RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14904
(233 letters)
>gnl|CDD|234625 PRK00090, bioD, dithiobiotin synthetase; Reviewed.
Length = 222
Score = 216 bits (554), Expect = 2e-71
Identities = 86/226 (38%), Positives = 125/226 (55%), Gaps = 10/226 (4%)
Query: 9 YFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNKY 68
F+TGT+T++GKT+++ AL ++ G S G KP+ SG + N D L +
Sbjct: 2 LFVTGTDTDVGKTVVTAALAQALREAGYSVAGYKPVQSGCE-----ETDRNGDALALQRL 56
Query: 69 SN--SLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIG 126
S YE +NPY F+ P+SP+ ++ LE I+ I L+ D++++EG G
Sbjct: 57 SGLPLDYE---DVNPYRFEEPLSPHLAAALEGVAIDLEKISAALRRLAQQYDLVLVEGAG 113
Query: 127 GFSVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVANHTQ 186
G VP ++ ADLA++L LP+ILV+ +K+GCIN+ LL+LEAI +RGL L GWVAN
Sbjct: 114 GLLVPLTEDLTLADLAKQLQLPVILVVGVKLGCINHTLLTLEAIRARGLPLAGWVANGIP 173
Query: 187 IVDTLFANENYIELTKYLNVTPLGRIPYLYNLNINLISHYLDFSSL 232
L EN L + L LG +PYL + + YLD L
Sbjct: 174 PEPGLRHAENLATLERLLPAPLLGELPYLAEAELAAAAEYLDLDLL 219
>gnl|CDD|223210 COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism].
Length = 223
Score = 192 bits (490), Expect = 8e-62
Identities = 84/225 (37%), Positives = 126/225 (56%), Gaps = 7/225 (3%)
Query: 9 YFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNKY 68
+F+TGT+T +GKT++S AL K++G S G KP+ +G+ + N D +L +
Sbjct: 5 FFVTGTDTGVGKTVVSAALAQALKQQGYSVAGYKPVQTGS-----EETAENSDALVLQRL 59
Query: 69 SNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGF 128
S L +LINPY FK P+SP+ ++ LE R I+ + L D++++EG GG
Sbjct: 60 S-GLDLSYELINPYRFKEPLSPHLAAELEGRTIDLEKLSQGLRQLLKKYDLVLVEGAGGL 118
Query: 129 SVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVANHTQIV 188
VP + ADLA +L LP+ILV+ +K+G IN+ LL++EA+ +RGL L GWVAN
Sbjct: 119 LVPLTEEYTFADLAVQLQLPVILVVGIKLGTINHTLLTVEALRARGLPLAGWVANGINPE 178
Query: 189 DTLFANENYIELTKYLNVTPLGRIPYLYNLNINLISHYLDFSSLF 233
+A N L K + LG IPYL + +D ++L
Sbjct: 179 LDHYAEINAT-LLKRIGAPLLGIIPYLPESEEEELGKLIDLAALL 222
>gnl|CDD|129447 TIGR00347, bioD, dethiobiotin synthase. Dethiobiotin synthase is
involved in biotin biosynthesis and catalyses the
reaction (CO2 + 7,8-diaminononanoate + ATP =
dethiobiotin + phosphate + ADP). The enzyme binds ATP
(see motif in first 12 residues of the SEED alignment)
and requires magnesium as a co-factor [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 166
Score = 142 bits (359), Expect = 9e-43
Identities = 62/174 (35%), Positives = 96/174 (55%), Gaps = 8/174 (4%)
Query: 10 FITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNKYS 69
F+TGT+T +GKT+ S AL ++ KK G S KP+ +G N D LL S
Sbjct: 1 FVTGTDTGVGKTVASSALAAKLKKAGYSVGYYKPVQTGIEKTN-------SDALLLQNIS 53
Query: 70 NSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGFS 129
+ ++ + +NPY F P+SP+ +++ E R I+ + L D +++EG GG
Sbjct: 54 GTALDWDE-VNPYAFALPLSPHIAADQEGRPIDLEELSKHLRTLEQKYDFVLVEGAGGLC 112
Query: 130 VPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVAN 183
VP + +ADL + L LP+ILV+ +K+G IN+ LL++E GL L G + N
Sbjct: 113 VPITEEYTTADLIKLLQLPVILVVRVKLGTINHTLLTVEHARQTGLTLAGVILN 166
>gnl|CDD|237083 PRK12374, PRK12374, putative dithiobiotin synthetase; Provisional.
