RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780900|ref|YP_003065313.1| homoserine dehydrogenase
[Candidatus Liberibacter asiaticus str. psy62]
(438 letters)
>gnl|CDD|30808 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 319 bits (818), Expect = 1e-87
Identities = 147/326 (45%), Positives = 202/326 (61%), Gaps = 8/326 (2%)
Query: 4 VLKVGVAGLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKNIDRGIDCLRYE-WF 62
+KVG+ GLGTVGS ++ + +++ + V A++ RD ++ R +D L E W
Sbjct: 3 TVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVADRDGSLVRDLDLLNAEVWT 62
Query: 63 DDPLIMAGE-----ADIDVFVELIGGEDYPAY--DAVRIALMRGCHVVTANKALIASHGK 115
D + G+ DIDV VEL+GG+ PA D AL G HVVTANKAL+A H
Sbjct: 63 TDGALSLGDEVLLDEDIDVVVELVGGDVEPAEPADLYLKALENGKHVVTANKALLALHYH 122
Query: 116 DLALLAQKNNAILNFEAAVAGGIPIIRILKNYVEYDEINRVYGIINGTCNYILSHMNNLG 175
+L A+KN L +EA V GGIPII++L+ + DEI + GI+NGT NYIL+ M G
Sbjct: 123 ELREAAEKNGVKLLYEATVGGGIPIIKLLRELLAGDEILSIRGILNGTTNYILTRMEEGG 182
Query: 176 LSFQDCLEEARRQGYAEGDATFDINGVDSSHKIAILSAIAFGIDTSVEGVYCEGISNITL 235
LSF+D L EA+ GYAE D T D+ G+D++ K+ IL+ +AFG +++ V EGI+ IT
Sbjct: 183 LSFEDALAEAQELGYAEADPTDDLEGIDAARKLVILARLAFGTPETLDDVEVEGITPITP 242
Query: 236 EDIRGAADFGYCIKFLAMARRKGKGIIRYVYPVLLKYDSVMALVDGITNAVVIETNGLGK 295
EDI A + GY IK + +A + GKGI V+P L+ D +A V+G+ NAV IET+ G
Sbjct: 243 EDIEFAKELGYVIKLVGIADKTGKGIEARVHPTLVPKDHPLASVNGVMNAVAIETDAYGP 302
Query: 296 LTMTGPGAGGSATASAVLGDICSIAK 321
L + GPGAGG TASAVL D+ IA+
Sbjct: 303 LVLYGPGAGGEVTASAVLSDLLRIAR 328
>gnl|CDD|144371 pfam00742, Homoserine_dh, Homoserine dehydrogenase.
Length = 179
Score = 218 bits (559), Expect = 2e-57
Identities = 90/178 (50%), Positives = 119/178 (66%)
Query: 139 PIIRILKNYVEYDEINRVYGIINGTCNYILSHMNNLGLSFQDCLEEARRQGYAEGDATFD 198
PIIR L+ + D I R+ GI+NGT NYIL+ M GLSF++ L+EA+ GYAE D T D
Sbjct: 1 PIIRTLRELLAGDRITRIEGILNGTTNYILTRMEEEGLSFEEALKEAQELGYAEADPTDD 60
Query: 199 INGVDSSHKIAILSAIAFGIDTSVEGVYCEGISNITLEDIRGAADFGYCIKFLAMARRKG 258
+ G+D++ K+ IL+ +AFG+ ++ V EGIS ITLEDI A + GY IK +A ARR
Sbjct: 61 VEGLDAARKLLILARLAFGLPVELDDVEVEGISPITLEDIEYAKELGYVIKLVAEARRDD 120
Query: 259 KGIIRYVYPVLLKYDSVMALVDGITNAVVIETNGLGKLTMTGPGAGGSATASAVLGDI 316
G+ V P L+ D +A VDG+ NAV+IET+ G L + GPGAGG TASAVL D+
Sbjct: 121 GGVEARVGPTLVPKDHPLANVDGVDNAVLIETDRYGPLVIYGPGAGGEPTASAVLSDL 178
>gnl|CDD|35676 KOG0455, KOG0455, KOG0455, Homoserine dehydrogenase [Amino acid
transport and metabolism].
