RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021156
(316 letters)
>gnl|CDD|215245 PLN02446, PLN02446,
(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase.
Length = 262
Score = 513 bits (1324), Expect = 0.0
Identities = 208/262 (79%), Positives = 238/262 (90%), Gaps = 3/262 (1%)
Query: 54 VRFRPCIDIHKGKVKQIVGSTLQDSKD---DGTKLVTNFESDKSAAEFANLYKEDGLTGG 110
VRFRPCIDIHKGKVKQIVGSTL+DSKD DG++LVTNFESDKSAAEFA +YK DGLTGG
Sbjct: 1 VRFRPCIDIHKGKVKQIVGSTLKDSKDGSEDGSELVTNFESDKSAAEFAEMYKRDGLTGG 60
Query: 111 HAIMLGADPLSKAAAIEALHAYPGGLQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQM 170
H IMLGAD S AAA+EAL AYPGGLQVGGG+NS+N++SY++ GA+HVIVTSYVF +GQ+
Sbjct: 61 HVIMLGADDASLAAALEALRAYPGGLQVGGGVNSENAMSYLDAGASHVIVTSYVFRDGQI 120
Query: 171 DLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEF 230
DLERLKDLVR+VGKQRLVLDLSCRKKDG+Y +VTDRWQKFSD+ +DE L+FLA+Y DEF
Sbjct: 121 DLERLKDLVRLVGKQRLVLDLSCRKKDGRYYVVTDRWQKFSDLAVDEETLEFLAAYCDEF 180
Query: 231 LVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSA 290
LVHGVDVEGK+LGID+ELVALLG++SPIPVTYAGGV ++ DLE++KVAG GRVDVTVGSA
Sbjct: 181 LVHGVDVEGKRLGIDEELVALLGEHSPIPVTYAGGVRSLDDLERVKVAGGGRVDVTVGSA 240
Query: 291 LDIFGGNLAYKDVVAWHAQQEA 312
LDIFGGNL Y DVVAWH QQ+
Sbjct: 241 LDIFGGNLPYDDVVAWHKQQKT 262
>gnl|CDD|162719 TIGR02129, hisA_euk, phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase, eukaryotic type. This
enzyme acts in the biosynthesis of histidine and has
been characterized in S. cerevisiae and Arabidopsis
where it complements the E. coli HisA gene. In
eukaryotes the gene is known as HIS6. In bacteria, this
gene is found in Fibrobacter succinogenes, presumably
due to lateral gene transfer from plants in the rumen
gut [Amino acid biosynthesis, Histidine family].
Length = 253
Score = 390 bits (1004), Expect = e-138
Identities = 141/256 (55%), Positives = 189/256 (73%), Gaps = 6/256 (2%)
Query: 54 VRFRPCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAI 113
+FRPCIDIH GKVKQIVG TL K L TNF SDK ++ +A LYK+DG+ G H I
Sbjct: 1 TKFRPCIDIHNGKVKQIVGGTLTSKKGSV--LKTNFVSDKPSSYYAKLYKDDGVKGCHVI 58
Query: 114 MLGADPLSKAAAIEALHAYPGGLQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQMDLE 173
MLG + + AA EALHAYPGGLQVGGGIN N+ +++EGA+HVIVTS++F G+ DL+
Sbjct: 59 MLGPN--NDDAAKEALHAYPGGLQVGGGINDTNAQEWLDEGASHVIVTSWLFTKGKFDLK 116
Query: 174 RLKDLVRVVGKQRLVLDLSCRKK-DGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLV 232
RLK++V +VGK RL++DLSCRK DG++ + ++WQ +D+ L+ L+ L+ Y DEFL+
Sbjct: 117 RLKEIVSLVGKDRLIVDLSCRKTQDGRWIVAMNKWQTITDLELNAETLEELSKYCDEFLI 176
Query: 233 HGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSALD 292
H DVEG GID+ELV+ LG++SPIP+TYAGG ++ DL+ + G+VD+T+GSALD
Sbjct: 177 HAADVEGLCKGIDEELVSKLGEWSPIPITYAGGAKSIDDLDLVDELSKGKVDLTIGSALD 236
Query: 293 IFGGN-LAYKDVVAWH 307
IFGGN + + D VAW+
Sbjct: 237 IFGGNLVKFTDCVAWN 252
>gnl|CDD|240074 cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase (HisA) and
the cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). The ProFAR isomerase catalyzes the
fourth step in histidine biosynthesis, an isomerisation
of the aminoaldose moiety of ProFAR to the aminoketose
of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene. The Imidazole glycerol phosphate synthase (IGPS)
catalyzes the fifth step of histidine biosynthesis, the
formation of the imidazole ring. IGPS converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria.
