKNYGCGSSREHAAWAPRDLGIKAVIAKSFARIHRNNLIKNG-LLPL 126
>gnl|CDD|238236 cd00404, Aconitase_swivel, Aconitase swivel domain. Aconitase
(aconitate hydratase) catalyzes the reversible
isomerization of citrate and isocitrate as part of the
TCA cycle. This is the aconitase swivel domain, which
undergoes swivelling conformational change in the enzyme
mechanism. The aconitase family contains the following
proteins: - Iron-responsive element binding protein
(IRE-BP). IRE-BP is a cytosolic protein that binds to
iron-responsive elements (IREs). IREs are stem-loop
structures found in the 5'UTR of ferritin, and delta
aminolevulinic acid synthase mRNAs, and in the 3'UTR of
transferrin receptor mRNA. IRE-BP also express aconitase
activity. - 3-isopropylmalate dehydratase
(isopropylmalate isomerase), the enzyme that catalyzes
the second step in the biosynthesis of leucine. -
Homoaconitase (homoaconitate hydratase), an enzyme that
participates in the alpha-aminoadipate pathway of lysine
biosynthesis and that converts cis-homoaconitate into
homoisocitric acid.
Length = 88
Score = 65.6 bits (160), Expect = 4e-14
Identities = 39/127 (30%), Positives = 52/127 (40%), Gaps = 42/127 (33%)
Query: 76 VVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKIII 135
V NI TD I PA ++I
Sbjct: 1 KVAGNITTDHISPAGPG----------------------------------------VVI 20
Query: 136 AGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLD-SEARLCEECS 194
N+G GSSREHA + L G AV+A+S+ARIFFRN V G + PL+ ++ +
Sbjct: 21 GDENYGTGSSREHAALELRLLGGRAVIAKSFARIFFRNLVDQG-LLPLEFADPEDYLKLH 79
Query: 195 TGDVVTI 201
TGD + I
Sbjct: 80 TGDELDI 86
>gnl|CDD|238811 cd01579, AcnA_Bact_Swivel, Bacterial Aconitase-like swivel domain.
Aconitase (aconitate hydratase or citrate hydrolyase)
catalyzes the reversible isomerization of citrate and
isocitrate as part of the TCA cycle. Cis-aconitate is
formed as an intermediate product during the course of
the reaction. This is the aconitase-like swivel domain,
which is believed to undergo swivelling conformational
change in the enzyme mechanism. This distinct subfamily
is found only in bacteria and archea. Its exact
characteristics are not known.
Length = 121
Score = 66.3 bits (162), Expect = 5e-14
Identities = 41/110 (37%), Positives = 54/110 (49%), Gaps = 12/110 (10%)
Query: 76 VVGDNIDTDQIIPA--EYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKI 133
VGDNI TD I+PA + L L SN + + + T+ R
Sbjct: 1 KVGDNITTDHIMPAGAKVLPL-RSN---IPAISEFVFHRVDPTFAER-----AKAAGPGF 51
Query: 134 IIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPL 183
I+ G N+G GSSREHA +A G AV+A+S+ARI N + G I PL
Sbjct: 52 IVGGENYGQGSSREHAALAPMYLGVRAVLAKSFARIHRANLINFG-ILPL 100
>gnl|CDD|223977 COG1048, AcnA, Aconitase A [Energy production and conversion].
Length = 861
Score = 68.9 bits (169), Expect = 2e-13
Identities = 45/196 (22%), Positives = 66/196 (33%), Gaps = 47/196 (23%)
Query: 76 VVGDNIDTDQIIPAEYLTLVPSNPD-------EYEKLGSYA------------------- 109
+GD+I TD I PA + E SY
Sbjct: 641 KLGDSITTDHISPAGSIKADSPAGKYLYEHGVERIDFNSYGSRRGNHEVMMRGTFANIRI 700
Query: 110 ---LIGLPATYTTRFIDEN--ETKTKYK------IIIAGGNFGCGSSREHAPVALGAAGC 158
++ YT + KYK +++AG N+G GSSR+ A G
Sbjct: 701 RNEMVPGEGGYTIHQPSGEIYDAAMKYKEEGIPLVVVAGKNYGTGSSRDWAAKGPRLLGV 760
Query: 159 SAVVAESYARIFFRNSVATG----EIYPLDSEARLCEECSTGDVVTIEIAESRLINHTTG 214
AV+AES+ RI N + G + ++ +L TI+I L N G
Sbjct: 761 KAVIAESFERIHRSNLIGMGVLPLQFPNGETYDKL----GLDGEETIDIG--GLENLKPG 814
Query: 215 KEYKLKPIGDLGPVID 230
+ GPV +
Sbjct: 815 ATVTVTVTRGDGPVEE 830
>gnl|CDD|235974 PRK07229, PRK07229, aconitate hydratase; Validated.
