RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013280
(446 letters)
>gnl|CDD|215402 PLN02754, PLN02754, chorismate synthase.
Length = 413
Score = 803 bits (2075), Expect = 0.0
Identities = 351/412 (85%), Positives = 373/412 (90%), Gaps = 5/412 (1%)
Query: 29 RQLPSPNVQILIRSRTPKKLQVKAAGSAFGTYFRVTTFGESHGGGVGCIIDGCPPRIPLS 88
R+L S +VQI +RSRT K LQ++AAGS FGTYFRVTTFGESHGGGVGC+IDGCPPRIPL+
Sbjct: 1 RRLSSASVQISLRSRTRKNLQIQAAGSTFGTYFRVTTFGESHGGGVGCVIDGCPPRIPLT 60
Query: 89 EADMQVDLDRRIVVSRRPGQSRITTPRKETDTCKIYSGVSEGVTTGTPIHVFVPNTDQRG 148
E DMQ DLDRR RPGQSRITTPRKETDTC+I SGVSEG+T GTPI VFVPNTDQRG
Sbjct: 61 EEDMQFDLDRR-----RPGQSRITTPRKETDTCEILSGVSEGMTLGTPIAVFVPNTDQRG 115
Query: 149 HDYSEMSVAYRPSHADATYDMKYGVRSVQGGGRSSARETIGRVAPGAVAKKILKQFAGTE 208
DYSEMSVAYRPSHADATYD KYGVR+VQGGGRSSARETIGRVA GAVAKKILKQFAGTE
Sbjct: 116 QDYSEMSVAYRPSHADATYDFKYGVRAVQGGGRSSARETIGRVAAGAVAKKILKQFAGTE 175
Query: 209 ILAYVSQAHNVVLPEDVVDHEMLTLDQVESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGG 268
ILAYVSQ H+VVLPED+VDHE LTL+Q+ESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGG
Sbjct: 176 ILAYVSQVHDVVLPEDLVDHETLTLEQIESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGG 235
Query: 269 VVTCIVRNCPRGLGSPVFDKLEAELAKAMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYT 328
VVTCIVRN PRGLGSPVFDKLEAELAKAMMSLPATKGFE+GSGFAGT LTGSEHNDEFY
Sbjct: 236 VVTCIVRNVPRGLGSPVFDKLEAELAKAMMSLPATKGFEIGSGFAGTLLTGSEHNDEFYM 295
Query: 329 DEFGNIRTRTNRSGGIQGGISNGEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRH 388
DE G IRTRTNRSGGIQGGISNGEII MRIAFKPTSTIG+KQNTVTR+ +ETEL ARGRH
Sbjct: 296 DEHGRIRTRTNRSGGIQGGISNGEIIVMRIAFKPTSTIGKKQNTVTRDGQETELRARGRH 355
Query: 389 DPCVVPRAVPMVEAMVALVLMDQLMAQHAQCHLFPINPDLQGTMKLPELEPA 440
DPCVVPRAVPMVEAMVALVL+DQLMAQ+AQC LFPINP LQ + + A
Sbjct: 356 DPCVVPRAVPMVEAMVALVLVDQLMAQYAQCELFPINPVLQEPLGIASPAAA 407
>gnl|CDD|143612 cd07304, Chorismate_synthase, Chorismase synthase, the enzyme
catalyzing the final step of the shikimate pathway.
Chorismate synthase (CS;
5-enolpyruvylshikimate-3-phosphate phospholyase;
1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C.
4.2.3.5) catalyzes the seventh and final step in the
shikimate pathway: the conversion of 5-
enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a
precursor for the biosynthesis of aromatic compounds.
This process has an absolute requirement for reduced FMN
as a co-factor which is thought to facilitate cleavage
of C-O bonds by transiently donating an electron to the
substrate, having no overall change its redox state.
Depending on the capacity of these enzymes to regenerate
the reduced form of FMN, chorismate synthases are
divided into two classes: Enzymes, mostly from plants
and eubacteria, that sequester CS from the cellular
environment, are monofunctiona,l while those that can
generate reduced FMN at the expense of NADPH, such as
found in fungi and the ciliated protozoan Euglena
gracilis, are bifunctional, having an additional
NADPH:FMN oxidoreductase activity. Recently,
bifunctionality of the Mycobacterium tuberculosis enzyme
(MtCS) was determined by measurements of both chorismate
synthase and NADH:FMN oxidoreductase activities. Since
shikimate pathway enzymes are present in bacteria, fungi
and apicomplexan parasites (such as Toxoplasma gondii,
Plasmodium falciparum, and Cryptosporidium parvum) but
absent in mammals, they are potentially attractive
targets for the development of new therapy against
infectious diseases such as tuberculosis (TB).
