RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780742|ref|YP_003065155.1| hypothetical protein
CLIBASIA_03145 [Candidatus Liberibacter asiaticus str. psy62]
(419 letters)
>gnl|CDD|31934 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 364 bits (937), Expect = e-101
Identities = 161/401 (40%), Positives = 223/401 (55%), Gaps = 33/401 (8%)
Query: 2 KKNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKIDGKLA 61
+L+IGAGGV VVAHK AQN D G++ IA R+ +KC++I + I GK+
Sbjct: 1 MMKILVIGAGGVGSVVAHKLAQNGD--GEVTIADRSKEKCARIAELI--------GGKVE 50
Query: 62 IHQVDALNIKAVVELIKKTNSQIIINVGSSFLNMSVLRACIDSNVAYIDTAIHESPLKIC 121
QVDA ++ A+V LIK ++IN F+++++L+ACI + V Y+DT+ +E P
Sbjct: 51 ALQVDAADVDALVALIKDF--DLVINAAPPFVDLTILKACIKTGVDYVDTSYYEEP---- 104
Query: 122 ESPPWYNNYEWSLLDECRTKSITAILGAGFDPGVVNAFARLAQDEYFDKITDIDIIDVNA 181
W L +E + ITA+LG GFDPG+ N A A E FD+I IDI
Sbjct: 105 ---------PWKLDEEAKKAGITAVLGCGFDPGITNVLAAYAAKELFDEIESIDIYVGGL 155
Query: 182 GKH---DKYFATNFDAEINLREFTGVVYSWQKNQWCVNKMFEISRTYDLPTVGQHKVYLS 238
G+H +AT + EINLRE+T W+ +W E ++ P +G VY
Sbjct: 156 GEHGDNPLGYATTWSPEINLREYTRPARYWENGKWVEVDPLEEREVFEFPVIGYGDVYAF 215
Query: 239 GHDEIHSLFKNIQG-ADIRFWMGFS-DHYINVFTVLKNIGLLSEQPIRTAENIEIAPLKI 296
HDE+ SL K I G RF M F ++ V L+++GLLS +P++ + EI PL+
Sbjct: 216 YHDELRSLVKTIPGVVRTRFEMTFRYPGHLEVIKALRDLGLLSREPVKVQQ--EIVPLEF 273
Query: 297 VKAVLPDPSSLAPNYQGKTCIGCLINGIYHGETREIFLYNICDHQNAYQEIASQGISYTA 356
+KAVLPDP SLAP+Y+ T IG + G G + +F YN+ DH AY E+ S ISYT
Sbjct: 274 LKAVLPDPLSLAPDYKDVTVIGVEVKGTKDGRDKTVF-YNVKDHAEAYSEVGSSAISYTT 332
Query: 357 GTPPVATAILIAQGIWDIGKMVNIEELPPKPFLGTLQRMGL 397
G P A L+A+G W+ +VN EEL P PFL L GL
Sbjct: 333 GVPAAIGAELLAEGEWETPGVVNPEELGPDPFLEKLLIRGL 373
>gnl|CDD|146194 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 384
Score = 280 bits (719), Expect = 5e-76
Identities = 119/405 (29%), Positives = 184/405 (45%), Gaps = 41/405 (10%)
Query: 5 VLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKIDGKLAIHQ 64
VLIIGAGGV VA A++ D+ +I +A R+L+K + K L+
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDVD-EITVADRSLEKAQALAA---PKLGLRFI----AIA 52
Query: 65 VDALNIKAVVELIKKTNSQIIINVGSSFLNMSVLRACIDSNVAYIDTAIHESPLKICESP 124
VDA N +A+ L+K+ ++IN+ FL+++VL+ACI++ V Y+DT+
Sbjct: 53 VDADNYEALAALLKEG--DLVINLAPPFLSLTVLKACIETGVHYVDTSY----------- 99
Query: 125 PWYNNYEWSLLDECRTKSITAILGAGFDPGVVNAFARLAQDEYFDKITDIDIIDVNAGKH 184
+ +L ++ + +TA+LG GFDPG+V+ FA+ A D+ D++ + + ++ G
Sbjct: 100 --LREAQLALHEKAKEAGVTAVLGCGFDPGLVSVFAKYALDDLADELAKVLSVKIHCGGR 157
Query: 185 DKY------FATNFDAEINLREFTGVVYSWQKNQWCVNKMFEISRTYDLP-TVGQHKVYL 237