Length = 233
Score = 204 bits (520), Expect = 5e-65
Identities = 84/255 (32%), Positives = 115/255 (45%), Gaps = 26/255 (10%)
Query: 55 RFRPCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIM 114
R P ID+ G V VG D+ + +N S + A YKE G G +
Sbjct: 1 RIIPVIDLKDGVVVHGVGGDR----DNYRPITSNLCSTSDPLDVARAYKELGFRGLYIAD 56
Query: 115 LGA---DPLSKAAAIEALHAYPGGLQVGGGINS-DNSLSYIEEGATHVIVTSYVFNNGQM 170
L A + A E A+P GL V GGI S +N+ +++ GA+ VIV + +
Sbjct: 57 LDAIMGRGDNDEAIRELAAAWPLGLWVDGGIRSLENAQEWLKRGASRVIVGTETLPSDD- 115
Query: 171 DLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEF 230
D +RL L G+QRLVL L R K +D E +L LA + +E
Sbjct: 116 DEDRLAAL----GEQRLVLSLDFRGGQLL---------KPTDFIGPEELLRRLAKWPEEL 162
Query: 231 LVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSA 290
+V +D G G D EL+ L + IPV AGGV ++ DLE +K +G V SA
Sbjct: 163 IVLDIDRVGSGQGPDLELLERLAARADIPVIAAGGVRSVEDLELLK--KLGASGALVASA 220
Query: 291 LDIFGGNLAYKDVVA 305
L G L +DVV
Sbjct: 221 LHDGG--LTLEDVVR 233
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 128 bits (325), Expect = 9e-36
Identities = 67/245 (27%), Positives = 101/245 (41%), Gaps = 17/245 (6%)
Query: 56 FRPCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIML 115
P ID+ GKV ++V + K + + A L G A
Sbjct: 4 IIPAIDLKDGKVVRLVQGDYGKETVYSDD--PLEVAKKWSDQGAEWLHLVDLDGAKA--- 58
Query: 116 GADPLSKAAAIEALHAYPGGLQVGGGINSDNSL-SYIEEGATHVIVTSYVFNNGQMDLER 174
G P + A E L A +QVGGGI S + + ++ G VI+ + N +
Sbjct: 59 GG-PRNLEAIKEILEATDVPVQVGGGIRSLEDVEALLDAGVARVIIGTAAVKN----PDL 113
Query: 175 LKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHG 234
+K+L G R+V+ L R DGK A+ WQ+ S V L+E L
Sbjct: 114 VKELCEEYG-DRIVVALDAR--DGKVAV--SGWQEDSGVELEELAKRLEEVGLAHILYTD 168
Query: 235 VDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSALDIF 294
+ +G G + +LV L + IPV +GGV+++ D++ +K G V VG AL
Sbjct: 169 ISRDGTLSGPNVDLVKELAEAVDIPVIASGGVSSLDDIKALKELS-GVEGVIVGRALYEG 227
Query: 295 GGNLA 299
L
Sbjct: 228 KFTLE 232
>gnl|CDD|216225 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins
involved in steps 4 and 6 of the histidine biosynthesis
pathway are contained in this family. Histidine is
formed by several complex and distinct biochemical
reactions catalyzed by eight enzymes. The enzymes in
this Pfam entry are called His6 and His7 in eukaryotes
and HisA and HisF in prokaryotes. The structure of HisA
is known to be a TIM barrel fold. In some archaeal HisA
proteins the TIM barrel is composed of two tandem
repeats of a half barrel . This family belong to the
common phosphate binding site TIM barrel family.
Length = 230
Score = 109 bits (276), Expect = 9e-29
Identities = 59/239 (24%), Positives = 101/239 (42%), Gaps = 23/239 (9%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIMLGA 117
P ID+ G+V ++ + + E A Y+E+G H + L A
Sbjct: 4 PAIDLKDGRVVRLY----KGDYFKNLVYAGDP------VELAKRYEEEGADELHFVDLDA 53
Query: 118 DPLSKAAAIEALH----AYPGGLQVGGGINSDNSLS-YIEEGATHVIVTSYVFNNGQMDL 172
+ ++ + +QVGGGI S + GA VI+ + N
Sbjct: 54 AKEGRPVNLDLIEEIAEEVFIPVQVGGGIRSLEDAERLLSAGADKVIIGTAAVKN----P 109
Query: 173 ERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLV 232
E +K+ G Q +V+ + +++DGK + + W++ + + E A E L+
Sbjct: 110 ELIKEAAEKFGSQCIVVAIDAKREDGK--VAINGWREETGIDAVEWAKKLEELGAGEILL 167
Query: 233 HGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSAL 291
+D +G G D EL L + IPV +GGV ++ DL+++ G+ V GSAL
Sbjct: 168 TDIDRDGTLSGPDLELTRELAEAVNIPVIASGGVGSLEDLKELFSEGV--DGVIAGSAL 224
>gnl|CDD|240083 cd04732, HisA, HisA. Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase catalyzes
the fourth step in histidine biosynthesis, an
isomerisation of the aminoaldose moiety of ProFAR to the
aminoketose of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene.
Length = 234
Score = 77.1 bits (191), Expect = 1e-16
Identities = 66/239 (27%), Positives = 106/239 (44%), Gaps = 25/239 (10%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIML-G 116
P ID+ GK ++ Q D T E A ++E G H + L G
Sbjct: 4 PAIDLKDGKCVRLY----QGDYDKKT------VYSDDPVEVAKKWEEAGAKWLHVVDLDG 53
Query: 117 A-DPLSK-AAAIEALHAYPGG-LQVGGGINSDNSL-SYIEEGATHVIVTSYVFNNGQMDL 172
A IE + G +QVGGGI S + ++ G + VI+ + N ++
Sbjct: 54 AKGGEPVNLELIEEIVKAVGIPVQVGGGIRSLEDIERLLDLGVSRVIIGTAAVKNPEL-- 111
Query: 173 ERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLV 232
+K+L++ G +R+V+ L + DGK A T W + S+V L+E F +
Sbjct: 112 --VKELLKEYGGERIVVGLDAK--DGKVA--TKGWLETSEVSLEELAKRFEELGVKAIIY 165
Query: 233 HGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSAL 291
+ +G G + EL L + IPV +GGV+++ D++ +K G+ V VG AL
Sbjct: 166 TDISRDGTLSGPNFELYKELAAATGIPVIASGGVSSLDDIKALKELGV--AGVIVGKAL 222
>gnl|CDD|232779 TIGR00007, TIGR00007, phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase. This protein family
consists of HisA,
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase, the enzyme catalyzing the fourth
step in histidine biosynthesis. It is closely related to
the enzyme HisF for the sixth step. Examples of this
enzyme in Actinobacteria have been found to be
bifunctional, also possessing phosphoribosylanthranilate
isomerase activity ; the trusted cutoff here has now
been raised to 275.0 to exclude the bifunctional group,
now represented by model TIGR01919. HisA from
Lactococcus lactis was reported to be inactive
(MEDLINE:93322317) [Amino acid biosynthesis, Histidine
family].