Length = 344
Score = 569 bits (1469), Expect = 0.0
Identities = 203/351 (57%), Positives = 241/351 (68%), Gaps = 9/351 (2%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRITTPRKETDT 120
FRVTTFGESHG +G +IDGCP +PL E D+Q +LDRR RPGQ R TTPR E D
Sbjct: 1 FRVTTFGESHGPALGVVIDGCPAGLPLDEEDIQKELDRR-----RPGQGRGTTPRIEKDE 55
Query: 121 CKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGV-RSVQGG 179
+I SGV EG TTGTPI + + N DQR DYS + RP HAD T +KYG +GG
Sbjct: 56 VEILSGVFEGKTTGTPIALLIRNKDQRSWDYSMLKTLPRPGHADYTGFLKYGGFDDRRGG 115
Query: 180 GRSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESN 239
GRSSARET RVA GAVAKK+LK+F G E++A+V + +D E L L++ E +
Sbjct: 116 GRSSARETAARVAAGAVAKKLLKEF-GIEVVAHVKSIGGIEDEPFDLDEEEL-LEEAEES 173
Query: 240 IVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMS 299
VRCPDPE EKM ID + GDSVGGVV + P GLGSPVFDKL+A LA+A+MS
Sbjct: 174 PVRCPDPEAEEKMKELIDEAKKEGDSVGGVVEVVATGVPAGLGSPVFDKLDARLAQALMS 233
Query: 300 LPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIA 359
+PA KG E+GSGF + GSE NDE Y DE G I+T+TN +GGI GGISNGE I R+A
Sbjct: 234 IPAVKGVEIGSGFEAARMRGSEVNDEIYYDE-GGIKTKTNNAGGILGGISNGEPIVFRVA 292
Query: 360 FKPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVEAMVALVLMD 410
FKPT +I + Q TV +ETEL +GRHDPC VPRAVP+VEAMVALVL D
Sbjct: 293 FKPTPSIAKPQKTVDLTGEETELAVKGRHDPCAVPRAVPVVEAMVALVLAD 343
>gnl|CDD|216398 pfam01264, Chorismate_synt, Chorismate synthase.
Length = 346
Score = 568 bits (1467), Expect = 0.0
Identities = 202/354 (57%), Positives = 241/354 (68%), Gaps = 10/354 (2%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRITTPRKETDT 120
FRVTTFGESHG +G +IDGCP +PL E D+Q +LDRR RPG R TT R E D
Sbjct: 1 FRVTTFGESHGPALGAVIDGCPAGLPLDEEDIQRELDRR-----RPGYGRGTTQRIEKDE 55
Query: 121 CKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGG 180
+I SGV EG TTGTPI + + N DQR DYSE+ RP HAD TY +KYG R +GGG
Sbjct: 56 VEILSGVFEGKTTGTPIALLIRNKDQRSWDYSEIKTRPRPGHADLTYFLKYGFRDYRGGG 115
Query: 181 RSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNI 240
RSSARET RVA GAVAKK+LK+ G E+ +YVS + E E ++VE +
Sbjct: 116 RSSARETAARVAAGAVAKKLLKEL-GIEVRSYVSSIGGIEADEADPAEE--DFEEVEKSP 172
Query: 241 VRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSL 300
VRCPDPE AE+M ID + GDS+GGVV + R P GLG PVFDKL+A+LAKA+MS+
Sbjct: 173 VRCPDPEAAERMEELIDEAKKEGDSLGGVVEVVARGVPAGLGEPVFDKLDADLAKALMSI 232
Query: 301 PATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAF 360
PA KG E+G GFA + GSE NDE Y D G IR +TN +GGI GGISNGE I +R+AF
Sbjct: 233 PAVKGVEIGDGFAAARMRGSEVNDEIYYDG-GRIRRKTNHAGGILGGISNGEPIVVRVAF 291
Query: 361 KPTSTIGRKQNTVTREKKE-TELIARGRHDPCVVPRAVPMVEAMVALVLMDQLM 413
KPT +I + Q TV E E E+ +GRHDPCVVPRAVP+ EAMVALVL D L+
Sbjct: 292 KPTPSIAKPQRTVDLETGEEAEIEVKGRHDPCVVPRAVPVAEAMVALVLADALL 345
>gnl|CDD|235438 PRK05382, PRK05382, chorismate synthase; Validated.