Length = 646
Score = 68.6 bits (169), Expect = 2e-13
Identities = 57/185 (30%), Positives = 85/185 (45%), Gaps = 40/185 (21%)
Query: 77 VGDNIDTDQIIPA--EYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKII 134
VGDNI TD I+PA ++L SN + + G+ T+ R ++ I+
Sbjct: 477 VGDNITTDHIMPAGAKWLPY-RSNIP---NISEFVFEGVDNTFPERAKEQGGG-----IV 527
Query: 135 IAGGNFGCGSSREHA---PVALGAAGCSAVVAESYARIFFRNSVATGEIYPL---DSE-- 186
+ G N+G GSSREHA P LG AV+A+S+ARI N + G I PL D
Sbjct: 528 VGGENYGQGSSREHAALAPRYLGVK---AVLAKSFARIHKANLINFG-ILPLTFADPADY 583
Query: 187 ARLCEECSTGDVVTI----EIAESR---LINHTTGKEYKLKPIGDLGP----VIDAGGIF 235
++ E GDV+ I E ++N T +E +++ L ++ AGG
Sbjct: 584 DKIEE----GDVLEIEDLREFLPGGPLTVVNVTKDEEIEVRH--TLSERQIEILLAGGAL 637
Query: 236 AYARK 240
+K
Sbjct: 638 NLIKK 642
>gnl|CDD|130409 TIGR01342, acon_putative, aconitate hydratase, putative, Aquifex
type. This model represents a small family of proteins
homologous (and likely functionally equivalent to)
aconitase 1. Members are found, so far in the anaerobe
Clostridium acetobutylicum, in the microaerophilic,
early-branching bacterium Aquifex aeolicus, and in the
halophilic archaeon Halobacterium sp. NRC-1. No member
is experimentally characterized [Energy metabolism, TCA
cycle].
Length = 658
Score = 61.2 bits (148), Expect = 7e-11
Identities = 45/110 (40%), Positives = 58/110 (52%), Gaps = 6/110 (5%)
Query: 76 VVGDNIDTDQIIPAEYLTL-VPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKII 134
++ DNI TD IIPA L SN E + + L + + R + K K II
Sbjct: 478 IMEDNITTDHIIPAGADILKFRSN---IEAISEFTLHRIDDEFAER-AKAADEKGKAGII 533
Query: 135 IAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLD 184
IAG N+G GSSREHA +A G AV+A+S+ARI N G I PL+
Sbjct: 534 IAGENYGQGSSREHAALAPMFLGVEAVIAKSFARIHHANLFNFG-ILPLE 582
>gnl|CDD|238837 cd01674, Homoaconitase_Swivel, Homoaconitase swivel domain. This
family includes homoaconitase and other uncharacterized
proteins of the Aconitase family. Homoaconitase is part
of an unusual lysine biosynthesis pathway found only in
filamentous fungi, in which lysine is synthesized via
the alpha-aminoadipate pathway. In this pathway,
homoaconitase catalyzes the conversion of
cis-homoaconitic acid into homoisocitric acid. The
reaction mechanism is believed to be similar to that of
other aconitases. This is the swivel domain, which is
believed to undergo swivelling conformational change in
the enzyme mechanism.