+ FA + E L E T W+ +W RT P G Y
Sbjct: 158 PEPKDNGLEFANTWSPEGLLEELTNPARYWENGKWVEVGWGSHERTIPFPYGHGPGYAYE 217
Query: 238 SGHDEIHSLFKNIQGA----DIRFWMGFSDHYINVFTVLKNIGLLSEQPIRTAENIEIAP 293
H+ +L + + F Y+ V +L ++GLL I P
Sbjct: 218 IYHNRPGTLTRVRSWLPEAGGVLFGTIRIPGYLTVIKLLGDLGLLRPTVHYAY----IPP 273
Query: 294 LKIVKAVLPDPSSLAPNYQGKTCIGCLINGIYH-GETREIFLYNICDHQNAYQEIASQGI 352
L +KA+L P+SL P Q K IG + GI G +YN+ + +E +
Sbjct: 274 LDALKALLESPASLGPEEQDKVRIGVEVEGIDKLGVLLTGHIYNVYGSGLSIEE-GRSAM 332
Query: 353 SYTAGTPPVATAILIAQGIWDIGKMVNIEE-LPPKPFLGTLQRMG 396
YT GTP A L+A G W +V EE L P PFL L +G
Sbjct: 333 PYTTGTPAQVAAALLAGGEWAKPGVVEPEEDLDPDPFLPALPYLG 377
>gnl|CDD|37944 KOG2733, KOG2733, KOG2733, Uncharacterized membrane protein
[Function unknown].
Length = 423
Score = 38.0 bits (88), Expect = 0.005
Identities = 33/155 (21%), Positives = 66/155 (42%), Gaps = 20/155 (12%)
Query: 4 NVLIIGAGGVA--HVV--AHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKIDGK 59
+V+I GA G ++V A + + +A R +K ++++ + +K +
Sbjct: 7 DVVIYGASGFTGKYIVEEAVSSQVFEGL--SLAVAGRNEKKLQEVLEKVGEK-TGTDLSS 63
Query: 60 LAIHQVDALNIKAVVELIKKTNSQIIIN-VGS-SFLNMSVLRACIDSNVAYIDTAIHESP 117
I D+ N ++ E+ K+ +I+N VG F V++ACI++ ++D
Sbjct: 64 SVILIADSANEASLDEMAKQAR--VIVNCVGPYRFHGEPVVKACIENGTHHVD------- 114
Query: 118 LKICESPPWYNNYEWSLLDECRTKSITAILGAGFD 152
I P + + D + K + + GFD
Sbjct: 115 --ISGEPQFMERMQLKYHDLAKEKGVYIVSACGFD 147
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of
Shikimate dehydrogenase. Shikimate dehydrogenase (DH)
is an amino acid DH family member. Shikimate pathway
links metabolism of carbohydrates to de novo
biosynthesis of aromatic amino acids, quinones and
folate. It is essential in plants, bacteria, and fungi
but absent in mammals, thus making enzymes involved in
this pathway ideal targets for broad spectrum
antibiotics and herbicides. Shikimate DH catalyzes the
reduction of 3-hydroshikimate to shikimate using the
cofactor NADH. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily
and include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 36.1 bits (84), Expect = 0.017
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 2 KKNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLK--IDGK 59
K VLI+GAGG A VA+ A+ I I +RTL+K + + + +D +
Sbjct: 19 GKKVLILGAGGAARAVAYALAELG--AAKIVIVNRTLEKAKALAERFGELGIAIAYLDLE 76
Query: 60 LAIHQVDAL 68
+ + D +
Sbjct: 77 ELLAEADLI 85
>gnl|CDD|35393 KOG0172, KOG0172, KOG0172, Lysine-ketoglutarate
reductase/saccharopine dehydrogenase [Amino acid
transport and metabolism].
