RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046320
(198 letters)
>gnl|CDD|215500 PLN02926, PLN02926, histidinol dehydrogenase.
Length = 431
Score = 248 bits (635), Expect = 1e-81
Identities = 130/237 (54%), Positives = 151/237 (63%), Gaps = 58/237 (24%)
Query: 2 EKIFGPGNKYVTAAKMILQLQFFPAILKKSHDKVQT------AQVLVIADRYPSPLHVAA 55
+KIFGPGN+YVTAAKMILQ S V ++VLVIAD+ +P+HVAA
Sbjct: 205 DKIFGPGNQYVTAAKMILQ---------NSEAMVSIDMPAGPSEVLVIADKTANPVHVAA 255
Query: 56 DLLSQ--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLP-----------NFMVFAREI 102
DLLSQ GPDSQ VLV VGD VD+ AIEEE+ QCQSLP +F+V AR++
Sbjct: 256 DLLSQAEHGPDSQVVLVAVGD-VDLDAIEEEVEKQCQSLPRGEIASKALGHSFIVVARDM 314
Query: 103 MRAITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES---------------- 146
AI+FSNLYAPEHLIV+ +D E W I+NAGS+ G WTPES
Sbjct: 315 AEAISFSNLYAPEHLIVNVEDAESWLDKIDNAGSVFLGRWTPESVGDYASGTNHVLPTYG 374
Query: 147 -ARMYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLRLQDI 190
ARMYGGVSLDSFLKY+TVQSL A MAE+EGLEAHKRA+TLRL DI
Sbjct: 375 YARMYGGVSLDSFLKYMTVQSLTEEGLQNLGPYVARMAEVEGLEAHKRAVTLRLGDI 431
>gnl|CDD|216133 pfam00815, Histidinol_dh, Histidinol dehydrogenase.
Length = 413
Score = 177 bits (452), Expect = 2e-54
Identities = 91/232 (39%), Positives = 120/232 (51%), Gaps = 55/232 (23%)
Query: 1 AEKIFGPGNKYVTAAKMILQLQF---FPAILKKSHDKVQTAQVLVIADRYPSPLHVAADL 57
+KIFGPGN YVTAAK ++ PA ++VLVIAD P VA+DL
Sbjct: 191 VDKIFGPGNIYVTAAKRLVSGLVDIDMPA---------GPSEVLVIADETADPDFVASDL 241
Query: 58 LSQ--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLP-----------NFMVFAREIMR 104
LSQ PDSQ VLV + + + +EEE+ Q + LP + +V +++
Sbjct: 242 LSQAEHDPDSQVVLVTDSEEL-AEEVEEEVERQLEQLPRKEIVRKALAHSAIVLVKDLEE 300
Query: 105 AITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES-----------------A 147
AI FSN YAPEHLI+ K+ EK I+NAGS+ G ++PES A
Sbjct: 301 AIEFSNQYAPEHLIIQTKNAEKLLGKIKNAGSIFLGAYSPESAGDYASGTNHVLPTYGYA 360
Query: 148 RMYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLRL 187
R Y G+S+ FLK +TVQ L T+AE EGLEAH A+ +RL
Sbjct: 361 RQYSGLSVADFLKRITVQELTEEGLKNVAETVMTLAEAEGLEAHAEAVRIRL 412
>gnl|CDD|119329 cd06572, Histidinol_dh, Histidinol dehydrogenase, HisD, E.C
1.1.1.23. Histidinol dehydrogenase catalyzes the last
two steps in the L-histidine biosynthesis pathway, which
is conserved in bacteria, archaea, fungi, and plants.
These last two steps are (i) the NAD-dependent oxidation
of L-histidinol to L-histidinaldehyde, and (ii) the
NAD-dependent oxidation of L-histidinaldehyde to
L-histidine. In most fungi and in the unicellular
choanoflagellate Monosiga bevicollis, the HisD domain is
fused with units that catalyze the second and third
biosynthesis steps in this same pathway.