Length = 230
Score = 71.1 bits (175), Expect = 2e-14
Identities = 63/244 (25%), Positives = 102/244 (41%), Gaps = 35/244 (14%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIML-G 116
P IDI GK ++ Q D T D E A ++E+G H + L G
Sbjct: 3 PAIDIKDGKCVRLY----QGDYDKET-----VYGD-DPVEAAKKWEEEGAERIHVVDLDG 52
Query: 117 A--------DPLSKAAAIEALHAYPGGLQVGGGINSDNSL-SYIEEGATHVIVTSYVFNN 167
A + K + +QVGGGI S + ++ G VI+ + N
Sbjct: 53 AKEGGPVNLPVIKKIVRETGVP-----VQVGGGIRSLEDVEKLLDLGVDRVIIGTAAVEN 107
Query: 168 GQMDLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYA 227
+ +K+L++ G +R+V+ L R G+ + W + S+V L+E
Sbjct: 108 ----PDLVKELLKEYGPERIVVSLDAR--GGE--VAVKGWLEKSEVSLEELAKRLEELGL 159
Query: 228 DEFLVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTV 287
+ + + +G G + EL L K +PV +GGV+++ DL +K G+ V V
Sbjct: 160 EGIIYTDISRDGTLSGPNFELTKELVKAVNVPVIASGGVSSIDDLIALKKLGVY--GVIV 217
Query: 288 GSAL 291
G AL
Sbjct: 218 GKAL 221
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 65.3 bits (160), Expect = 2e-12
Identities = 74/248 (29%), Positives = 112/248 (45%), Gaps = 43/248 (17%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIML-G 116
P +D+ GK Q+V + GT+ V+ + A+ + + G H + L G
Sbjct: 7 PAVDMKGGKCVQLVQG------EPGTETVS-YGDPVEVAK---RWVDAGAETLHLVDLDG 56
Query: 117 ADPLSK--AAAIEA-LHAYPGGLQVGGGINS-DNSLSYIEEGATHVIV-TSYVFNNGQMD 171
A + A AIE + A +Q+GGGI S +++ S ++ G VI+ T+ V N
Sbjct: 57 AFEGERKNAEAIEKIIEAVGVPVQLGGGIRSAEDAASLLDLGVDRVILGTAAVENP---- 112
Query: 172 LERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFL 231
E +++L G +R+++ L KDG+ +V W + + A F
Sbjct: 113 -EIVRELSEEFGSERVMVSLDA--KDGE--VVIKGWTEKTG-------YTP-VEAAKRFE 159
Query: 232 VHG--------VDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRV 283
G VDVEG G++ E V L IPV +GGVTT+ DL +K AG
Sbjct: 160 ELGAGSILFTNVDVEGLLEGVNTEPVKELVDSVDIPVIASGGVTTLDDLRALKEAGAA-- 217
Query: 284 DVTVGSAL 291
V VGSAL
Sbjct: 218 GVVVGSAL 225
>gnl|CDD|132611 TIGR03572, WbuZ, glycosyl amidation-associated protein WbuZ. This
clade of sequences is highly similar to the HisF
protein, but generally represents the second HisF
homolog in the genome where the other is an authentic
HisF observed in the context of a complete histidine
biosynthesis operon. The similarity between these WbuZ
sequences and true HisFs is such that often the closest
match by BLAST of a WbuZ is a HisF. Only by making a
multiple sequence alignment is the homology relationship
among the WbuZ sequences made apparent. WbuZ genes are
invariably observed in the presence of a homolog of the
HisH protein (designated WbuY) and a proposed N-acetyl
sugar amidotransferase designated in WbuX in E. coli ,
IfnA in P. aeriginosa and PseA in C. jejuni. Similarly,
this trio of genes is invariably found in the context of
saccharide biosynthesis loci. It has been shown that the
WbuYZ homologs are not essential components of the
activity expressed by WbuX, leading to the proposal that
these to proteins provide ammonium ions to the
amidotransferase when these are in low concentration.
WbuY (like HisH) is proposed to act as a glutaminase to
release ammonium. In histidine biosynthesis this is also
dispensible in the presence of exogenous ammonium ion.
HisH and HisF form a complex such that the ammonium ion
is passed directly to HisF where it is used in an
amidation reaction causing a subsequent cleavage and
cyclization. In the case of WbuYZ, the ammonium ion
would be passed from WbuY to WbuZ. WbuZ, being
non-essential and so similar to HisF that a sugar
substrate is unlikely, would function instead as a
amoonium channel to the WbuX protein which does the
enzymatic work.