Length = 445
Score = 35.7 bits (82), Expect = 0.023
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 1 MKKNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSI 48
KK VL++G+G V+ VA ++ D+ ++ +ASRTL+ ++ I
Sbjct: 1 TKKGVLLLGSGFVSRPVADFLSRKKDV--NVTVASRTLKDAEALVKGI 46
>gnl|CDD|30518 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 34.1 bits (78), Expect = 0.069
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 15/85 (17%)
Query: 3 KNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKIDGKLAI 62
K VLI+GAGG A VA A+ I + +RT ++ ++ D A
Sbjct: 127 KRVLILGAGGAARAVAFALAEAG--AKRITVVNRTRERAEELADL--------FGELGAA 176
Query: 63 HQVDALNIKAVVELIKKTNSQIIIN 87
+ AL +L + ++IN
Sbjct: 177 VEAAALA-----DLEGLEEADLLIN 196
>gnl|CDD|144908 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase.
This family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyses the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyses the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 134
Score = 32.3 bits (74), Expect = 0.28
Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 26/94 (27%)
Query: 3 KNVLIIGAGGVA-----HVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKID 57
K VL+IGAG +A H+++ I IA+RTL+K ++ +
Sbjct: 13 KKVLLIGAGEMARLAAKHLLSKGAK-------KITIANRTLEKAKELAE----------- 54
Query: 58 GKLAIHQVDALNIKAVVELIKKTNSQIIINVGSS 91
+ +V+AL + + EL+ + I+I+ S+
Sbjct: 55 -EFGGEEVEALPLDELEELLA--EADIVISATSA 85
>gnl|CDD|145810 pfam02844, GARS_N, Phosphoribosylglycinamide synthetase, N
domain. Phosphoribosylglycinamide synthetase catalyses
the second step in the de novo biosynthesis of purine.
The reaction catalysed by Phosphoribosylglycinamide
synthetase is the ATP- dependent addition of
5-phosphoribosylamine to glycine to form
5'phosphoribosylglycinamide. This domain is related to
the N-terminal domain of biotin carboxylase/carbamoyl
phosphate synthetase (see pfam00289).
Length = 99
Score = 32.0 bits (74), Expect = 0.34
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 4 NVLIIGAGGVAHVVAHKCAQNNDI 27
VL++G+GG H +A K AQ+ +
Sbjct: 1 KVLVVGSGGREHALAWKLAQSPRV 24
>gnl|CDD|35458 KOG0237, KOG0237, KOG0237, Glycinamide ribonucleotide synthetase
(GARS)/Aminoimidazole ribonucleotide synthetase (AIRS)
[Nucleotide transport and metabolism].
Length = 788
Score = 31.8 bits (72), Expect = 0.35
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 1 MKKNVLIIGAGGVAHVVAHKCAQN 24
+ NVL+IG+GG H +A K Q+
Sbjct: 1 ERVNVLVIGSGGREHALAWKLKQS 24
>gnl|CDD|30500 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 31.7 bits (72), Expect = 0.36
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 4 NVLIIGAGGVAHVVAHKCAQNNDIL 28
VL+IG+GG H +A K AQ+ +L
Sbjct: 2 KVLVIGSGGREHALAWKLAQSPLVL 26
>gnl|CDD|30722 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 31.4 bits (71), Expect = 0.52
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 2 KKNVLIIGAGGVAHVVA-HKCAQNNDILGDINIASRTLQKCSKIID 46
K VL+IGAG + +VA H + + I IA+RTL++ ++
Sbjct: 178 DKKVLVIGAGEMGELVAKHLAEKG---VKKITIANRTLERAEELAK 220
>gnl|CDD|29457 cd02761, MopB_FmdB-FwdB, The MopB_FmdB-FwdB CD contains the
molybdenum/tungsten formylmethanofuran dehydrogenases,
subunit B (FmdB/FwdB), and other related proteins.
Formylmethanofuran dehydrogenase catalyzes the first
step in methane formation from CO2 in methanogenic
archaea and some eubacteria. Members of this CD belong
to the molybdopterin_binding (MopB) superfamily of
proteins..