Length = 390
Score = 166 bits (423), Expect = 3e-50
Identities = 85/225 (37%), Positives = 108/225 (48%), Gaps = 56/225 (24%)
Query: 1 AEKIFGPGNKYVTAAKMILQLQFFPAILKKSHDKVQTA---QVLVIADRYPSPLHVAADL 57
+KI GPGN YVTAAK + I D A +VLVIAD +P VAADL
Sbjct: 176 VDKIVGPGNIYVTAAKR--LVSGDVGI-----D--MPAGPSEVLVIADETANPEFVAADL 226
Query: 58 LSQ--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLP------------NFMVFAREIM 103
LSQ PDSQ +LV +A+EEE+ Q LP ++ ++
Sbjct: 227 LSQAEHDPDSQAILVTT-SEELAEAVEEEVERQLAELPRREIAAKSLLDYGAIILVDDLE 285
Query: 104 RAITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES----------------- 146
AI +N YAPEHL + +D E+ I NAGS+ G +TPE+
Sbjct: 286 EAIELANEYAPEHLELQTEDPEELLEKIRNAGSIFLGPYTPEALGDYAAGPNHVLPTGGT 345
Query: 147 ARMYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAH 179
AR Y G+S+D FLK +TVQ AT+AE EGLEAH
Sbjct: 346 ARFYSGLSVDDFLKRITVQEYSKEGLRALAPAVATLAEAEGLEAH 390
>gnl|CDD|234853 PRK00877, hisD, bifunctional histidinal dehydrogenase/ histidinol
dehydrogenase; Reviewed.
Length = 425
Score = 161 bits (409), Expect = 8e-48
Identities = 78/231 (33%), Positives = 107/231 (46%), Gaps = 56/231 (24%)
Query: 3 KIFGPGNKYVTAAKMILQLQF---FPAILKKSHDKVQTAQVLVIADRYPSPLHVAADLLS 59
KI GPGN YVTAAK ++ A +++LVIAD P VAADLLS
Sbjct: 205 KIVGPGNIYVTAAKRLVFGVVGIDMIA---------GPSEILVIADETADPDFVAADLLS 255
Query: 60 Q--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLPN------------FMVFAREIMRA 105
Q PD+Q +LV + + +A+ E+ Q +LP ++ ++ A
Sbjct: 256 QAEHDPDAQSILVTTSEEL-AEAVAAEVERQLATLPRAEIARASLEGQGAIILVDDLEEA 314
Query: 106 ITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES-----------------AR 148
I SN YAPEHL + +D I NAG++ G +TPES AR
Sbjct: 315 IELSNAYAPEHLEIQTEDPRALLDRIRNAGAIFLGPYTPESLGDYAAGPNHVLPTSGTAR 374
Query: 149 MYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLRL 187
G+S+ FLK +V L T+AE EGL+AH RA+ +RL
Sbjct: 375 FSSGLSVYDFLKRSSVIELSKEGLKALGPAIVTLAEAEGLDAHARAVRVRL 425
>gnl|CDD|232808 TIGR00069, hisD, histidinol dehydrogenase. This model describes a
polypeptide sequence catalyzing the final step in
histidine biosynthesis, found sometimes as an
independent protein and sometimes as a part of a
multifunctional protein [Amino acid biosynthesis,
Histidine family].