Length = 129
Score = 56.9 bits (137), Expect = 2e-10
Identities = 36/98 (36%), Positives = 50/98 (51%), Gaps = 12/98 (12%)
Query: 79 DNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKY-KIIIAG 137
DN++TD I P +Y P++ ++ + E TKTK I+++G
Sbjct: 4 DNLNTDGIYPGKYTYQDDITPEKMAEV-----------CMENYDSEFSTKTKQGDILVSG 52
Query: 138 GNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSV 175
NFG GSSRE A AL A G VV+ S+ IF RNS+
Sbjct: 53 FNFGTGSSREQAATALLAKGIPLVVSGSFGNIFSRNSI 90
>gnl|CDD|129245 TIGR00139, h_aconitase, homoaconitase. Homoaconitase is known only
as a fungal enzyme from two species, where it is part of
an unusual lysine biosynthesis pathway. Because This
model is based on just two sequences from a narrow
taxonomic range, it may not recognize distant orthologs,
should any exist. Homoaconitase, aconitase, and
3-isopropylmalate dehydratase have similar overall
structures, but 3-isopropylmalate dehydratase is split
into large (leuC) and small (leuD) chains in eubacteria.
Several pairs of archaeal proteins resemble leuC and
leuD over their lengths but are even closer to the
respective domains of homoaconitase, and their identity
is uncertain [Amino acid biosynthesis, Aspartate
family].
Length = 712
Score = 56.6 bits (136), Expect = 3e-09
Identities = 38/103 (36%), Positives = 53/103 (51%), Gaps = 10/103 (9%)
Query: 73 LCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYK 132
L + DNI+TD I P +Y T P E K+ + A + T +
Sbjct: 535 LVFCDADNINTDGIYPGKY-TYQDDVPKE--KMAQVCMENYDAEFRT-------KAHEGD 584
Query: 133 IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSV 175
I+++G NFGCGSSRE A A+ A G + VV+ S+ IF RNS+
Sbjct: 585 ILVSGFNFGCGSSREQAATAILAKGINLVVSGSFGNIFSRNSI 627
>gnl|CDD|238812 cd01580, AcnA_IRP_Swivel, Aconitase A swivel domain. This is the
major form of the TCA cycle enzyme aconitate hydratase,
also known as aconitase and citrate hydro-lyase. It
includes bacterial and archaeal aconitase A, and the
eukaryotic cytosolic form of aconitase. This group also
includes sequences that have been shown to act as an
iron-responsive element (IRE) binding protein in animals
and may have the same role in other eukaryotes. This is
the aconitase-like swivel domain, which is believed to
undergo swivelling conformational change in the enzyme
mechanism.
Length = 171
Score = 50.4 bits (121), Expect = 7e-08
Identities = 43/151 (28%), Positives = 59/151 (39%), Gaps = 46/151 (30%)
Query: 76 VVGDNIDTDQIIPA----------EYLTLVPSNPDEYEKLGS------------------ 107
++GD++ TD I PA +YL P ++ GS
Sbjct: 1 LLGDSVTTDHISPAGSIAKDSPAGKYLAERGVKPRDFNSYGSRRGNDEVMMRGTFANIRL 60
Query: 108 -YALIGLPATYTTRFIDENETKT------KYK------IIIAGGNFGCGSSREHAPVALG 154
L+ TT E + +YK +I+AG +G GSSR+ A A G
Sbjct: 61 RNKLVPGTEGGTTHHPPTGEVMSIYDAAMRYKEEGVPLVILAGKEYGSGSSRDWA--AKG 118
Query: 155 AA--GCSAVVAESYARIFFRNSVATGEIYPL 183
G AV+AES+ RI N V G I PL
Sbjct: 119 PFLLGVKAVIAESFERIHRSNLVGMG-ILPL 148
>gnl|CDD|131386 TIGR02333, 2met_isocit_dHY, 2-methylisocitrate dehydratase,
Fe/S-dependent. Members of this family appear in an
operon for the degradation of propionyl-CoA via
2-methylcitrate. This family is homologous to aconitases
A and B and appears to act the part as
2-methylisocitrate dehydratase, the enzyme after PrpD
and before PrpB. In Escherichia coli, which lacks a
member of this family, 2-methylisocitrate dehydratase
activity was traced to aconitase B (TIGR00117)
(PMID:12473114).
Length = 858
Score = 48.1 bits (114), Expect = 2e-06
Identities = 35/84 (41%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 104 KLGSYALIGLPATYTTRFIDENETKTKYK---IIIAGGNFGCGSSREHAPVALGAAGCSA 160
K GS A I P TR + ET K IIIAG ++G GSSR+ A + AG A
Sbjct: 703 KQGSLARIE-PEGKVTRMWEAIETYMNRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEA 761
Query: 161 VVAESYARIFFRNSVATGEIYPLD 184
+VAE + RI N V G + PL+
Sbjct: 762 IVAEGFERIHRTNLVGMG-VLPLE 784
>gnl|CDD|237246 PRK12881, acnA, aconitate hydratase; Provisional.