Length = 415
Score = 29.5 bits (66), Expect = 1.7
Identities = 23/112 (20%), Positives = 42/112 (37%), Gaps = 11/112 (9%)
Query: 67 ALNIKAVVELIKKTNSQIIINVGSSFLNMSVLRACIDSNVAYIDTAIHESPLKI--CESP 124
NI+A + L+K +N + F + + + T + P ++
Sbjct: 253 HRNIEAAIRLVKA------LNEYTKFALLPLRGHYNVRGFNQVLTWLTGYPFRVDFSRGY 306
Query: 125 PWYNNYEWSLLDECRTKSITAILGAGFDPGVVNAFARLAQDEYFDKITDIDI 176
P YN E++ +D A+L DP F + A ++ +I I I
Sbjct: 307 PRYNPGEFTAVDLLAEGEADALLIIASDPP--AHFPQSAV-KHLAEIPVIVI 355
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 28.4 bits (64), Expect = 3.4
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 3 KNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIID 46
K VL+IGAG + + A A + +I IA+RT ++ ++
Sbjct: 179 KKVLVIGAGEMGELAAKHLAAKG--VAEITIANRTYERAEELAK 220
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus
jannaschii, exhibit both MDH and LDH activities.
Tetrameric MDHs, including those from phototrophic
bacteria, are more similar to LDHs than to other MDHs.
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH-like MDHs are part
of the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 28.6 bits (65), Expect = 3.7
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 7 IIGAGGVAHVVAHKCAQNNDILGDI 31
IIGAG V +A A LGD+
Sbjct: 3 IIGAGNVGATLAQLLALKE--LGDV 25
>gnl|CDD|34111 COG4408, COG4408, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 431
Score = 28.4 bits (63), Expect = 4.1
Identities = 12/62 (19%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 3 KNVLIIGAGGVAHVVAHKCAQNNDILGDINIASRTLQKCSKIIDSIYKKKSLKIDGKLAI 62
VL++G G VA +A + + D + + +R + ++ ++ L + G+
Sbjct: 5 LPVLLLGTGPVAIQLAVDLSAHGD--ARLGLYNRPSTRSERLKQALALTPQLYLQGQGEA 62
Query: 63 HQ 64
H+
Sbjct: 63 HR 64
>gnl|CDD|35894 KOG0675, KOG0675, KOG0675, Calnexin [Posttranslational
modification, protein turnover, chaperones].
Length = 558
Score = 28.1 bits (62), Expect = 4.7
Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 16/102 (15%)
Query: 309 PNYQGKTCIGCLINGIYHGE--TREIF--LYNICDHQNAYQEIASQGISYTAGTPP---- 360
PNY+GK + + N Y G R+I Y D I++ G+ + +
Sbjct: 351 PNYKGKWILPMIDNPNYQGIWKPRKIPNPDYFEDDKPFTLTPISAVGLELWSMSSNILFD 410
Query: 361 ---VATAILIAQGI----WDIGKMVNIEELPPKPFLGTLQRM 395
+ I +A+ I W + K E P +
Sbjct: 411 NIIITKDIEVAEDIANFTWLL-KAAAEREKPFVQQVMEAAEG 451
>gnl|CDD|31442 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid
metabolism].
Length = 307
Score = 27.5 bits (61), Expect = 6.5
Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 22/92 (23%)
Query: 3 KNVLIIGAG----GVAHVVAHKCAQNNDILGDIN--IASRTLQKCSKIIDSIYKKKSLKI 56
K V +IGAG G+A V A A + +L DI+ R L K ++ + +K L
Sbjct: 4 KKVAVIGAGVMGAGIAAVFA--LAGYDVVLKDISPEALERALAYIEKNLEKLVEKGKLTE 61
Query: 57 DGK-------------LAIHQVDALNIKAVVE 75
+ A+ D L I+AVVE
Sbjct: 62 EEADAALARITPTTDLAALKDAD-LVIEAVVE 92
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 27.7 bits (62), Expect = 7.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 3 KNVLIIGAGGVAHVVA 18
VL++GAGGV + A
Sbjct: 136 DTVLVLGAGGVGLLAA 151
>gnl|CDD|111045 pfam02106, Fanconi_C, Fanconi anaemia group C protein.
Length = 559
Score = 27.5 bits (61), Expect = 7.6
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 43 KIIDSIYKKKSLKIDGKLAIHQVDALNIKAVVELIKKTNSQ 83
+I+D I++ L+ DG + + + + VE ++K N Q
Sbjct: 293 RIVDEIFRNALLETDGAPEVLALIQVFTQCFVEALEKENKQ 333
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.137 0.412
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,103,059
Number of extensions: 272690
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 673
Number of HSP's successfully gapped: 23
Length of query: 419
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 323
Effective length of database: 4,189,273
Effective search space: 1353135179
Effective search space used: 1353135179
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: 59 (26.4 bits)