Length = 393
Score = 159 bits (406), Expect = 9e-48
Identities = 84/230 (36%), Positives = 114/230 (49%), Gaps = 56/230 (24%)
Query: 3 KIFGPGNKYVTAAKMILQLQF---FPAILKKSHDKVQTAQVLVIADRYPSPLHVAADLLS 59
KI GPGN YVTAAK ++ PA ++VLVIAD +P VAADLLS
Sbjct: 174 KIVGPGNIYVTAAKKLVFGDVGIDMPA---------GPSEVLVIADETANPEFVAADLLS 224
Query: 60 Q--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLPN------------FMVFAREIMRA 105
Q PD+Q +LV + + +A++EEI Q +LP ++ ++ A
Sbjct: 225 QAEHDPDAQAILVTTSEEL-AEAVQEEIERQLATLPRREIARKSLEDNGAIILVDDLEEA 283
Query: 106 ITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES-----------------AR 148
I SN YAPEHL + K+ E+ I NAGS+ G +TPE+ AR
Sbjct: 284 IEISNDYAPEHLELQTKNPEELLPKIRNAGSIFLGPYTPEAAGDYAAGPNHVLPTGGTAR 343
Query: 149 MYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLR 186
Y G+S+ FLK +TVQ L T+AE EGLEAH ++ +R
Sbjct: 344 FYSGLSVLDFLKRITVQRLSKEGLAELAPAVETLAEAEGLEAHANSVRIR 393
>gnl|CDD|223219 COG0141, HisD, Histidinol dehydrogenase [Amino acid transport and
metabolism].
Length = 425
Score = 148 bits (375), Expect = 6e-43
Identities = 79/238 (33%), Positives = 112/238 (47%), Gaps = 62/238 (26%)
Query: 2 EKIFGPGNKYVTAAKMILQLQFFPAILKKSHDKV---QTA---QVLVIADRYPSPLHVAA 55
+KI GPGN YVTAAK ++ V A +VLVIAD +P VAA
Sbjct: 200 DKIVGPGNAYVTAAKRLVS------------GVVGIDMIAGPSEVLVIADETANPDFVAA 247
Query: 56 DLLSQ--RGPDSQGVLVIVGDGVDIKAIEEEIRMQCQSLPNF------------MVFARE 101
DLLSQ PD+Q +LV + + +A+E + Q ++LP ++ +
Sbjct: 248 DLLSQAEHDPDAQAILVTDSEEL-AEAVEAAVERQLETLPRAEIARKALENYGAIILVDD 306
Query: 102 IMRAITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES--------------- 146
+ A+ SN YAPEHL + ++ + I NAGS+ G ++PES
Sbjct: 307 LDEAVEISNEYAPEHLELQTENPRELLGKIRNAGSIFLGHYSPESLGDYAAGPNHVLPTS 366
Query: 147 --ARMYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLRLQDI 190
AR G+S+ FLK TVQ L T+AE EGL AH A+ +RL+ +
Sbjct: 367 GTARFSSGLSVYDFLKRSTVQELSEEGLARLAETVITLAEAEGLTAHAEAVRIRLERL 424
>gnl|CDD|237103 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 89.2 bits (222), Expect = 4e-21
Identities = 62/247 (25%), Positives = 92/247 (37%), Gaps = 72/247 (29%)
Query: 1 AEKIFGPGNKYVTAAKMILQLQFFPAILKKSHDKVQT------AQVLVIADRYPSPLHVA 54
+ + GPGN YV AK L +V + LVIAD P VA
Sbjct: 198 VDMLVGPGNAYVAEAKRQL------------FGRVGIDLFAGPTETLVIADDTADPELVA 245
Query: 55 ADLLSQ--RGPDSQGVLVI----VGDGVDIKAIEEEIRMQCQSLPNFMVFAREIMR---- 104
DLL Q GP+S VL+ + + V + IE + LP A R
Sbjct: 246 TDLLGQAEHGPNSPAVLITTSRKLAEEV-LAEIERLL----AILPT-ADVASAAWRDYGE 299
Query: 105 ---------AITFSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPES--------- 146
+ ++ YA EH+ V +D + + + N G++ GE T +
Sbjct: 300 VILCDDLEEMVAEADRYASEHVQVMTEDPDWFLENMTNYGALFLGERTNVAYGDKVIGTN 359
Query: 147 --------ARMYGGVSLDSFLKYVTVQSL------------ATMAEIEGLEAHKRAITLR 186
AR GG+ + FLK VT Q + + + +EG E H R +R
Sbjct: 360 HVLPTSGAARYTGGLWVGKFLKTVTYQRVTDEASAEIGEYCSRLCRLEGFEGHARQADIR 419
Query: 187 LQDIAAR 193
++ R
Sbjct: 420 VRRYGGR 426
>gnl|CDD|172308 PRK13770, PRK13770, histidinol dehydrogenase; Provisional.