Length = 889
Score = 46.1 bits (110), Expect = 8e-06
Identities = 42/154 (27%), Positives = 58/154 (37%), Gaps = 52/154 (33%)
Query: 76 VVGDNIDTDQIIPA----------EYLTLVPSNPDEYEKLGSYA------LIGLPATYT- 118
V+GD+I TD I PA +YL N SY + + T+
Sbjct: 664 VLGDSITTDHISPAGAIKADSPAGKYLK---ENGVPKADFNSYGSRRGNHEVMMRGTFAN 720
Query: 119 ---------------TRFIDENETKT------KYK------IIIAGGNFGCGSSREHAPV 151
T E + +Y+ ++IAG +G GSSR+ A
Sbjct: 721 VRIKNLMIPGKEGGLTLHQPSGEVLSIYDAAMRYQAAGTPLVVIAGEEYGTGSSRDWA-- 778
Query: 152 ALGA--AGCSAVVAESYARIFFRNSVATGEIYPL 183
A G G AV+AES+ RI N V G + PL
Sbjct: 779 AKGTRLLGVKAVIAESFERIHRSNLVGMG-VLPL 811
>gnl|CDD|240263 PTZ00092, PTZ00092, aconitate hydratase-like protein; Provisional.
Length = 898
Score = 45.4 bits (108), Expect = 2e-05
Identities = 28/62 (45%), Positives = 34/62 (54%), Gaps = 11/62 (17%)
Query: 130 KYK------IIIAGGNFGCGSSREHAPVALGAA--GCSAVVAESYARIFFRNSVATGEIY 181
KYK I++AG +G GSSR+ A A G G AV+AES+ RI N V G I
Sbjct: 765 KYKQEGVPLIVLAGKEYGSGSSRDWA--AKGPYLQGVKAVIAESFERIHRSNLVGMG-IL 821
Query: 182 PL 183
PL
Sbjct: 822 PL 823
>gnl|CDD|236445 PRK09277, PRK09277, aconitate hydratase; Validated.
Length = 888
Score = 44.7 bits (107), Expect = 2e-05
Identities = 40/141 (28%), Positives = 55/141 (39%), Gaps = 53/141 (37%)
Query: 76 VVGDNIDTDQIIPA----------EYLTLVPSNPDEYEKLGSYA---------------- 109
++GD+I TD I PA +YL + E + SY
Sbjct: 663 LLGDSITTDHISPAGAIKADSPAGKYLL---EHGVEPKDFNSYGSRRGNHEVMMRGTFAN 719
Query: 110 -------LIGLPATYTTRFIDENETKT------KYK------IIIAGGNFGCGSSREHAP 150
+ G+ YT R E E + KYK ++IAG +G GSSR+ A
Sbjct: 720 IRIRNEMVPGVEGGYT-RHFPEGEVMSIYDAAMKYKEEGTPLVVIAGKEYGTGSSRDWAA 778
Query: 151 --VALGAAGCSAVVAESYARI 169
L G AV+AES+ RI
Sbjct: 779 KGTRL--LGVKAVIAESFERI 797
>gnl|CDD|233363 TIGR01341, aconitase_1, aconitate hydratase 1. This model
represents one form of the TCA cycle enzyme aconitate
hydratase, also known as aconitase and citrate
hydro-lyase. It is found in bacteria, archaea, and
eukaryotic cytosol. It has been shown to act also as an
iron-responsive element binding protein in animals and
may have the same role in other eukaryotes [Energy
metabolism, TCA cycle].