Length = 232
Score = 54.2 bits (131), Expect = 1e-08
Identities = 38/162 (23%), Positives = 67/162 (41%), Gaps = 11/162 (6%)
Query: 136 LQVGGGINSDNSLSYI-EEGATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCR 194
L VGGGI S + GA V + + N + +++ R G Q +V+ + +
Sbjct: 77 LTVGGGIRSLEDAKKLLSLGADKVSINTAALENPDL----IEEAARRFGSQCVVVSIDVK 132
Query: 195 KK--DGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALL 252
K+ Y + +D ++ + E + A E L++ +D +G G D EL+ +
Sbjct: 133 KELDGSDYKVYSDNGRRATGRDPVEWAREAEQLGAGEILLNSIDRDGTMKGYDLELIKTV 192
Query: 253 GKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSALDIF 294
IPV GG ++ DL V + +A +F
Sbjct: 193 SDAVSIPVIALGGAGSLDDL----VEVALEAGASAVAAASLF 230
Score = 37.2 bits (87), Expect = 0.005
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 222 FLASYADEFLVHGVDVEGKKLG--IDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAG 279
+ A ADE +V +D++ K G EL++ L + +P+T GG+ ++ D +K+ G
Sbjct: 39 YNAKGADELIV--LDIDASKRGREPLFELISNLAEECFMPLTVGGGIRSLEDAKKLLSLG 96
Query: 280 IGRV 283
+V
Sbjct: 97 ADKV 100
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 50.3 bits (121), Expect = 3e-07
Identities = 34/158 (21%), Positives = 63/158 (39%), Gaps = 10/158 (6%)
Query: 139 GGGINS-DNSLSYIEEGATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCRKK- 196
GGGI + + + G V + + + + + + G Q +V+ + +K
Sbjct: 80 GGGIKTLEQAKKIFSLGVEKVSINTAALEDPDL----ITEAAERFGSQSVVVSIDVKKNL 135
Query: 197 DGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGKYS 256
GK+ + T K E ++ A A E L++ +D +G G D EL+
Sbjct: 136 GGKFDVYTHNGTKKLKKDPLELAKEYEALGAGEILLNSIDRDGTMKGYDLELLKSFRNAL 195
Query: 257 PIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSALDIF 294
IP+ GG ++ D+ V I + +A +F
Sbjct: 196 KIPLIALGGAGSLDDI----VEAILNLGADAAAAGSLF 229
Score = 32.2 bits (74), Expect = 0.23
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 222 FLASYADEFLVHGVDVEGKKLG--IDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAG 279
F DE +V +D++ K G + EL+ L +P+ Y GG+ T+ +KI G
Sbjct: 39 FNEKEVDELIV--LDIDASKRGSEPNYELIENLASECFMPLCYGGGIKTLEQAKKIFSLG 96
Query: 280 IGRV 283
+ +V
Sbjct: 97 VEKV 100
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 49.7 bits (120), Expect = 4e-07
Identities = 52/178 (29%), Positives = 84/178 (47%), Gaps = 26/178 (14%)
Query: 123 AAAIEA-LHAYPGGLQVGGGINSDNSLS-YIEEGATHVIVTSYVFNNGQMDLERLKDLVR 180
IEA + A +QVGGGI S ++ ++ G + VI+ + N ++ +K+ +
Sbjct: 63 LELIEAIVKAVDIPVQVGGGIRSLETVEALLDAGVSRVIIGTAAVKNPEL----VKEACK 118
Query: 181 ------VVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHG 234
VVG LD +DGK A TD W + S V ++ F + +
Sbjct: 119 KFPGKIVVG-----LDA----RDGKVA--TDGWLETSGVTAEDLAKRFEDAGVKAIIYTD 167
Query: 235 VDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVD-VTVGSAL 291
+ +G G + E L PIPV +GGV+++ D++ +K G+G V+ V VG AL
Sbjct: 168 ISRDGTLSGPNVEATRELAAAVPIPVIASGGVSSLDDIKALK--GLGAVEGVIVGRAL 223
>gnl|CDD|240082 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). Imidazole glycerol phosphate synthase
(IGPS) catalyzes the fifth step of histidine
biosynthesis, the formation of the imidazole ring. IGPS
converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria.
Length = 243
Score = 46.7 bits (112), Expect = 4e-06
Identities = 36/140 (25%), Positives = 65/140 (46%), Gaps = 6/140 (4%)
Query: 136 LQVGGGINS-DNSLSYIEEGATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCR 194
L VGGGI S +++ + GA V + S N ++ ++++ + G Q +V+ + +
Sbjct: 74 LTVGGGIRSLEDARRLLRAGADKVSINSAAVENPEL----IREIAKRFGSQCVVVSIDAK 129
Query: 195 KK-DGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLG 253
++ DG Y + T +K + + E + A E L+ +D +G K G D EL+ +
Sbjct: 130 RRGDGGYEVYTHGGRKPTGLDAVEWAKEVEELGAGEILLTSMDRDGTKKGYDLELIRAVS 189
Query: 254 KYSPIPVTYAGGVTTMADLE 273
IPV +GG
Sbjct: 190 SAVNIPVIASGGAGKPEHFV 209
>gnl|CDD|237439 PRK13586, PRK13586,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 232
Score = 41.3 bits (97), Expect = 3e-04
Identities = 35/149 (23%), Positives = 61/149 (40%), Gaps = 16/149 (10%)
Query: 136 LQVGGGINSDNSLS-YIEEGATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCR 194
+QVGGGI + ++ ++ VF N + D+VR +G R+++ S
Sbjct: 76 IQVGGGIRDIEKAKRLLSLDVNALVFSTIVFTNFNL----FHDIVREIGSNRVLV--SID 129
Query: 195 KKDGKYAIVT---DRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVAL 251
+ K ++ ++ + D L+ L + + EG GID +
Sbjct: 130 YDNTKRVLIRGWKEKSMEVIDGIKKVNELELLG-----IIFTYISNEGTTKGIDYNVKDY 184
Query: 252 LGKYSPIPVTYAGGVTTMADLEKIKVAGI 280
+ YAGGV++ ADLE +K G
Sbjct: 185 ARLIRGLK-EYAGGVSSDADLEYLKNVGF 212
>gnl|CDD|167709 PRK04128, PRK04128,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 228
Score = 40.1 bits (94), Expect = 6e-04
Identities = 45/157 (28%), Positives = 76/157 (48%), Gaps = 19/157 (12%)
Query: 136 LQVGGGINSDNSLSYIEE-GATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCR 194
+QVGGG+ + S+ E G +VI+ + F DLE L+ + + LD+
Sbjct: 76 VQVGGGLRTYESIKDAYEIGVENVIIGTKAF-----DLEFLEKVTSEFEGITVSLDV--- 127
Query: 195 KKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGK 254
K G+ I W + S + +++ + L +Y + F+ ++ +G GI+ E+ G
Sbjct: 128 -KGGR--IAVKGWLEESSIKVED-AYEMLKNYVNRFIYTSIERDGTLTGIE-EIERFWGD 182
Query: 255 YSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSAL 291