Length = 416
Score = 54.9 bits (132), Expect = 4e-09
Identities = 49/228 (21%), Positives = 89/228 (39%), Gaps = 50/228 (21%)
Query: 2 EKIFGPGNKYVTAAKMILQLQFFPAILKKSHDKVQ-TAQVLVIADRYPSPLHVAADLLSQ 60
+KI GPGN++V AK L Q D++ ++ +I D + D+ +Q
Sbjct: 194 DKIVGPGNQFVAYAKKYLFGQV-------GIDQIAGPTEIALIIDETADLDAIVYDVFAQ 246
Query: 61 RGPDSQG-VLVIVGDGVDIKAIEEEIRMQCQSLP------------NFMVFAREIMRAIT 107
D VI D +K +E I ++ ++++ A A
Sbjct: 247 AEHDELARTYVISEDAQVLKDLESRIAKALPNVDRYDIVSKSIANQHYLIHASNFDEACH 306
Query: 108 FSNLYAPEHLIVSAKDTEKWESIIENAGSMLFGEWTPE-----------------SARMY 150
N APEH + + + + ++ G++ G ++PE +AR
Sbjct: 307 VMNTIAPEHASIQTVNPQPYIEKVKYVGALFIGHYSPEVIGDYVAGPSHVLPTNRTARFT 366
Query: 151 GGVSLDSFLKYVTVQSLAT------------MAEIEGLEAHKRAITLR 186
G+S++ FL TV L+ +A +E L H+++I +R
Sbjct: 367 NGLSVNDFLTRNTVIHLSKDTFEQIADSAQHIAHVEALYNHQQSILIR 414
>gnl|CDD|172307 PRK13769, PRK13769, histidinol dehydrogenase; Provisional.
Length = 368
Score = 30.2 bits (68), Expect = 0.58
Identities = 50/207 (24%), Positives = 80/207 (38%), Gaps = 39/207 (18%)
Query: 6 GPGNKYVTAAKMILQLQFFPAILKKSHDKVQTAQVLVIADRYPSPLHVAADLLSQ--RGP 63
GPG YV AAK +L D ++ LV+ P L+Q GP
Sbjct: 172 GPGGLYVQAAKYVLSQYV-------GIDGIEGPTELVVYAEGVPPEVAVRGALAQLEHGP 224
Query: 64 DSQGVLVIVGDGVDIKAIEEEIRMQCQSL--PNFMVFAREIMRAITFSNLYAPEHLIVSA 121
S L+ D +KA EE R + S P + + A+ F + APEHL V
Sbjct: 225 TSFAYLLST-DAELLKAAEEIYRRERTSSMGPLEVRKVAGVEEAVRFIDEIAPEHLEVWG 283
Query: 122 KDTEKWESIIENAGSMLFGEWTPE---------------SARMYGGVSLDSFLKYVTV-- 164
+ + + N G++ +P +AR G ++ +F+K + V
Sbjct: 284 RREVAYR--VRNVGAVSVNMPSPYLDYVAGISHVLPTGGTARWRGIITPLTFMKPIGVAE 341
Query: 165 --------QSLATMAEIEGLEAHKRAI 183
++ +AE EG + H+ A+
Sbjct: 342 AVGELELAEAARRLAEYEGFQYHREAL 368
>gnl|CDD|99979 cd03807, GT1_WbnK_like, This family is most closely related to the
GT1 family of glycosyltransferases. WbnK in Shigella
dysenteriae has been shown to be involved in the type 7
O-antigen biosynthesis.