Length = 876
Score = 43.6 bits (103), Expect = 5e-05
Identities = 43/153 (28%), Positives = 59/153 (38%), Gaps = 42/153 (27%)
Query: 76 VVGDNIDTDQIIPA----------EYLTLVPSNPDEYEKLGS------------YALI-- 111
++GD+I TD I PA +YL + ++ GS +A I
Sbjct: 653 LLGDSITTDHISPAGSITKDSPAGKYLQERGVSRRDFNSYGSRRGNHEVMMRGTFANIRI 712
Query: 112 ------GLPATYTTRFIDENETKT-----KYK------IIIAGGNFGCGSSREHAPVALG 154
G YT F D +YK ++IAG +G GSSR+ A
Sbjct: 713 KNLMVKGKEGGYTVHFPDGKVASVYDAAMQYKKEGTPLVVIAGKEYGSGSSRDWAAKGTK 772
Query: 155 AAGCSAVVAESYARIFFRNSVATGEIYPLDSEA 187
G AV+AES+ RI N V G + PL
Sbjct: 773 LLGVKAVIAESFERIHRSNLVGMG-VIPLQFPQ 804
>gnl|CDD|215047 PLN00070, PLN00070, aconitate hydratase.
Length = 936
Score = 39.4 bits (92), Expect = 0.001
Identities = 26/60 (43%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 130 KYK------IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPL 183
KYK II+AG +G GSSR+ A G AV+A+S+ RI N V G I PL
Sbjct: 801 KYKSEGHDTIILAGAEYGSGSSRDWAAKGPMLLGVKAVIAKSFERIHRSNLVGMG-IIPL 859
>gnl|CDD|238810 cd01578, AcnA_Mitochon_Swivel, Mitochondrial aconitase A swivel
domain. Aconitase (also known as aconitate hydratase and
citrate hydro-lyase) catalyzes the reversible
isomerization of citrate and isocitrate as part of the
TCA cycle. This is the aconitase swivel domain, which
undergoes swivelling conformational change in the enzyme
mechanism. In eukaryotes two isozymes of aconitase are
known to exist: one found in the mitochondrial matrix
and the other found in the cytoplasm. This is the
mitochondrial form. The mitochondrial product is coded
by a nuclear gene. Most members of this subfamily are
mitochondrial but there are some bacterial members.
Length = 149
Score = 37.4 bits (87), Expect = 0.002
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 133 IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARI 169
++I N+G GSSREHA + G A++ +S+ARI
Sbjct: 72 VVIGDENYGEGSSREHAALEPRHLGGRAIITKSFARI 108
>gnl|CDD|173273 PRK14812, PRK14812, hypothetical protein; Provisional.
Length = 119
Score = 35.9 bits (82), Expect = 0.004
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 143 GSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGE---IYPLDSEARLCEECSTGDVV 199
GSSREHA AL G V+A S+ I + N + G + P + +L + T D V
Sbjct: 3 GSSREHAAWALADYGFKVVIAGSFGDIHYNNELNNGMLPIVQPREVREKLAQLKPT-DQV 61
Query: 200 TIEIAESRLIN 210
T+++ + ++I+
Sbjct: 62 TVDLEQQKIIS 72
>gnl|CDD|233362 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
This model represents mitochondrial forms of the TCA
cycle enzyme aconitate hydratase, also known as
aconitase and citrate hydro-lyase [Energy metabolism,
TCA cycle].
Length = 745
Score = 35.2 bits (81), Expect = 0.030
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 133 IIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARI 169
+++A N+G GS+REHA + G ++ +S+ARI
Sbjct: 625 VVVAEHNYGEGSAREHAALEPRHLGGRIIITKSFARI 661
>gnl|CDD|224034 COG1109, {ManB}, Phosphomannomutase [Carbohydrate transport and
metabolism].
Length = 464
Score = 30.4 bits (69), Expect = 0.94
Identities = 17/94 (18%), Positives = 29/94 (30%), Gaps = 7/94 (7%)
Query: 82 DTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPA----TYTTRFIDENETKTKYKIIIAG 137
D ++ I A V + +LG I + +D + K+++
Sbjct: 126 DIEEEIEAILAEEVDLPRPSWGELGRLKRIPDALDRYIEFIKSLVDVDLKLRGLKVVVDC 185
Query: 138 GNFGCGSSREHAPVALGAAGCSAVVAESYARIFF 171
N G++ AP L G V F
Sbjct: 186 AN---GAAGLVAPRLLKELGAEVVSINCDPDGLF 216
>gnl|CDD|172019 PRK13382, PRK13382, acyl-CoA synthetase; Provisional.