I YAGGV++ D+ K+A IG V +G AL
Sbjct: 183 EEFI---YAGGVSSAEDV--KKLAEIGFSGVIIGKAL 214
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 39.3 bits (92), Expect = 0.001
Identities = 57/235 (24%), Positives = 92/235 (39%), Gaps = 44/235 (18%)
Query: 53 AVRFRPCIDIHKGKV-KQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDG----- 106
A R PC+D+ G+V K + L+D+ D E A Y E+G
Sbjct: 3 AKRIIPCLDVRDGRVVKGVQFLNLRDAGD--------------PVELAQRYDEEGADELV 48
Query: 107 ---LTGGH---AIMLGADPLSKAAAIEALHAYPGGLQVGGGINS-DNSLSYIEEGATHV- 158
+T M+ D + + A + P L VGGGI S ++ + GA V
Sbjct: 49 FLDITASSEGRTTMI--DVVERTAETVFI---P--LTVGGGIKSIEDVDKLLRAGADKVS 101
Query: 159 IVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCRKK----DGKYAIVTDRWQKFSDVY 214
I T+ V N E + +L G Q +V+ + ++ Y + ++ + +
Sbjct: 102 INTAAVKNP-----ELIYELADRFGSQCIVVAIDAKRVYVNSYCWYEVYIYGGRESTGLD 156
Query: 215 LDERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTM 269
E + A E L+ +D +G K G D EL + + IPV +GG
Sbjct: 157 AVEWAKEVEKLGAGEILLTSMDKDGTKSGYDLELTKAVSEAVKIPVIASGGAGKP 211
>gnl|CDD|172156 PRK13587, PRK13587,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 234
Score = 37.9 bits (88), Expect = 0.003
Identities = 37/151 (24%), Positives = 68/151 (45%), Gaps = 20/151 (13%)
Query: 136 LQVGGGINSDNSL-SYIEEGATHVIVTSYVFNNGQMDLERLKDLVRVV-GKQRLVLDLSC 193
++VGGGI + + + Y G + IV + G D + LK++ G+ L +D
Sbjct: 79 IEVGGGIRTKSQIMDYFAAGINYCIVGT----KGIQDTDWLKEMAHTFPGRIYLSVDAYG 134
Query: 194 RKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFL--VHGVDV--EGKKLGIDDELV 249
I + W++ D L+ + F+ +D L + D+ +GK G + EL
Sbjct: 135 ED------IKVNGWEE--DTELN--LFSFVRQLSDIPLGGIIYTDIAKDGKMSGPNFELT 184
Query: 250 ALLGKYSPIPVTYAGGVTTMADLEKIKVAGI 280
L K + IPV +GG+ D++++ +
Sbjct: 185 GQLVKATTIPVIASGGIRHQQDIQRLASLNV 215
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 36.4 bits (85), Expect = 0.011
Identities = 34/148 (22%), Positives = 61/148 (41%), Gaps = 19/148 (12%)
Query: 136 LQVGGGINS-DNSLSYIEEGATHV-IVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSC 193
L VGGGI S +++ + GA V I ++ V D E + + G Q +V+ +
Sbjct: 77 LTVGGGIRSVEDARKLLRAGADKVSINSAAV-----KDPELITEAADRFGSQCIVVAIDA 131
Query: 194 RKK-DGKYAIVTDRWQKFS---DVYLDERVLDFLASYAD----EFLVHGVDVEGKKLGID 245
++ DG+ ++ F+ +++ + E L+ +D +G K G D
Sbjct: 132 KRVPDGEN----GWYEVFTHGGREDTGLDAVEWAKEVEELGAGEILLTSMDRDGTKAGYD 187
Query: 246 DELVALLGKYSPIPVTYAGGVTTMADLE 273
EL + + IPV +GG
Sbjct: 188 LELTRAVREAVNIPVIASGGAGKPEHFV 215
Score = 27.5 bits (62), Expect = 9.7
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 258 IPVTYAGGVTTMADLEKIKVAGIGRVDV 285
IP+T GG+ ++ D K+ AG +V +
Sbjct: 75 IPLTVGGGIRSVEDARKLLRAGADKVSI 102
>gnl|CDD|238244 cd00429, RPE, Ribulose-5-phosphate 3-epimerase (RPE). This enzyme
catalyses the interconversion of D-ribulose 5-phosphate
(Ru5P) into D-xylulose 5-phosphate, as part of the
Calvin cycle (reductive pentose phosphate pathway) in
chloroplasts and in the oxidative pentose phosphate
pathway. In the Calvin cycle Ru5P is phosphorylated by
phosphoribulose kinase to ribulose-1,5-bisphosphate,
which in turn is used by RubisCO
(ribulose-1,5-bisphosphate carboxylase/oxygenase) to
incorporate CO2 as the central step in carbohydrate
synthesis.
Length = 211
Score = 34.8 bits (81), Expect = 0.031
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 136 LQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQMDLERLKDL 178
++V GGIN + E GA ++ S +F + E +K+L
Sbjct: 169 IEVDGGINLETIPLLAEAGADVLVAGSALFGSDDYA-EAIKEL 210
>gnl|CDD|233107 TIGR00734, hisAF_rel, hisA/hisF family protein. This model models
a family of proteins found so far in three archaeal
species: Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, and Archaeoglobus fulgidus.
This protein is homologous to
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase (HisA) and, with lower similarity, to
the cyclase HisF, both of which are enzymes of histidine
biosynthesis. Each species with this protein also
encodes HisA. The function of this protein is unknown
[Unknown function, General].
Length = 221
Score = 32.6 bits (74), Expect = 0.17
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 217 ERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIK 276
E V DFL S+ +V + G G + EL+ + S PV GG++ + DLE +K
Sbjct: 144 EEVRDFLNSFDYGLIVLDIHSVGTMKGPNLELLTKTLELSEHPVMLGGGISGVEDLELLK 203
Query: 277 VAGIGRVDVTVGSAL 291
G+ V V +A+
Sbjct: 204 EMGVS--AVLVATAV 216
>gnl|CDD|172604 PRK14114, PRK14114,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 32.7 bits (74), Expect = 0.18
Identities = 38/128 (29%), Positives = 57/128 (44%), Gaps = 21/128 (16%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIMLG- 116
P ID+ +GKV ++V G K T F +K AE E+G T H + L
Sbjct: 5 PAIDLFRGKVARMV---------KGKKENTIF-YEKDPAELVEKLIEEGFTLIHVVDLSK 54
Query: 117 --ADPLSKAAAIEALHAYPGGLQVGGGINSDNSLSYIEE----GATHVIVTSYVFNNGQM 170
+ + +E L + +Q+GGGI SL Y E+ G IV+S V +
Sbjct: 55 AIENSVENLPVLEKLSEFAEHIQIGGGI---RSLDYAEKLRKLGYRRQIVSSKVLEDPSF 111
Query: 171 DLERLKDL 178
L+ LK++
Sbjct: 112 -LKFLKEI 118
>gnl|CDD|224329 COG1411, COG1411, Uncharacterized protein related to proFAR
isomerase (HisA) [General function prediction only].