Length = 365
Score = 29.1 bits (66), Expect = 1.6
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 54 AADLLSQRGPDSQGVLVIVGDGVDIKAIEEEIRMQ 88
AA LL ++ P++ L++VGDG D +E +
Sbjct: 214 AAALLLKKFPNA--RLLLVGDGPDRANLELLALKE 246
>gnl|CDD|234262 TIGR03567, FMN_reduc_SsuE, FMN reductase, SsuE family. Members of
this protein family use NAD(P)H to reduce FMN and
regenerate FMNH2. Members include the homodimeric,
NAD(P)H-dependent enzyme SsuE from Escherichia coli,
which serves as a partner to an FMNH2-dependent
alkanesulfonate monooxygenase. It is induced by sulfate
starvation. The NADH-dependent enzyme MsuE from
Pseudomonas aeruginosa is outside the scope of this
model (see model TIGR03566) [Central intermediary
metabolism, Sulfur metabolism].
Length = 171
Score = 28.0 bits (63), Expect = 2.5
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 14/56 (25%)
Query: 25 PAILKKSHDKVQTAQVLVIADRYPSPLHVAA---------DLLSQRGPDSQGVLVI 71
PAI K + +V A +V+A +P++ A+ DLL QR + VL I
Sbjct: 54 PAI-KAATAQVAQADGVVVA----TPVYKASYSGVLKALLDLLPQRALRGKVVLPI 104
>gnl|CDD|238798 cd01557, BCAT_beta_family, BCAT_beta_family: Branched-chain
aminotransferase catalyses the transamination of the
branched-chain amino acids leusine, isoleucine and
valine to their respective alpha-keto acids,
alpha-ketoisocaproate, alpha-keto-beta-methylvalerate
and alpha-ketoisovalerate. The enzyme requires pyridoxal
5'-phosphate (PLP) as a cofactor to catalyze the
reaction. It has been found that mammals have two foms
of the enzyme - mitochondrial and cytosolic forms while
bacteria contain only one form of the enzyme. The
mitochondrial form plays a significant role in skeletal
muscle glutamine and alanine synthesis and in interorgan
nitrogen metabolism.Members of this subgroup are widely
distributed in all three forms of life.
Length = 279
Score = 28.3 bits (64), Expect = 2.6
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 14/61 (22%)
Query: 131 IENAGSM-LFGEW-----TPESARMYGGVSLDSFLKYVTVQSLATMAEIEGLEAHKRAIT 184
+ G+M +F TP S L +T S+ +A G++ +R IT
Sbjct: 174 VAEVGTMNIFFVKDGELITPPLD--------GSILPGITRDSILELARDLGIKVEERPIT 225
Query: 185 L 185
Sbjct: 226 R 226
>gnl|CDD|223825 COG0754, Gsp, Glutathionylspermidine synthase [Amino acid transport
and metabolism].
Length = 387
Score = 28.1 bits (63), Expect = 3.6
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 127 WESIIENAGSMLFGEWTPESARMYGGVSLDSFLKYVTVQSLATMAEIEGLEAH 179
E++IE FG RM + D+ TVQ L A+ G E
Sbjct: 156 QEALIER-----FGRLYELRDRMGFSICQDTAEDRGTVQYLQDCAQEAGFETE 203
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 28.0 bits (63), Expect = 4.1
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 107 TFSNLYAPEHLIVSAKDTEK-WESIIENAGS 136
T N Y + L KDT++ W SI+ N GS
Sbjct: 460 TVKNKYLEKLLEEKGKDTDEVWSSILTNEGS 490
>gnl|CDD|166653 PLN03012, PLN03012, Camelliol C synthase.
Length = 759
Score = 28.1 bits (62), Expect = 4.2
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 11/59 (18%)
Query: 6 GPGNKYVTAAKMILQLQFFPAILKKSHDKVQTAQVLV------IADRYPSPLHVAADLL 58
G G Y++ K I + + S + VQTA L+ A+R P PLH AA L+
Sbjct: 657 GWGESYLSCPKKI----YIAQEGEIS-NLVQTAWALMGLIHAGQAERDPIPLHRAAKLI 710
>gnl|CDD|215768 pfam00174, Oxidored_molyb, Oxidoreductase molybdopterin binding
domain. This domain is found in a variety of
oxidoreductases. This domain binds to a molybdopterin
cofactor. Xanthine dehydrogenases, that also bind
molybdopterin, have essentially no similarity.