Length = 537
Score = 30.1 bits (68), Expect = 1.1
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 179 EIYPLDSEARLCEECSTGDVVTIEIAESRLIN-HTTG--KEYK--LKPIGDLGPVIDAGG 233
EI LD + R E TG+V TI + + +T+G K++ GD+G + + G
Sbjct: 375 EIRILDQDFR---EVPTGEVGTIFVRNDTQFDGYTSGSTKDFHDGFMASGDVGYLDENGR 431
Query: 234 IFAYARKTGMIAS 246
+F R MI S
Sbjct: 432 LFVVGRDDEMIVS 444
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 28.9 bits (64), Expect = 2.6
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 160 AVVAESYARIFFRNSVATGEIYPLDSEARLCEEC 193
A+V E YAR+F A G+IY D E C C
Sbjct: 168 AIVKEFYARVF-----ANGDIYRADYEGLYCVNC 196
>gnl|CDD|236424 PRK09238, PRK09238, bifunctional aconitate hydratase
2/2-methylisocitrate dehydratase; Validated.
Length = 835
Score = 29.0 bits (66), Expect = 3.0
Identities = 41/171 (23%), Positives = 63/171 (36%), Gaps = 44/171 (25%)
Query: 75 YVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATY--TTRFIDENET----- 127
+ V +TD + PA S PD I L A R +
Sbjct: 171 FKVTGETNTDDLSPAPDAW---SRPD----------IPLHALAMLKNRRPGPIKQIEELK 217
Query: 128 KTKYKIIIAGGNFGCGSSREHA--PVA--LG----------AAGCSAVVAESYARIFFRN 173
K + + G G GSSR+ A V +G A G V+ A IFF
Sbjct: 218 KKGHPVAYVGDVVGTGSSRKSATNSVLWHMGEDIPYVPNKRAGG--VVLGGKIAPIFFNT 275
Query: 174 SVATGEIYPLDSEARLCEECSTGDVVTIEIAESRLINHTTGK---EYKLKP 221
+G + P++ + + + GDV+ I + + I + TG+ +KLK
Sbjct: 276 MEDSGAL-PIELDV---SKLNMGDVIDIYPYKGK-IRNETGEVIATFKLKT 321
>gnl|CDD|217906 pfam04115, Ureidogly_hydro, Ureidoglycolate hydrolase.
Ureidoglycolate hydrolase (EC:3.5.3.19) carried out the
third step in the degradation of allantoin.
Length = 156
Score = 27.5 bits (62), Expect = 4.9
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 196 GDVVTIEIAESRLINH-TTGKEYKLKPIGDLGPVIDAG-GIF 235
GDV+ + A +IN T G+ + L + GP AG +F
Sbjct: 17 GDVIETDGAPDFIINQGTAGRYHDLARVDFAGPGGRAGISLF 58
>gnl|CDD|237336 PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
Length = 214
Score = 27.3 bits (61), Expect = 7.2
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 81 IDTDQIIPAEYL-TLVPSNPDEYEKLGSYALIGLPATYTTRFIDEN 125
I+T+++I + +L TL P++Y++ IG T IDE+
Sbjct: 15 INTNELIISSFLHTLKTYYPNQYKREDVLPFIGPSLHDTFSKIDES 60
>gnl|CDD|222888 PHA02582, 10, baseplate wedge subunit and tail pin; Provisional.
Length = 604
Score = 27.3 bits (61), Expect = 7.8
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 178 GEIYPLDSEA-RLCEECSTGDVVTIE 202
GE+ PLD ++ RL + C+ GD V I
Sbjct: 218 GELVPLDGKSIRLRQPCNAGDTVQIV 243
>gnl|CDD|235855 PRK06707, PRK06707, amidase; Provisional.
Length = 536
Score = 27.2 bits (60), Expect = 8.6
Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 37 GNGRAAVTFQRAVSVIPKATSADSRATKEPTATFHGLCYVVGDNIDTDQIIP 88
G +VT + + + +A D ++ + +G+ VV DN+ T +++P
Sbjct: 105 GITLNSVT-EINPNAMEEARKLDQERSRNKKSNLYGIPVVVKDNVQTAKVMP 155
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
0.316 0.133 0.385
Gapped
Lambda K H
0.267 0.0813 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,487,905
Number of extensions: 1170977
Number of successful extensions: 1025
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1003
Number of HSP's successfully gapped: 45
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.0 bits)