Length = 231
Score = 125 bits (315), Expect = 2e-35
Identities = 76/233 (32%), Positives = 121/233 (51%), Gaps = 26/233 (11%)
Query: 9 YFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAY-----LNNKNKIWFNEDVN 63
+FITGT+T++GKT++S ALL +G + G KP+A G+ L NK+
Sbjct: 5 FFITGTDTSVGKTVVSRALLQALASQGKTVAGYKPVAKGSKETPEGLRNKDA-------- 56
Query: 64 LLNKYSNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILE 123
L+ + +S+ + +NP +S SS + IN + + N LS D +++E
Sbjct: 57 LVLQSVSSIELPYEAVNPI----ALSEEESSVAHSCPINYTLMSNGLANLSEKVDHVVVE 112
Query: 124 GIGGFSVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVAN 183
G GG+ +D ++ + LP+++V+ ++ GCIN+ALL+ +AI + GL LIGWVAN
Sbjct: 113 GTGGWRSLMNDLRPLSEWVVQEQLPVLMVVGIQEGCINHALLTAQAIANDGLPLIGWVAN 172
Query: 184 HTQIVDTLFANENYIE----LTKYLNVTPLGRIPYLYNLNINLISHYLDFSSL 232
+I L +Y E L K L +G +PYL + Y+D S L
Sbjct: 173 --RINPGL---AHYAEIIDVLGKKLPAPLIGELPYLPRAEQRELGQYIDLSML 220
>gnl|CDD|222178 pfam13500, AAA_26, AAA domain. This domain is found in a number of
proteins involved in cofactor biosynthesis such as
dethiobiotin synthase and cobyric acid synthase. This
domain contains a P-loop motif.
Length = 197
Score = 116 bits (292), Expect = 2e-32
Identities = 68/212 (32%), Positives = 105/212 (49%), Gaps = 19/212 (8%)
Query: 8 HYFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNK 67
F+TGT+T +GKT++S L+ K RG+ KPI SG + D L+ +
Sbjct: 2 TIFVTGTDTGVGKTVVSLGLVRALK-RGVKVGYWKPIQSGLV--------DDGDSELVKR 52
Query: 68 YSNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGG 127
+ PY P+SP+ ++ LE I+ I+ L D +++EG GG
Sbjct: 53 LLGLDQTR-EHPEPYRLSAPLSPHLAARLEGVTIDLEKIVK---KLPKDADPLVVEGAGG 108
Query: 128 FSVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVANHTQI 187
VP ++N + D+A LGLP+ILV +G IN+ LL++EA+ SRG+ ++G + N
Sbjct: 109 LMVPLNENLLNIDIAANLGLPVILVARGGLGTINHTLLTIEALRSRGINILGVILNGVP- 167
Query: 188 VDTLFANENYIELTKYLNVTPLGRIPYLYNLN 219
N + + V LG IPYL +L
Sbjct: 168 -----NPANVEAIEAFSGVPVLGVIPYLPDLT 194
>gnl|CDD|239383 cd03109, DTBS, Dethiobiotin synthetase (DTBS) is the penultimate
enzyme in the biotin biosynthesis pathway in Escherichia
coli and other microorganisms. The enzyme catalyzes
formation of the ureido ring of dethiobiotin from
(7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon
dioxide. The enzyme utilizes carbon dioxide instead of
hydrogen carbonate as substrate and is dependent on ATP
and divalent metal ions as cofactors.