Length = 144
Score = 27.1 bits (61), Expect = 4.6
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 140 GEWTPESARMYGGVSLDSFLKYVTVQSLATMAEIEGLEAHKRAIT--LRLQDIAARQV 195
G W+ +A + GV L L+ + A EG + T L L+D V
Sbjct: 38 GNWSIGNAE-WTGVPLRDLLELAGPKPDAKYVLFEGADGGTGGYTTSLPLEDALDPDV 94
>gnl|CDD|182111 PRK09850, PRK09850, pseudouridine kinase; Provisional.
Length = 313
Score = 27.3 bits (60), Expect = 5.1
Identities = 11/41 (26%), Positives = 23/41 (56%)
Query: 98 FAREIMRAITFSNLYAPEHLIVSAKDTEKWESIIENAGSML 138
+ + ++ S +Y + LIV ++T + S+++N G ML
Sbjct: 68 YGQSLLTQTNQSGVYVDKCLIVPGENTSSYLSLLDNTGEML 108
>gnl|CDD|235425 PRK05349, PRK05349, Na(+)-translocating NADH-quinone reductase
subunit B; Provisional.
Length = 405
Score = 27.1 bits (61), Expect = 5.9
Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 102 IMRAITFSNLYAP--EHLIVSA 121
+M AI F+NL+AP ++ +V A
Sbjct: 373 MMLAILFANLFAPLFDYFVVQA 394
>gnl|CDD|99982 cd03811, GT1_WabH_like, This family is most closely related to the
GT1 family of glycosyltransferases. WabH in Klebsiella
pneumoniae has been shown to transfer a GlcNAc residue
from UDP-GlcNAc onto the acceptor GalUA residue in the
cellular outer core.
Length = 353
Score = 27.3 bits (61), Expect = 6.4
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 54 AADLLSQRGPDSQGVLVIVGDGVDIKAIEEEIR 86
A LL + GPD++ LVI+GDG + +E +
Sbjct: 210 AFALLRKEGPDAR--LVILGDGPLREELEALAK 240
>gnl|CDD|233420 TIGR01452, PGP_euk, phosphoglycolate/pyridoxal phosphate
phosphatase family. PGP is an essential enzyme in the
glycolate salvage pathway in higher organisms
(photorespiration in plants). Phosphoglycolate results
from the oxidase activity of RubisCO in the Calvin cycle
when concentrations of carbon dioxide are low relative
to oxygen. In mammals, PGP is found in many tissues,
notably in red blood cells where P-glycolate is and
important activator of the hydrolysis of
2,3-bisphosphoglycerate, a major modifier of the oxygen
affinity of hemoglobin. Pyridoxal phosphate (PLP,
Vitamin B6) phosphatase is involved in the degradation
of PLP in mammals and is widely distributed in human
tissues including erythrocyes. The enzymes described
here are members of the Haloacid dehalogenase
superfamily of hydrolase enzymes (pfam00702). Unlike the
bacterial PGP equivalog (TIGR01449), which is a member
of class (subfamily) I, these enzymes are members of
class (subfamily) II. These two families have almost
certainly arisen from convergent evolution (although
these two ancestors may themselves have diverged from a
more distant HAD superfamily progenitor). The primary
seed sequence for this model comes from Chlamydomonas
reinhardtii, a photosynthetic alga. The enzyme has been
purified and characterized and these data are fully
consistent with the assignment of function as a PGPase
involved in photorespiration. The second seed, from Homo
sapiens chromosome 22 has been characterized as a
pyridoxal phosphatase. Biochemical characterization of
partially purified PGP's from various tissues including
red blood cells have been performed while one gene for
PGP has been localized to chromosome 16p13.3. The
sequence used here maps to chromosome 22. There is
indeed a related gene on chromosome 16 (and it is
expressed, since EST's are found) which shows 46%
identity and 59% positives by BLAST2 (E=1e-66). The
chromosome 16 gene is not in evidence in nraa but
translated from the genomic sequence would score 372.4
(E=7.9e-113) versus This model, well above trusted. The
third seed, from C. elegans, is only supported by
sequence similarity. This model is limited to eukaryotic
species including S. pombe and S. cerevisiae, although
several archaea score between the trusted and noise
cutoffs. This model is closely related to a family of
bacterial sequences including the E. coli NagD and B.
subtilus AraL genes which are characterized by the
ability to hydrolyze para-nitrophenylphosphate (pNPPases
or NPPases). The chlamydomonas PGPase d.