Length = 364
Score = 90.5 bits (224), Expect = 7e-19
Identities = 72/255 (28%), Positives = 117/255 (45%), Gaps = 31/255 (12%)
Query: 95 ALMRGCHVVTANKALIAS---HGKDLALLAQKNNAILNFEAAVAGGIPIIRILKNYVEY- 150
+ G + T NK +S H LAL K+ + EA V G+PII L +
Sbjct: 108 FVDLGICIATPNKKAFSSTLEHYDKLAL-HSKSPRFIRHEATVGAGLPIISSLNEIISTG 166
Query: 151 DEINRVYGIINGTCNYILSHMNN---LGLSFQDCLEEARRQGYAEGDATFDINGVDSSHK 207
DE++++ GI +GT +YI + +++ LSF D ++ A++ GY E D D+NG+D + K
Sbjct: 167 DEVHKIEGIFSGTLSYIFNELSDGKPGTLSFSDVVKAAKKLGYTEPDPRDDLNGMDVARK 226
Query: 208 IAILSAIAFGIDTSVEGVYCEGISNITLEDIRGAADFGYCI--------KFLAMARRKGK 259
+ IL+ I S++ E + L + A +F + + + + A +GK
Sbjct: 227 VTILARILGVRVESMDSFPVESLIPEPLPSLMSADEFLHGLVKLDQNIEERVKEASSEGK 286
Query: 260 GIIRYV-------YPVLLK-----YDSVMALVDGITNAVVIETNGLGK--LTMTGPGAGG 305
++R+V V + A + G N + I T L + G GAG
Sbjct: 287 -VLRFVGVIDVANKSVQVGIEKYDKSHPFARLRGSDNIISIYTKRYKTQPLVIQGAGAGA 345
Query: 306 SATASAVLGDICSIA 320
+ TA+ VLGDI I
Sbjct: 346 AVTAAGVLGDIIKIQ 360
>gnl|CDD|146203 pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding
domain. This domain adopts a Rossmann NAD binding fold.
The C-terminal domain of homoserine dehydrogenase
contributes a single helix to this structural domain,
which is not included in the Pfam model.
Length = 116
Score = 50.8 bits (122), Expect = 8e-07
Identities = 30/129 (23%), Positives = 49/129 (37%), Gaps = 21/129 (16%)
Query: 11 GLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKNIDRGIDCLRYEWFDDPLIMAG 70
G G +GS L+ + + ++ + A++ RD + R D +
Sbjct: 1 GCGAIGSGLLELL--LRQQ----EEIPLELVAVADRDL-----LSKARAALLGDEPVTLD 49
Query: 71 E------ADIDVFVELIGGEDYPAYDAVRIALMRGCHVVTANKALIAS--HGKDLALLAQ 122
DV VE + A + V AL G HVVTA+K +A + L A+
Sbjct: 50 LDDLVADPRPDVVVEC-ASSEAVA-EYVLKALKAGKHVVTASKGALADLALRERLREAAE 107
Query: 123 KNNAILNFE 131
+ + FE
Sbjct: 108 ASGVRVYFE 116
>gnl|CDD|153153 cd04881, ACT_HSDH-Hom, ACT_HSDH_Hom CD includes the C-terminal ACT
domain of the NAD(P)H-dependent, homoserine
dehydrogenase (HSDH) and related domains. The
ACT_HSDH_Hom CD includes the C-terminal ACT domain of
the NAD(P)H-dependent, homoserine dehydrogenase (HSDH)
encoded by the hom gene of Bacillus subtilis and other
related sequences. HSDH reduces aspartate semi-aldehyde
to the amino acid homoserine, one that is required for
the biosynthesis of Met, Thr, and Ile from Asp. Neither
the enzyme nor the aspartate pathway is found in the
animal kingdom. This mostly bacterial HSDH group has a
C-terminal ACT domain and is believed to be involved in
enzyme regulation. A C-terminal deletion in the
Corynebacterium glutamicum HSDH abolished allosteric
inhibition by L-threonine. Members of this CD belong to
the superfamily of ACT regulatory domains.