Length = 134
Score = 64.3 bits (157), Expect = 3e-13
Identities = 32/96 (33%), Positives = 53/96 (55%), Gaps = 1/96 (1%)
Query: 118 DVIILEGIGGFSVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKL 177
D +++EG GG VP ++ +AD+A++L LP ILV +G IN+A L++EA +G+ L
Sbjct: 40 DFVLVEGAGGLCVPLKEDFTNADVAKELNLPAILVTSAGLGSINHAFLTIEAARIKGIIL 99
Query: 178 IGWVANHTQIVDTLFANENYIELTKYLNVTPLGRIP 213
G + N + L N + + + LG +P
Sbjct: 100 NGVLGNVIVEKEGLATL-NVETIERLTGIPVLGIVP 134
Score = 41.6 bits (98), Expect = 5e-05
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 11 ITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYL 50
GT T+IGKT+ + L K++G +KP+ + ++
Sbjct: 3 GFGTGTDIGKTVATAILARALKEKGYRVAPLKPVQTYDFV 42
>gnl|CDD|232946 TIGR00379, cobB, cobyrinic acid a,c-diamide synthase. This model
describes cobyrinic acid a,c-diamide synthase, the cobB
(cbiA in Salmonella) protein of cobalamin biosynthesis.
It is responsible for the amidation of carboxylic groups
at positions A and C of either cobyrinic acid or
hydrogenobrynic acid. NH(2) groups are provided by
glutamine and one molecule of ATP hydrogenolyzed for
each amidation [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 449
Score = 48.3 bits (115), Expect = 1e-06
Identities = 48/216 (22%), Positives = 84/216 (38%), Gaps = 56/216 (25%)
Query: 11 ITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNKYSN 70
I GT++ +GKT IS ++ +R + ++P G
Sbjct: 4 IAGTSSGVGKTTISTGIMKALSRRKL---RVQPFKVGP---------------------- 38
Query: 71 SLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGF-- 128
I+P +F + S NL++ ++ + I C++ S TD I+EG+ G
Sbjct: 39 ------DYIDP-MFHTQATGRPSRNLDSFFMSEAQIQECFHRHSKGTDYSIIEGVRGLYD 91
Query: 129 -SVPFHDNENSADLAEKLGLPIILVIDLK-----IGCINNALLSLEAINSRGLKLIGWVA 182
D ++A +A+ L PI+LV++ + I S + G+KL G +
Sbjct: 92 GISAITDYGSTASVAKALDAPIVLVMNCQRLSRSAAAIVLGYRSFD----PGVKLKGVIL 147
Query: 183 NHTQIVDTLFANENYIELTK-----YLNVTPLGRIP 213
N +E ++E K + LG IP
Sbjct: 148 NRVG-------SERHLEKLKIAVEPLRGIPILGVIP 176
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 46.8 bits (112), Expect = 3e-06
Identities = 32/149 (21%), Positives = 61/149 (40%), Gaps = 37/149 (24%)
Query: 10 FITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGA-YLNNKNKIWFNEDVNLLNKY 68
I GT++ GKT ++ L+ ++RG+ ++P G Y
Sbjct: 4 VIAGTSSGSGKTTVTLGLMRALRRRGLK---VQPFKVGPDY------------------- 41
Query: 69 SNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGF 128
I+P + + S NL++ ++ + + + D+ ++EG+ G
Sbjct: 42 ----------IDPG-YHTAATGRPSRNLDSWMMGEEGVRALFARAAADADIAVIEGVMGL 90
Query: 129 --SVPFHDNENS-ADLAEKLGLPIILVID 154
+ S ADLA+ LG P++LV+D
Sbjct: 91 FDGRGSATDTGSTADLAKLLGAPVVLVVD 119
>gnl|CDD|215526 PLN02974, PLN02974, adenosylmethionine-8-amino-7-oxononanoate
transaminase.