Length = 359
Score = 561 bits (1449), Expect = 0.0
Identities = 198/360 (55%), Positives = 240/360 (66%), Gaps = 14/360 (3%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRITTPRKETDT 120
FRVTTFGESHG +G +IDGCP +PL+E D+Q +LDRR RPG SR TT R E D
Sbjct: 3 FRVTTFGESHGPALGAVIDGCPAGLPLTEEDIQKELDRR-----RPGYSRGTTMRIEPDE 57
Query: 121 CKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGG 180
+I SGV EG TTGTPI + + NTDQR DYSE+ RP HAD TY +KYG R +GGG
Sbjct: 58 VEILSGVFEGKTTGTPIALLIRNTDQRSKDYSEIKTRPRPGHADYTYFLKYGFRDYRGGG 117
Query: 181 RSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNI 240
RSSARET RVA GAVAKK+LK+ G E+ +V Q + D + E ++ ++N
Sbjct: 118 RSSARETAARVAAGAVAKKLLKEL-GIEVRGHVVQIGGIEADLDWEEVE----ERADANP 172
Query: 241 VRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSL 300
VRCPDPE E+M ID + GDS+GGVV + P GLG PVFDKL+A+LA A+MS+
Sbjct: 173 VRCPDPEAEEEMEELIDEAKKEGDSLGGVVEVVAEGVPAGLGEPVFDKLDADLAHALMSI 232
Query: 301 PATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAF 360
A KG E+G GFA L GSE NDE Y + I TN +GGI GGISNGE I +R+AF
Sbjct: 233 NAVKGVEIGDGFAAARLRGSEVNDEIY---YTGIGRLTNHAGGILGGISNGEPIVVRVAF 289
Query: 361 KPTSTIGRKQNTVT-REKKETELIARGRHDPCVVPRAVPMVEAMVALVLMDQLMAQHAQC 419
KPT +I + Q TV R + TEL +GRHDPCVVPRAVP+ EAMVALVL D L+ + Q
Sbjct: 290 KPTPSIRKPQRTVDIRTGEPTELATKGRHDPCVVPRAVPVAEAMVALVLADHLLRKRDQL 349
>gnl|CDD|223160 COG0082, AroC, Chorismate synthase [Amino acid transport and
metabolism].
Length = 369
Score = 522 bits (1346), Expect = 0.0
Identities = 199/372 (53%), Positives = 242/372 (65%), Gaps = 17/372 (4%)
Query: 53 AGSAFGTYFRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRIT 112
G+ FG FRVTTFGESHG +G +IDGCP + LSE D+Q +LDRR RPG SR T
Sbjct: 1 MGNTFGRLFRVTTFGESHGPALGAVIDGCPAGLELSEEDIQKELDRR-----RPGYSRGT 55
Query: 113 TPRKETDTCKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYG 172
T RKE D +I SGV EG TTGTPI + + NTDQR DYS + RP HAD TY +KYG
Sbjct: 56 TMRKEKDEVEILSGVFEGKTTGTPIALLIENTDQRSKDYSMIKDPPRPGHADYTYGIKYG 115
Query: 173 VRSVQGGGRSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLT 232
R +GGGRSSARET RVA GAVAKK+L++ G E+L +V + + L
Sbjct: 116 FRDYRGGGRSSARETAARVAAGAVAKKLLREL-GIEVLGHVVSIGGIEADDS------LD 168
Query: 233 LDQVESNI--VRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLE 290
++VE VRCPDPE E+M ID + GDS+GGVV + P GLG PVFDKL+
Sbjct: 169 FEEVEQRASPVRCPDPEAEEEMEELIDKAKKEGDSIGGVVEVVAEGVPAGLGEPVFDKLD 228
Query: 291 AELAKAMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISN 350
A+LA A+MS+PA KG E+G GF + GSE NDE D G I +TN +GGI GGI+N
Sbjct: 229 AKLAHALMSIPAVKGVEIGDGFEAARMRGSEANDEITLD--GGIVRKTNNAGGILGGITN 286
Query: 351 GEIINMRIAFKPTSTIGRKQNTVTRE-KKETELIARGRHDPCVVPRAVPMVEAMVALVLM 409
GE I +R+AFKPT +I + Q TV E +E E +GRHDPCVVPRAVP+VEAMVALVL
Sbjct: 287 GEPIVVRVAFKPTPSIYKPQRTVDLETGEEVEASTKGRHDPCVVPRAVPVVEAMVALVLA 346
Query: 410 DQLMAQHAQCHL 421
D L+ + Q
Sbjct: 347 DHLLRKFGQDPD 358
>gnl|CDD|232792 TIGR00033, aroC, chorismate synthase. Homotetramer (noted in
E.coli) suggests reason for good conservation [Amino
acid biosynthesis, Aromatic amino acid family].