Length = 79
Score = 42.1 bits (100), Expect = 3e-04
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 354 YFIRLTIRNFEGILDKITSQMSDFNISLRLFSCPHQEENSQEFS--VFMITHKVSGKLIR 411
Y++RLT+++ G+L KIT +++ IS+ Q+E + V ++TH+ S +
Sbjct: 1 YYLRLTVKDKPGVLAKITGILAEHGISIESV---IQKEADGGETAPVVIVTHETSEAALN 57
Query: 412 DAIE 415
A+
Sbjct: 58 AALA 61
>gnl|CDD|31898 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 32.2 bits (73), Expect = 0.29
Identities = 27/146 (18%), Positives = 54/146 (36%), Gaps = 19/146 (13%)
Query: 5 LKVGVAGLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKNIDRGIDCLRYEWFDD 64
LKVG+ G G +G L+ ++ F+ ++ D++ ++ +
Sbjct: 1 LKVGIVGCGAIGKFLLELVRDGRVDFE----------LVAVYDRDEEKAKE--LEASVGR 48
Query: 65 PLIM---AGEADIDVFVELIGGEDYPAYDAVRIALMRGCHVVTANKALIASHGKDLAL-- 119
+ A++D+ VE E + V L G V+ + +A G L
Sbjct: 49 RCVSDIDELIAEVDLVVEAASPE--AVREYVPKILKAGIDVIVMSVGALADEGLRERLRE 106
Query: 120 LAQKNNAILNFEAAVAGGIPIIRILK 145
LA+ A + + GG+ + +
Sbjct: 107 LAKCGGARVYLPSGAIGGLDALAAAR 132
>gnl|CDD|144849 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilize NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 31.8 bits (73), Expect = 0.35
Identities = 24/131 (18%), Positives = 48/131 (36%), Gaps = 22/131 (16%)
Query: 5 LKVGVAGLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKNIDRGIDCLRYEWFDD 64
L+VG+ G G +G +R++ + + + +V + + + + D
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAE-------LVGVLDPDPARAEAVAESFGVPAYSD 53
Query: 65 PLIMAGEADIDVFVELIGGEDYPAYDAVRIALMRGCHVV-------TANKALIASHGKDL 117
+ + D+D + ++ AL G HV+ T +A K+L
Sbjct: 54 LEELLADPDVDAVS--VATPPGLHFELALAALEAGKHVLVEKPLATTVEEA------KEL 105
Query: 118 ALLAQKNNAIL 128
LA+K L
Sbjct: 106 VELAEKKGVRL 116
>gnl|CDD|38031 KOG2820, KOG2820, KOG2820, FAD-dependent oxidoreductase [General
function prediction only].
Length = 399
Score = 31.5 bits (71), Expect = 0.46
Identities = 13/79 (16%), Positives = 25/79 (31%), Gaps = 13/79 (16%)
Query: 1 MAGVLKVGVAGLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKN----------- 49
M V + G G G + + KR + L+Q S S+ +
Sbjct: 4 MVKSRDVIIVGAGVFGLSTAYELAKRGDKILLLEQFPLPHSRGSSHGISRIIRPAYAEDK 63
Query: 50 -IDRGIDCLRYEWFDDPLI 67
+ ++ +W + P
Sbjct: 64 YMSMVLEAYE-KWRNLPEE 81
>gnl|CDD|29380 cd01412, SIRT5_Af1_CobB, SIRT5_Af1_CobB: Eukaryotic, archaeal and
prokaryotic group (class3) which includes human sirtuin
SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli
CobB; and are members of the SIR2 family of proteins,
silent information regulator 2 (Sir2) enzymes which
catalyze NAD+-dependent protein/histone deacetylation.
Sir2 proteins have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
CobB is a bacterial sirtuin that deacetylates acetyl-CoA
synthetase at an active site lysine to stimulate its
enzymatic activity. .
Length = 224
Score = 30.9 bits (70), Expect = 0.67
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 9/54 (16%)
Query: 61 WFDDPL------IMAGEADIDVFVELIG--GEDYPAYDAVRIALMRGCHVVTAN 106
WF + L + A D+F+ +IG G YPA A RG V+ N
Sbjct: 146 WFGESLPLALLEAVEALAKADLFL-VIGTSGVVYPAAGLPEEAKERGARVIEIN 198
>gnl|CDD|176235 cd08274, MDR9, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(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. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. 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.