Length = 817
Score = 45.9 bits (109), Expect = 9e-06
Identities = 42/163 (25%), Positives = 72/163 (44%), Gaps = 18/163 (11%)
Query: 82 YLFKYPISPYTSSNLENRIINTSHIINCYN-YL-------SNLTDVI-ILEGIGGFSVPF 132
+ ++ +SP+ ++ E R ++ ++ N L S V+ ++E GG + P
Sbjct: 141 FAWRRAVSPHLAARREGRGVSDDEVLEAVNRSLREVGANESGGGRVLALVETAGGVASPG 200
Query: 133 HDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAINSRGLKLIGWVANHTQIVDTLF 192
DL L LP ILV D ++G I+ L + E++ RG ++ V I D
Sbjct: 201 PSGTLQCDLYRPLRLPAILVGDGRLGGISATLAAYESLLLRGYDVVAVV-----IEDHGL 255
Query: 193 ANENYIELTKYL-NVTPLGRIPYL-YNLNINLISHYLDFSSLF 233
+NE L YL N P+ +P + + +L + D S F
Sbjct: 256 SNEKA--LLSYLSNRVPVFVLPPVPEDPGDDLDEWFDDSKSTF 296
Score = 35.8 bits (83), Expect = 0.017
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 9 YFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASG 47
+ + G NT +GKT++S L + R + +KP+ +G
Sbjct: 30 FAVWGANTAVGKTLVSAGLAAAAASRRSPVLYVKPVQTG 68
>gnl|CDD|216631 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyze amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well as
the plasmid partitioning proteins of the MinD/ParA
family.
Length = 217
Score = 41.3 bits (97), Expect = 1e-04
Identities = 39/220 (17%), Positives = 67/220 (30%), Gaps = 24/220 (10%)
Query: 10 FITGTNTNIGKTIISCALLSEFKKRGISCIGMKP----IASGAYLNNKNKIWFNEDVNLL 65
I GT +GKT ++ L KRG + + S + + ++
Sbjct: 2 AIAGTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANNSSYLGKVEEVLPEGLEIVDA 61
Query: 66 NKYSN--SLYEFTKLINPYLFK--YPISPYTSSNLENRIINTSHIIN-CYNYLSNLTDVI 120
+ ++ ++P L S L S + + + D +
Sbjct: 62 QALQAIAAAIVPSRNLDPLLLIPSNLSLENFESELIVEGKRESRLRAALESLIKLAYDYV 121
Query: 121 ILEGIGGFSVPFHDNENSADLAEKLGLPIILVIDLKIGC--INNALLSLEAIN-SRGLKL 177
I++G G A L ILV+ ++ + A LE I L +
Sbjct: 122 IIDGPPGLGEL---------TANALVAADILVVPIEPEGVAVEGAQRLLELIEDLGVLDI 172
Query: 178 IGWVANHTQIVDTLFANENYIELTKYLNVTPL---GRIPY 214
+G V N D L + + L G IP
Sbjct: 173 LGVVLNKVDRGDERHLKNEIEALERKTGIPVLVLLGVIPR 212
>gnl|CDD|184379 PRK13896, PRK13896, cobyrinic acid a,c-diamide synthase;
Provisional.
Length = 433
Score = 39.0 bits (91), Expect = 0.001
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 111 NYLSNLTDVIILEGIGGFSVPFHDNENS--ADLAEKLGLPIILVIDLKIG 158
NY D+ ++EG+ G +D + S A +AE L LP++LV+D K G
Sbjct: 72 NYYRGEGDICVVEGVMGL----YDGDVSSTAMVAEALDLPVVLVVDAKAG 117
>gnl|CDD|234896 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase; Validated.