Length = 229
Score = 32.4 bits (74), Expect = 0.19
Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 217 ERVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIK 276
E V D +V + G K G D EL+ + + S PV GGV M DLE +
Sbjct: 141 ETVKDLNYRRDPGLIVLDIGAVGTKSGPDYELLTKVLELSEHPVLLGGGVGGMEDLELLL 200
Query: 277 VAGIGRVDVTVGSAL 291
G+ V V +AL
Sbjct: 201 GMGVS--GVLVATAL 213
>gnl|CDD|240303 PTZ00170, PTZ00170, D-ribulose-5-phosphate 3-epimerase;
Provisional.
Length = 228
Score = 32.3 bits (74), Expect = 0.21
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 109 GGHAIMLGADPLSKAAAIEALHAYPG-GLQVGGGINSDNSLSYIEEGATHVIVTSYVF-- 165
GG + M D + K E YP +QV GGIN + + GA ++ S +F
Sbjct: 152 GGQSFM--HDMMPKVR--ELRKRYPHLNIQVDGGINLETIDIAADAGANVIVAGSSIFKA 207
Query: 166 NNGQMDLERLKDLVR 180
+ + +E L++ V+
Sbjct: 208 KDRKQAIELLRESVQ 222
>gnl|CDD|130974 TIGR01919, hisA-trpF,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide
isomerase/N-(5'phosphoribosyl)anthranilate isomerase.
This model represents a bifunctional protein posessing
both hisA
(1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase) and trpF
(N-(5'phosphoribosyl)anthranilate isomerase) activities.
Thus, it is involved in both the histidine and
tryptophan biosynthetic pathways. Enzymes with this
property have been described only in the Actinobacteria
(High-GC gram-positive). The enzyme is closely related
to the monofunctional HisA proteins (TIGR00007) and in
Actinobacteria, the classical monofunctional TrpF is
generally absent.
Length = 243
Score = 31.9 bits (72), Expect = 0.31
Identities = 47/240 (19%), Positives = 83/240 (34%), Gaps = 25/240 (10%)
Query: 58 PCIDIHKGKVKQIVGSTLQDSKDDGTKLVTNFES-DKSAAEFANLYKEDGLTGG--HAIM 114
P +D++ G ++ SK L + + ++ AE+ +L D GG + +M
Sbjct: 7 PAVDVNGGAAVRLQQGA-GGSKTYYGSLESAAKWWEQGGAEWIHLVDLDAAFGGGNNEMM 65
Query: 115 LGADPLSKAAAIEALHAYPGGLQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQMDLER 174
L E + ++ GG D+SL G NG
Sbjct: 66 LE----------EVVKLLVVVEELSGGRRDDSSLRAALTGGRAR-------VNGGTAALE 108
Query: 175 LKDLV-RVVGK-QRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLV 232
V+ +V +DG++ + +R E + L S +V
Sbjct: 109 NPWWAAAVIRYGGDIVAVGLDVLEDGEWHTLGNRGWS-DGGGDLEVLERLLDSGGCSRVV 167
Query: 233 HGVDVEGKKLGIDDE-LVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDVTVGSAL 291
+ G +E L+ ++ + V +GG + + DL IK G V V +G L
Sbjct: 168 VTDSKKDGLSGGPNELLLEVVAARTDAIVAASGGSSLLDDLRAIKYLDEGGVSVAIGGKL 227
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 31.0 bits (70), Expect = 0.54
Identities = 33/178 (18%), Positives = 54/178 (30%), Gaps = 29/178 (16%)
Query: 112 AIMLGADPLSKAAAIEALHAYPGGLQVGGGINSDN------SLSYIEEGATHVIVTSYVF 165
+ A+ K E L V IN + + GA V + V
Sbjct: 36 SDPEEAETDDKEVLKEVAAETDLPLGVQLAINDAAAAVDIAAAAARAAGADGVEIHGAVG 95
Query: 166 NNGQMDLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLAS 225
+ DLE +++L V ++V+ LS + +
Sbjct: 96 YLAREDLELIRELREAVPDVKVVVKLS-----------------PTGELAAAAAEEAGV- 137
Query: 226 YADEFLVHGVDVEG---KKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGI 280
DE + G + I D L+ L + S +PV GG+ D + G
Sbjct: 138 --DEVGLGNGGGGGGGRDAVPIADLLLILAKRGSKVPVIAGGGINDPEDAAEALALGA 193
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 29.4 bits (66), Expect = 0.55
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 71 VGSTLQDSKDDGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIMLGADPLSKAAAIEALH 130
+G QD +D +L+ F+S + EF + GL G A +D +AAI LH
Sbjct: 6 IGKIPQDVYED--RLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLH 63
Query: 131 AYPGGLQVGGGI 142
Y L G +
Sbjct: 64 NYE--LPEGCCL 73
>gnl|CDD|223237 COG0159, TrpA, Tryptophan synthase alpha chain [Amino acid
transport and metabolism].