Length = 350
Score = 30.7 bits (70), Expect = 0.88
Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 32/114 (28%)
Query: 3 GVLKVGVAGLGTVGSALIRSIQKREGRFKDLDQHSFVVSAISARDKN-----------ID 51
VL G +G VGSAL++ + KR G +V A++ K I
Sbjct: 180 TVLVTGASGG--VGSALVQ-LAKRRGA---------IVIAVAGAAKEEAVRALGADTVIL 227
Query: 52 RGIDCLRYEWFDDPLIMAGEADIDVFVELIGGEDYPAYDAVRIALMRGCHVVTA 105
R L G +DV +++GG +P D +R L G VTA
Sbjct: 228 RDAPLLADA------KALGGEPVDVVADVVGGPLFP--DLLR-LLRPGGRYVTA 272
>gnl|CDD|35308 KOG0085, KOG0085, KOG0085, G protein subunit Galphaq/Galphay, small
G protein superfamily [Signal transduction mechanisms].
Length = 359
Score = 30.4 bits (68), Expect = 0.91
Identities = 10/54 (18%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 341 VIHCDGVYEEEKEYFIRLTIRNFEGILDKITSQMSDFNISLRLFSCPHQEENSQ 394
+IH G EE+++ F +L +N + + M I + + ++
Sbjct: 61 IIHGAGYSEEDRKGFTKLVYQNIFTAMQAMIRAMETLKI---PYKREENKAHAS 111
>gnl|CDD|38742 KOG3534, KOG3534, KOG3534, p53 inducible protein PIR121 [General
function prediction only].
Length = 1253
Score = 29.2 bits (65), Expect = 2.1
Identities = 12/57 (21%), Positives = 22/57 (38%)
Query: 381 LRLFSCPHQEENSQEFSVFMITHKVSGKLIRDAIECFNGKSDAIRYSCVICIENFES 437
L S + SQ S+F+ T ++ +E G + + IC+ +E
Sbjct: 195 LTAMSDTQAVQESQNLSMFLATQNKIKDDLKLQLETIEGYEELLCDVVNICVHMYEH 251
>gnl|CDD|146841 pfam04404, ERF, ERF superfamily. The DNA single-strand annealing
proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52,
function in RecA-dependent and RecA-independent DNA
recombination pathways. This family includes proteins
related to ERF.
Length = 158
Score = 28.1 bits (63), Expect = 5.1
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 361 RNFEGILDKITSQMSDFNISLRLFSCPHQEENSQEFSV-FMITH 403
+ E IL+ I +S +SL + + V +TH
Sbjct: 29 ASLEDILEAIKPALSKHGLSLVQRVEIIEGSDRGYVEVTTTLTH 72
>gnl|CDD|133249 cd00066, G-alpha, G protein alpha subunit. The alpha subunit of G
proteins contains the guanine nucleotide binding site.
The heterotrimeric GNP-binding proteins are signal
transducers that communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 317
Score = 27.5 bits (62), Expect = 7.4
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 342 IHCDGVYEEEKEYFIRLTIRN-FEGILDKITSQMSDFNISLRLFSCPHQEENSQEFSVF- 399
+H DG EEE + + N + + + M NI F P E+++++ F
Sbjct: 23 LHGDGFSEEELREYRPVIYSNILQSM-KALLEAMERLNIP---FGDPENEKDAKKILSFA 78
Query: 400 -MITHKVSGKLIRDAIECF 417
+ + +AI+
Sbjct: 79 PELEEGELPPELAEAIKEL 97
>gnl|CDD|144034 pfam00295, Glyco_hydro_28, Glycosyl hydrolases family 28. Glycosyl
hydrolase family 28 includes polygalacturonase
EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A),
EC:3.2.1.-. These enzymes is important in cell wall
metabolism.
Length = 325
Score = 27.3 bits (61), Expect = 9.6
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 13/53 (24%)
Query: 210 ILSAIAFGIDTSVEGVYCEG-----------ISNITLEDIRGAADFGYCIKFL 251
+S +A+ I ++ YC+G IS+IT ++I G + +K L
Sbjct: 240 EMSNVAYPIV--IDQDYCDGKPCGKPTSGVKISDITFKNITGTSASATAVKLL 290
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
0.321 0.138 0.403
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,160,547
Number of extensions: 281290
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 707
Number of HSP's successfully gapped: 22
Length of query: 438
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 341
Effective length of database: 4,167,664
Effective search space: 1421173424
Effective search space used: 1421173424
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 (21.9 bits)
S2: 59 (26.5 bits)