Length = 451
Score = 38.6 bits (91), Expect = 0.002
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 106 IINCYNYLSNLTDVIILE-------GIGGFSVPFHDNENSADLAEKLGLPIILVID 154
+ + + D+ ++E G G D ++AD+A+ LG P++LV+D
Sbjct: 71 VRALFARAAQGADIAVIEGVMGLFDGAGSDP----DEGSTADIAKLLGAPVVLVVD 122
>gnl|CDD|235537 PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
Length = 684
Score = 35.5 bits (83), Expect = 0.022
Identities = 35/184 (19%), Positives = 69/184 (37%), Gaps = 51/184 (27%)
Query: 10 FITGTNTNIGKTIISCALLSEFKKRGISCIG-MKPIASGAYLNNKNKIWFNEDVNLLNKY 68
++ T T +G T +S L+ +++G+ +G KPIA
Sbjct: 6 YLAPTGTGVGLTSVSLGLMRALERKGVK-VGFFKPIAQPPL------------------- 45
Query: 69 SNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGF 128
++ E L+ S + ++ I+ Y+ L+ DV+++EG
Sbjct: 46 --TMSEVEALLA-------------SGQLDELLEE--IVARYHALAKDCDVVLVEG---- 84
Query: 129 SVP--FHDNENS--ADLAEKLGLPIILVIDLK----IGCINNALLSLEAI-NSRGLKLIG 179
P H E S A++A+ LG ++LV L+ + ++ ++G
Sbjct: 85 LDPTRKHPFEFSLNAEIAKNLGAEVVLVSSGGNDTPEELAERIELAASSFGGAKNANILG 144
Query: 180 WVAN 183
+ N
Sbjct: 145 VIIN 148
>gnl|CDD|217370 pfam03102, NeuB, NeuB family. NeuB is the prokaryotic
N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes
the direct formation of Neu5Ac (the most common sialic
acid) by condensation of phosphoenolpyruvate (PEP) and
N-acetylmannosamine (ManNAc). This reaction has only
been observed in prokaryotes; eukaryotes synthesise the
9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P
instead of ManNAc. Such eukaryotic enzymes are not
present in this family. This family also contains SpsE
spore coat polysaccharide biosynthesis proteins.
Length = 240
Score = 34.7 bits (81), Expect = 0.024
Identities = 22/57 (38%), Positives = 24/57 (42%), Gaps = 10/57 (17%)
Query: 124 GIGGFSVPFHDNENSADLAEKLGLPIILVIDLKI--GCINNALLSLEAINSRGLKLI 178
GI FS PF S D E LG+P KI G I N L L I G +I
Sbjct: 68 GIEFFSTPFD--LESVDFLESLGVPAY-----KIASGEITNLPL-LRYIAKTGKPVI 116
>gnl|CDD|223926 COG0857, Pta, BioD-like N-terminal domain of phosphotransacetylase
[General function prediction only].
Length = 354
Score = 34.6 bits (80), Expect = 0.037
Identities = 31/149 (20%), Positives = 59/149 (39%), Gaps = 14/149 (9%)
Query: 9 YFITGTNTNIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIWFNEDVNLLNKY 68
+ T T +GKT IS LL +++G+ KPI K + +
Sbjct: 5 LLLIPTETGVGKTSISLGLLRALEQKGLKVAYFKPIG-----TRTGKDADDLTEEDIRAT 59
Query: 69 SNSLYEFTKLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIG-G 127
S+SL P + + S+ ++ ++ I+ Y L+ DV+++EG
Sbjct: 60 SSSL----TYAEPLVLSFAEV-LLSTGQDDVLLEE--ILANYAELAKDADVVVVEGDVPT 112
Query: 128 FSVPFHDNENSADLAEKLGLPIILVIDLK 156
P+ + + ++A+ L +LV
Sbjct: 113 REGPY-ALDLNYEIAKNLNAAAVLVARAL 140
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 33.4 bits (77), Expect = 0.083
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 125 IGGFSVPFHDNENSADLAEKLGLPIILVIDL-----KIGCINNALLSL 167
IGG+++ D L E++G+ + + D ++ + NA L+L
Sbjct: 158 IGGYNLGGGDLRELKRLLEEMGIRVNALFDGGTTVEELRELGNAKLNL 205
>gnl|CDD|223895 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 31.1 bits (71), Expect = 0.46
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 139 ADLAEKLGLPIILVID 154
LAEK GLPII ID
Sbjct: 143 MKLAEKFGLPIITFID 158
>gnl|CDD|180595 PRK06504, PRK06504, acetyl-CoA acetyltransferase; Provisional.
Length = 390
Score = 30.9 bits (70), Expect = 0.59
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 14/56 (25%)
Query: 166 SLEAINSRGLKLI---GWV--ANHTQIVD----TLFANENYIELTKYLNVTPLGRI 212
+LE I G+KLI G + A +QI D + NE + K L V PL RI
Sbjct: 223 TLEGI--AGVKLIAEGGRLTAATASQICDGASGVMVVNERGL---KALGVKPLARI 273
>gnl|CDD|224409 COG1492, CobQ, Cobyric acid synthase [Coenzyme metabolism].