Length = 265
Score = 31.0 bits (71), Expect = 0.75
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 9/94 (9%)
Query: 216 DERVLDFLASYADEFL----VHGV-DVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMA 270
+ L +A A F+ GV ELV + KY+ +PV G+++
Sbjct: 159 PDERLKKIAEAASGFIYYVSRMGVTGARNPVSADVKELVKRVRKYTDVPVLVGFGISSPE 218
Query: 271 DLEKIKVAGIGRVDVTVGSAL-DIFGGNLAYKDV 303
++ A G V VGSA+ I L + +
Sbjct: 219 QAAQVAEAADG---VIVGSAIVKIIEEGLDEEAL 249
>gnl|CDD|224004 COG1078, COG1078, HD superfamily phosphohydrolases [General
function prediction only].
Length = 421
Score = 31.2 bits (71), Expect = 0.80
Identities = 26/96 (27%), Positives = 39/96 (40%), Gaps = 9/96 (9%)
Query: 168 GQMDLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLD------ERVLD 221
G +DLER+ ++RVV + LV+ + + I R+ + VY E +L
Sbjct: 189 GLIDLERILRVLRVVEGR-LVISEKGIEAIESFLIS--RYLMYQQVYFHPVSRIAEAMLR 245
Query: 222 FLASYADEFLVHGVDVEGKKLGIDDELVALLGKYSP 257
A E D E + D EL+ALL
Sbjct: 246 RALKRAIELYDLDFDAEEFRRLDDFELLALLRDLLD 281
>gnl|CDD|130231 TIGR01163, rpe, ribulose-phosphate 3-epimerase. This family
consists of Ribulose-phosphate 3-epimerase, also known
as pentose-5-phosphate 3-epimerase (PPE). PPE converts
D-ribulose 5-phosphate into D-xylulose 5-phosphate in
Calvin's reductive pentose phosphate cycle. It has been
found in a wide range of bacteria, archebacteria, fungi
and plants [Energy metabolism, Pentose phosphate
pathway].
Length = 210
Score = 30.3 bits (69), Expect = 0.93
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 136 LQVGGGINSDNSLSYIEEGATHVIVTSYVFNN 167
++V GG+N DN+ E GA ++ S +F
Sbjct: 168 IEVDGGVNDDNARELAEAGADILVAGSAIFGA 199
>gnl|CDD|183832 PRK12935, PRK12935, acetoacetyl-CoA reductase; Provisional.
Length = 247
Score = 30.4 bits (68), Expect = 0.95
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 81 DGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIMLGAD 118
+G K+V N+ S K AAE NL E G G + AD
Sbjct: 29 EGAKVVINYNSSKEAAE--NLVNELGKEGHDVYAVQAD 64
>gnl|CDD|234296 TIGR03653, arch_L6P, archaeal ribosomal protein L6P. Members of
this protein family are the archaeal ribosomal protein
L6P. The top-scoring proteins not selected by this model
are eukaryotic cytosolic ribosomal protein L9. Bacterial
ribosomal protein L6 scores lower and is described by a
distinct model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 170
Score = 29.6 bits (67), Expect = 1.3
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 235 VDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDV 285
V VEG K+ I++ LG+ +P GGV E++ V GI + DV
Sbjct: 94 VKVEGNKVVIEN----FLGEKAPRRAKIPGGVKVKVKGEEVIVTGIDKEDV 140
>gnl|CDD|223114 COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate
transport and metabolism].
Length = 220
Score = 29.8 bits (68), Expect = 1.4
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 7/64 (10%)
Query: 126 IEALHAYPGG-----LQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQMD--LERLKDL 178
I L A ++V GGIN + GA + S +F + L+
Sbjct: 157 IRELRAMIDERLDILIEVDGGINLETIKQLAAAGADVFVAGSALFGADDYKATIRELRGE 216
Query: 179 VRVV 182
+
Sbjct: 217 LLKA 220
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 29.9 bits (68), Expect = 1.5
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 218 RVLDFLASYADEFLVHGVDVEGKKLGIDDELVALLGKYSPI------PVTY-AGGVTTMA 270
V+ S DE V DV+G ++DE V + + P P TY G +
Sbjct: 167 YVIMVRISDGDESFVFASDVQGP---LNDEAVEFILEKKPDVVIIGGPPTYLLGRRLSEE 223
Query: 271 DLEK 274
DLEK
Sbjct: 224 DLEK 227
>gnl|CDD|235515 PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated.
Length = 220
Score = 28.6 bits (65), Expect = 3.0
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 136 LQVGGGINSDNSLSYIEEGATHVIVTSYVFNNGQM 170
++V GGIN+DN E GA + S VF
Sbjct: 173 IEVDGGINADNIKECAEAGADVFVAGSAVFGAPDY 207
>gnl|CDD|240077 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase
(KGPDC) and D-arabino-3-hexulose-6-phosphate synthase
(HPS). KGPDC catalyzes the formation of L-xylulose
5-phosphate and carbon dioxide from 3-keto-L-gulonate
6-phosphate as part of the anaerobic pathway for
L-ascorbate utilization in some eubacteria. HPS
catalyzes the formation of
D-arabino-3-hexulose-6-phosphate from D-ribulose
5-phosphate and formaldehyde in microorganisms that can
use formaldehyde as a carbon source. Both catalyze
reactions that involve the Mg2+-assisted formation and
stabilization of 1,2-enediolate reaction intermediates.