Length = 351
Score = 456 bits (1176), Expect = e-160
Identities = 207/358 (57%), Positives = 250/358 (69%), Gaps = 8/358 (2%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRITTPRKETDT 120
FRVTTFGESHG VG IIDGCP +PL+E D+Q DLDRR RPG SR T RKE D
Sbjct: 1 FRVTTFGESHGKAVGAIIDGCPAGLPLTEEDIQPDLDRR-----RPGYSRGTRMRKENDE 55
Query: 121 CKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGG 180
+I SGV EG TTG PI + + N D R DYS++ RP HAD TY +KYG+ +GGG
Sbjct: 56 VEILSGVFEGKTTGAPIALMIRNKDVRSSDYSDIRTFPRPGHADYTYWLKYGIDDYRGGG 115
Query: 181 RSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNI 240
RSSARET RVA GAVAKK+L + +G EI+AYV+Q V +P D E ++V+S+
Sbjct: 116 RSSARETAARVAAGAVAKKLLAETSGIEIVAYVTQIGEVEIPRVYYDPE--EKERVDSSP 173
Query: 241 VRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSL 300
VRCPDPE ++M+A ID + GDS+GGVV C+ RN P GLG P+FDKL+A LA AMMS+
Sbjct: 174 VRCPDPEAEKEMVAEIDKAKKDGDSIGGVVECVARNVPVGLGEPLFDKLDARLAHAMMSI 233
Query: 301 PATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAF 360
PA KG E+G GF + GSE NDEF ++ G IR +TN SGGI GGI+NGE I +RIAF
Sbjct: 234 PAVKGVEIGDGFELASMRGSEANDEFVFED-GGIRRKTNNSGGILGGITNGEPIRVRIAF 292
Query: 361 KPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVEAMVALVLMDQLMAQHAQ 418
KPT TIG+ Q TV + +E L +GRHDPCVVPRAVP+VEAM ALVL D L+ Q A
Sbjct: 293 KPTPTIGKPQKTVDLDTEEPALATKGRHDPCVVPRAVPVVEAMTALVLADALLEQRAS 350
>gnl|CDD|171518 PRK12463, PRK12463, chorismate synthase; Reviewed.