Length = 486
Score = 30.7 bits (70), Expect = 0.72
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 110 YNYLSNLTDVIILEGIGGFSVPFHDNENSADL-----AEKLGLPIILVIDLKIG 158
L DV+++EG G P N D+ AE P+ILV D+ G
Sbjct: 119 LERLDREYDVVVIEGAGS---PAEINLRDRDIANMGVAEIADAPVILVGDIDRG 169
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 30.3 bits (69), Expect = 0.95
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 131 PFHDNENSADLAEKLGLPIILVIDLKIGCINN 162
P HD N ++ ++ LP+I +ID G IN
Sbjct: 273 PAHD-FNDYEVGKRHNLPLINIIDED-GRINE 302
>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
ATP-binding and catalytic domain of bacterial DNA
topoisomerases I and III, and eukaryotic DNA
topoisomerase III and eubacterial and archael reverse
gyrases. Topoisomerases clevage single or double
stranded DNA and then rejoin the broken phosphodiester
backbone. Proposed catalytic mechanism of single
stranded DNA cleavage is by phosphoryl transfer through
a tyrosine nucleophile using acid/base catalysis. Tyr is
activated by a nearby group (not yet identified) acting
as a general base for nucleophilic attack on the 5'
phosphate of the scissile bond. Arg and Lys stabilize
the pentavalent transition state. Glu then acts as a
proton donor for the leaving 3'-oxygen, upon cleavage of
the scissile strand.
Length = 381
Score = 29.9 bits (68), Expect = 1.0
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 178 IGWVANHTQIVDTLFANENYIELTK-YLNVTPLGRIPYLYNLNINLISHYLDFSSL 232
IG + + I++TL + Y+E K L T LG + L L H+ +
Sbjct: 297 IGRPSTYASIIETLL-DRGYVEKEKKKLIPTELGFA--VIEL---LEKHFPELVDP 346
>gnl|CDD|234830 PRK00766, PRK00766, hypothetical protein; Provisional.
Length = 194
Score = 29.2 bits (66), Expect = 1.3
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 9/50 (18%)
Query: 119 VIILEGI--GGFSVPFHDNENSADLAEKLGLPIILVIDLK--IGCINNAL 164
VI+L+GI GGF+V D E +L + GLP+I+V+ K I +AL
Sbjct: 74 VIMLDGITYGGFNVV--DIE---ELYRETGLPVIVVMRKKPDFEAIESAL 118
>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal. This model
describes topoisomerase I from archaea. These enzymes
are involved in the control of DNA topology. DNA
topoisomerase I belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 618
Score = 29.8 bits (67), Expect = 1.5
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 167 LEAINSRGLKLIGWVANHTQIVDTLFANENYIELTKYLNVTPLG 210
+ + SRGL G A +I++TL+ YIE K + VTPLG
Sbjct: 474 IREMESRGL---GTKATRARIIETLY-KRGYIEGKKSIKVTPLG 513
>gnl|CDD|234838 PRK00784, PRK00784, cobyric acid synthase; Provisional.
Length = 488
Score = 29.3 bits (67), Expect = 1.8
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 106 IINCYNYLSNLTDVIILEGIGGFS-VPFHDNENSADL-----AEKLGLPIILV--ID 154
++ + L+ DV+++EG G + + D D+ AE P+ILV ID
Sbjct: 115 VLESLDRLAAEYDVVVVEGAGSPAEINLRDR----DIANMGFAEAADAPVILVADID 167
>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal. This
model represents the archaeal branch of the MinD family.
MinD, a weak ATPase, works in bacteria with MinC as a
generalized cell division inhibitor and, through
interaction with MinE, prevents septum placement
inappropriate sites. Often several members of this
family are found in archaeal genomes, and the function
is uncharacterized. More distantly related proteins
include flagellar biosynthesis proteins and ParA
chromosome partitioning proteins. The exact roles of the
various archaeal MinD homologs are unknown.