Length = 202
Score = 28.7 bits (65), Expect = 3.3
Identities = 31/142 (21%), Positives = 48/142 (33%), Gaps = 29/142 (20%)
Query: 152 EEGATHVIVTSYVFNNGQMDLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFS 211
+ GA V V G L +K V+ KK GK V
Sbjct: 75 KAGADIVTVL------GAAPLSTIKKAVKAA------------KKYGKEVQV-----DLI 111
Query: 212 DVYLDERVLDFLASYADEFLVH-GVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMA 270
V E+ L D ++H G+D + ++ + + K + V AGG+T
Sbjct: 112 GVEDPEKRAKLLKLGVDIVILHRGIDAQAAGGWWPEDDLKKVKKLLGVKVAVAGGIT--- 168
Query: 271 DLEKIKVAGIGRVD-VTVGSAL 291
+ + D V VG A+
Sbjct: 169 -PDTLPEFKKAGADIVIVGRAI 189
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 28.3 bits (64), Expect = 3.5
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 235 VDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADLEKIKVAGIGRVDV 285
V V+G ++ I++ LG+ SP GGV E + V GI + DV
Sbjct: 100 VKVQGNEVVIEN----FLGEKSPRRAKILGGVKVKVKGEDVIVEGIDKEDV 146
>gnl|CDD|224373 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 467
Score = 29.0 bits (65), Expect = 3.8
Identities = 29/122 (23%), Positives = 50/122 (40%), Gaps = 21/122 (17%)
Query: 170 MDLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADE 229
D E +K + VV Q+ +L YA D W++F+ + ++ +V L+++ D
Sbjct: 167 FDPEVMKAALEVVKDQKPLL----------YAATEDNWKEFAKLAVEYKVPLVLSAFNDL 216
Query: 230 FLVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGG---VTTMADLEKIKVAGIGRVDVT 286
+ + V + GI D ++ P TY GG T + I+ A I D
Sbjct: 217 DDLKNLAVTYAQAGIKDIVLD--------PGTYPGGEGLKDTFDNFVMIRRAAIEGFDKD 268
Query: 287 VG 288
Sbjct: 269 FA 270
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 28.3 bits (64), Expect = 4.2
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 117 ADPLSKAAAIEALHAYPGGLQVG--GGINSDNSLSYIEEGATHVIVTSYVFNNGQM---D 171
A+ + A ++AL ++ GG++ DN+ Y+ G V + S++ + D
Sbjct: 135 AEVVGGPAMLKALAGPFPQVRFCPTGGVSLDNAADYLAAGVVAVGLGSWLVPKDLIAAGD 194
Query: 172 LERLKDLVR 180
+R+ +L R
Sbjct: 195 WDRITELAR 203
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 28.5 bits (64), Expect = 4.8
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 14/58 (24%)
Query: 187 LVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEFLVHGVDVEGKKLGI 244
L+L L+ R D + A+ RWQ+ S L LDF V++EGK LG+
Sbjct: 110 LLLALATRLPDYQQAVAAGRWQQSSQFCL----LDFPI----------VELEGKTLGL 153
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 243
Score = 28.4 bits (64), Expect = 4.9
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 81 DGTKLVTNFESDKSAAEFANLYKEDGLTGGHAIMLGADPLSKAAAIEAL 129
DG +V N+ S K+AAE E GG AI + AD +S + + L
Sbjct: 26 DGASVVVNYASSKAAAEEVVAEIEAA--GGKAIAVQAD-VSDPSQVARL 71
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 28.6 bits (64), Expect = 5.2
Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 2/102 (1%)
Query: 171 DLERLKDLVRVVGKQRLVLDLSCRKKDGKYAIVTDRWQKFSDVYLDERVLDFLASYADEF 230
+LE LK + + K +L+ R+K GK + D + E + +
Sbjct: 727 ELEELKKELEKLEKALELLE-ELREKLGKAGLRADILRNLLAQIEAEANEILSKLSLNRY 785
Query: 231 LVHGVDVEGKKLGIDDELVALLGKYSPIPVTYAGGVTTMADL 272
+ + + G +V G+ PI T +GG +A L
Sbjct: 786 DLRRLTIRKDGNGGLVVVVYDGGEVRPI-KTLSGGERFLASL 826
>gnl|CDD|233965 TIGR02660, nifV_homocitr, homocitrate synthase NifV. This family
consists of the NifV clade of homocitrate synthases,
most of which are found in operons for nitrogen
fixation. Members are closely homologous to enzymes that
include 2-isopropylmalate synthase, (R)-citramalate
synthase, and homocitrate synthases associated with
other processes. The homocitrate made by this enzyme
becomes a part of the iron-molybdenum cofactor of
nitrogenase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other, Central intermediary
metabolism, Nitrogen fixation].
Length = 365
Score = 28.4 bits (64), Expect = 6.0
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 118 DPLSKAAAIEAL-HAYPGGLQVGG----GINSDNSLSYIEEGATHVIVT 161
DP S + AL A L++ G+ + N+L+ + GATHV T
Sbjct: 169 DPFSTYELVRALRQAVDLPLEMHAHNDLGMATANTLAAVRAGATHVNTT 217
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein
which is localized in the photoreceptor outer segment
discs. Mutation/s in its genetic loci is implicated in
the recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 28.4 bits (63), Expect = 7.2
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 203 VTDRWQKFSDVYLDERVLDFLASYADEF 230
+TDR+ + ++ YL+ VLD SY DE
Sbjct: 505 ITDRFLRLANQYLECLVLDKFESYDDEV 532
>gnl|CDD|238807 cd01573, modD_like, ModD; Quinolinate phosphoribosyl transferase
(QAPRTase or QPRTase) present in some modABC operons in
bacteria, which are involved in molybdate transport. In
general, QPRTases are part of the de novo synthesis
pathway of NAD in both prokaryotes and eukaryotes. They
catalyse the reaction of quinolinic acid (QA) with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to produce nicotinic acid mononucleotide (NAMN),
pyrophosphate and carbon dioxide.
Length = 272
Score = 27.6 bits (62), Expect = 9.0
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 123 AAAIEALHAYPGGLQV--GGGINSDNSLSYIEEGATHVIVTS 162
A + L + + + GGIN +N+ +Y GA ++VTS
Sbjct: 218 AELVPKLRSLAPPVLLAAAGGINIENAAAYAAAGA-DILVTS 258
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
0.317 0.135 0.387
Gapped
Lambda K H
0.267 0.0836 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,250,807
Number of extensions: 1611180
Number of successful extensions: 1760
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1721
Number of HSP's successfully gapped: 69
Length of query: 316
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 219
Effective length of database: 6,635,264
Effective search space: 1453122816
Effective search space used: 1453122816
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 (21.7 bits)
S2: 59 (26.3 bits)