Length = 279
Score = 27.1 bits (60), Expect = 6.4
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 42 VIADRYPSPLHVAADLLSQRGPDSQGVLVIVGDGV----DIKAIE 82
+A++ S AA LL Q + V VI +G+ D I
Sbjct: 62 GLAEQLFSSALCAARLLRQPPDAPKAVYVIGEEGLRAELDAAGIR 106
>gnl|CDD|224796 COG1884, Sbm, Methylmalonyl-CoA mutase, N-terminal domain/subunit
[Lipid metabolism].
Length = 548
Score = 26.9 bits (60), Expect = 7.6
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 43 IADRYPSPLHVAADLLSQRGPDSQGVLVI--VGD-GVDIKAIEE 83
+ + L VA DL + RG DS VG GV I +++
Sbjct: 94 LLAAGQTGLSVAFDLPTLRGYDSDHPRAEGEVGKAGVAIDTLKD 137
>gnl|CDD|99974 cd03801, GT1_YqgM_like, This family is most closely related to the
GT1 family of glycosyltransferases and named after YqgM
in Bacillus licheniformis about which little is known.
Glycosyltransferases catalyze the transfer of sugar
moieties from activated donor molecules to specific
acceptor molecules, forming glycosidic bonds. The
acceptor molecule can be a lipid, a protein, a
heterocyclic compound, or another carbohydrate residue.
This group of glycosyltransferases is most closely
related to the previously defined glycosyltransferase
family 1 (GT1). The members of this family may transfer
UDP, ADP, GDP, or CMP linked sugars. The diverse
enzymatic activities among members of this family
reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in certain bacteria and archaea.
Length = 374
Score = 27.0 bits (60), Expect = 7.9
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 54 AADLLSQRGPDSQGVLVIVGDGVDIKAIEEEIR 86
A L + PD + LVIVGDG + +E
Sbjct: 220 ALAKLRKEYPDVR--LVIVGDGPLREELEALAA 250
>gnl|CDD|132132 TIGR03088, stp2, sugar transferase, PEP-CTERM/EpsH1 system
associated. Members of this family include a match to
the pfam00534 Glycosyl transferases group 1 domain.
Nearly all are found in species that encode the
PEP-CTERM/exosortase system predicted to act in protein
sorting in a number of Gram-negative bacteria. In
particular, these transferases are found proximal to a
particular variant of exosortase, EpsH1, which appears
to travel with a conserved group of genes summarized by
Genome Property GenProp0652. The nature of the sugar
transferase reaction catalyzed by members of this clade
is unknown and may conceivably be variable with respect
to substrate by species, but we hypothesize a conserved
substrate.
Length = 374
Score = 26.6 bits (59), Expect = 8.5
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 47 YPSPLHVAADLLSQRGPDSQGV-LVIVGDGVDIKAIEEEIR 86
P+ + A L+ Q ++ + LVIVGDG A E+ +R
Sbjct: 209 QPTLVRAFALLVRQLPEGAERLRLVIVGDGPARGACEQMVR 249
>gnl|CDD|237517 PRK13807, PRK13807, maltose phosphorylase; Provisional.
Length = 756
Score = 26.8 bits (60), Expect = 9.0
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 112 YAPEHLIVSAKDTEKWESIIEN 133
AP L V+ ++ KW+ I++
Sbjct: 517 EAPARLNVTEEELAKWQDIVDK 538
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
0.320 0.134 0.376
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,149,051
Number of extensions: 955474
Number of successful extensions: 1047
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1013
Number of HSP's successfully gapped: 54
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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: 56 (25.4 bits)