Length = 251
Score = 28.9 bits (65), Expect = 1.9
Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 10/103 (9%)
Query: 111 NYLSNLTDVIILEGIGGFSVPFHDNENSADLAEKLGLPIILVIDLKIGCINNALLSLEAI 170
+ + TD ++++ G E A A ++LV++ +I I +AL +
Sbjct: 103 KEIIDDTDFLLIDAPAGL-------ERDAVTALAAADELLLVVNPEISSITDALKTKIVA 155
Query: 171 NSRGLKLIGWVANHTQIVDTLFANENYIELTKYLNVTPLGRIP 213
G ++G V N T E E+ L V LG +P
Sbjct: 156 EKLGTAILGVVLNRVTRDKTELGRE---EIETILEVPVLGVVP 195
>gnl|CDD|148738 pfam07302, AroM, AroM protein. This family consists of several
bacterial and archaeal AroM proteins. In Escherichia
coli the aroM gene is cotranscribed with aroL. The
function of this family is unknown.
Length = 221
Score = 28.8 bits (65), Expect = 2.2
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 14/75 (18%)
Query: 77 KLINPYLFKYPISPYTSSNLENRIINTSHIINCYNYLSNLTDVIILEGIGGFSVPFHDNE 136
KL+ + SPY S E+R+ + + L D+I+L+ IG +
Sbjct: 147 KLVKEVVVVA-ASPYHGS--EDRLEEAAREL-----LDQGADLIVLDCIG-----YT-QA 192
Query: 137 NSADLAEKLGLPIIL 151
L E LG P++L
Sbjct: 193 MKDMLQEALGKPVLL 207
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 28.9 bits (66), Expect = 2.5
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 128 FSVPFHDNENSADLAEKLGLPIILVID 154
+VP HD + + A+K GLPI VI+
Sbjct: 335 MAVPAHD-QRDFEFAKKYGLPIKPVIE 360
>gnl|CDD|222257 pfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This
is a family of the conserved region of Leucine-tRNA
ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.
Length = 178
Score = 28.2 bits (64), Expect = 2.8
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 128 FSVPFHDNENSADLAEKLGLPIILVI 153
+VP HD + + A+K LPI VI
Sbjct: 109 MAVPAHD-QRDFEFAKKYNLPIKQVI 133
>gnl|CDD|221794 pfam12825, DUF3818, Domain of unknown function in PX-proteins
(DUF3818). This domain is found on proteins carrying a
PX domain. Its function is unknown.
Length = 340
Score = 28.4 bits (64), Expect = 3.5
Identities = 6/35 (17%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 41 MKPIASGAYLNNKNKIWFNEDVNLLNKYSNSLYEF 75
++ + + Y+++ + V+L++++ S Y+F
Sbjct: 277 LEKVINQLYISDPFNV-VQAFVDLVDRHEQSFYKF 310
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse gyrase,
found in both archaeal and bacterial thermophiles. This
enzyme, a fusion of a type I topoisomerase domain and a
helicase domain, introduces positive supercoiling to
increase the melting temperature of DNA double strands.
Generally, these gyrases are encoded as a single
polypeptide. An exception was found in Methanopyrus
kandleri, where enzyme is split within the topoisomerase
domain, yielding a heterodimer of gene products
designated RgyB and RgyA [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1171
Score = 28.3 bits (63), Expect = 3.9
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 178 IGWVANHTQIVDTLFANENYIELTKYLNVTPLGRIPYLYNLNINLISHYLDFSS 231
IG + + IV+ L +E +L T LG Y Y L + Y S
Sbjct: 1088 IGRPSTYATIVEKLLRRGYVVESKGFLIPTKLGIEVYNY-----LTNRYPKLVS 1136
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 27.9 bits (63), Expect = 3.9
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 49 YLNNKNKIWFNEDVNLLNKYS 69
+LN + NE V L +YS
Sbjct: 163 FLNTPAAVAINEAVELAKRYS 183
>gnl|CDD|200452 cd11313, AmyAc_arch_bac_AmyA, Alpha amylase catalytic domain found
in archaeal and bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes firmicutes, bacteroidetes, and proteobacteria.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 336
Score = 27.5 bits (62), Expect = 6.7
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 168 EAINSRGLK-LIGWVANHT 185
+ + RG+K ++ WVANHT
Sbjct: 83 DEAHDRGMKVILDWVANHT 101
>gnl|CDD|235580 PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase
subunit alpha; Validated.
Length = 319
Score = 27.4 bits (62), Expect = 6.9
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 139 ADLAEKLGLPIILVID 154
+AEK GLPII ID
Sbjct: 144 MKMAEKFGLPIITFID 159
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 27.5 bits (62), Expect = 7.1
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 132 FHDNENSADLAEKLGLPIILVIDLKIG 158
F+ + +LAEK P+I++ D +
Sbjct: 337 FYLAAEAFNLAEKYQTPVIVLSDQYLA 363
>gnl|CDD|107330 cd06335, PBP1_ABC_ligand_binding_like_2, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 347
Score = 27.2 bits (61), Expect = 7.3
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 157 IGCIN--NALLSLEAINSRGLKLIGWVANHTQIVDTLFANENYI 198
+G ++ AL +LE I + LIG A T I A NYI
Sbjct: 72 LGGLHTPVALANLEFIQQNKIPLIGPWAAGTPITRNG-APPNYI 114
>gnl|CDD|184998 PRK15038, PRK15038, autoinducer 2 import system permease LsrD;
Provisional.
Length = 330
Score = 27.5 bits (61), Expect = 7.4
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 113 LSNLTDVIILEGIGGFSVPFHDNENSADLAEKLGLPIILVI 153
LS + EGIGGF + F D N + LGLP+ L+I
Sbjct: 133 LSGMAGATGYEGIGGFPMAFTDFAN----LDVLGLPVPLII 169
>gnl|CDD|214663 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding
domain. Bacterial DNA topoisomerase I and III,
Eukaryotic DNA topoisomeraes III, reverse gyrase alpha
subunit.
Length = 259
Score = 27.2 bits (61), Expect = 7.6
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 178 IGWVANHTQIVDTLFANENYIELTK-YLNVTPLGRI 212
IG + + I++TL + Y+ K L T LG
Sbjct: 224 IGRPSTYASIIETLL-DRGYVTKKKKKLIPTELGIA 258
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 27.0 bits (60), Expect = 7.9
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 4 KNFLHYFITGTNTNIGKTIISCALLSEFKKRGISCI 39
+N + G GKT ++ A+ +E K GIS +
Sbjct: 106 ENLVLLGPPGV----GKTHLAIAIGNELLKAGISVL 137
>gnl|CDD|215817 pfam00248, Aldo_ket_red, Aldo/keto reductase family. This family
includes a number of K+ ion channel beta chain
regulatory domains - these are reported to have
oxidoreductase activity.
Length = 277
Score = 26.9 bits (60), Expect = 9.5
Identities = 7/41 (17%), Positives = 14/41 (34%)
Query: 17 NIGKTIISCALLSEFKKRGISCIGMKPIASGAYLNNKNKIW 57
++ + + LL ++ GI I P+ G
Sbjct: 161 SLLRRLAEEGLLELCQENGIGIIAYSPLGGGLLTGKYTSEA 201
>gnl|CDD|234062 TIGR02924, ICDH_alpha, isocitrate dehydrogenase. This family of
mainly alphaproteobacterial enzymes is a member of the
isocitrate/isopropylmalate dehydrogenase superfamily
described by pfam00180. Every member of the seed of this
model appears to have a TCA cycle lacking only a
determined isocitrate dehydrogenase. The precise
identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH --
1.1.1.42) is unclear [Energy metabolism, TCA cycle].
Length = 473
Score = 27.0 bits (60), Expect = 9.8
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 49 YLNNKNKIWFNEDV-NLLNKYSNSLYEFTKLINPYLF 84
++ NKI N D+ NLLN+ + K+ YLF
Sbjct: 431 FIAKTNKIISNTDINNLLNRLEQKKIDVVKMEKLYLF 467
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
0.321 0.140 0.416
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,887,595
Number of extensions: 1129186
Number of successful extensions: 1400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1385
Number of HSP's successfully gapped: 72
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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: 57 (25.7 bits)