Length = 390
Score = 179 bits (454), Expect = 6e-52
Identities = 135/380 (35%), Positives = 196/380 (51%), Gaps = 32/380 (8%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRIVVSRRPGQSRITTPRKETDT 120
R T GESHG + I++G P + L+ + +L RR + G R + ETDT
Sbjct: 1 MRYITAGESHGPQLTVILEGVPAGLTLAAEHINKELLRR-----QKGHGRGRRMQIETDT 55
Query: 121 CKIYSGVSEGVTTGTPIHVFVPNTD---------------QRGHDYSEMSVAYRPSHADA 165
+I SGV G+T G+PI + V N D + + RP HAD
Sbjct: 56 VEIVSGVRHGMTLGSPITLIVKNDDFKHWTKVMGAEPISEKESKEMKRTITKPRPGHADL 115
Query: 166 TYDMKYGVRSVQGG-GRSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPED 224
+KYG R ++ RSSARET RVA GAVAK+ILK+ G EI +V + V
Sbjct: 116 NGAIKYGHRDIRNVLERSSARETTVRVAAGAVAKQILKEL-GVEIAGHVLEIGGV----K 170
Query: 225 VVDHEMLTLDQV----ESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRG 280
L+++++ E++ VRC D ++M+ AID + GDS+GG+V I P G
Sbjct: 171 AKHISNLSIEEIQTITENSPVRCLDKTVEQEMMDAIDNAKSSGDSIGGIVEVIAEGMPIG 230
Query: 281 LGSPV-FD-KLEAELAKAMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRT 338
+GS V +D KL+A+LA A+MS+ A KG E+G GF GS+ +DE DE +T
Sbjct: 231 VGSYVHYDRKLDAKLAGAIMSINAFKGAEIGVGFEAARQPGSKVHDEILWDEEQGYTRKT 290
Query: 339 NRSGGIQGGISNGEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVP 398
N +GG++GG++ G I +R KP T+ + +V + KE + R D C VP A
Sbjct: 291 NNAGGLEGGMTTGMPIVVRGVMKPIPTLYKPLASVDIDTKEAFQASIERSDSCAVPAAGV 350
Query: 399 MVEAMVALVLMDQLMAQHAQ 418
+ E++VA L L+ Q +
Sbjct: 351 VAESVVAWELAHALVEQFGK 370
>gnl|CDD|128624 smart00329, BPI2, BPI/LBP/CETP C-terminal domain. Bactericidal
permeability-increasing protein (BPI) /
Lipopolysaccharide-binding protein (LBP) / Cholesteryl
ester transfer protein (CETP) C-terminal domain.
Length = 202
Score = 36.5 bits (85), Expect = 0.013
Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 10/84 (11%)
Query: 14 PRTDGSLGSLLPDLRRQLPSPNVQILIRSRTPKKLQVKAAGSAFGTYFRVTTFGESHGGG 73
T G+L+P++ Q P +Q+ I +P ++ ++ G+ + V F
Sbjct: 43 LLTTCCFGTLVPEVAEQYPDSTLQLEISVLSPPRVTLQPGGATVYIHASVKVF------- 95
Query: 74 VGCIIDGCPPRIPLSEADMQVDLD 97
I R L + ++
Sbjct: 96 ---AILPDSSRASLFLMSVDTNVS 116
>gnl|CDD|213280 cd05912, OSB_CoA_lg, O-succinylbenzoate-CoA ligase (also known as
O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or
MenE). O-succinylbenzoic acid-CoA synthase catalyzes
the coenzyme A (CoA)- and ATP-dependent conversion of
o-succinylbenzoic acid to o-succinylbenzoyl-CoA. The
reaction is the fourth step of the biosynthesis pathway
of menaquinone (vitamin K2). In certain bacteria,
menaquinone is used during fumarate reduction in
anaerobic respiration. In cyanobacteria, the product of
the menaquinone pathway is phylloquinone
(2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used
exclusively as an electron transfer cofactor in
Photosystem 1. In green sulfur bacteria and
heliobacteria, menaquinones are used as loosely bound
secondary electron acceptors in the photosynthetic
reaction center.
Length = 407
Score = 32.2 bits (74), Expect = 0.58
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 10/62 (16%)
Query: 1 MASSVASKTFLAAPRTDGSLGSLLPDLRRQLPSPNVQILIRSRTPKKLQVKAAGSAFGTY 60
AS VA+ GS+G L P ++ I + ++ V+ G Y
Sbjct: 225 TASQVATLKPDDFLAKLGSVGKPL---------PGRELRIVNPQDGEILVRGPSLFLG-Y 274
Query: 61 FR 62
Sbjct: 275 LP 276
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor (ARF-GEF);
Provisional.
Length = 1780
Score = 31.7 bits (72), Expect = 0.93
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 9 TFLAAPRTDGSLGSLLPDLRRQLPSPNVQILIRSRTPKKLQVKAAGSAFGTY 60
TF AAP+ + + + + +++ + P KLQ AA G+Y
Sbjct: 993 TFFAAPQNESD--------KSKQAKSPILPVLKRKGPGKLQYAAAAVRRGSY 1036
>gnl|CDD|221709 pfam12684, DUF3799, PDDEXK-like domain of unknown function
(DUF3799). This family of proteins is functionally
uncharacterized. This family of proteins is found in
bacteria and viruses. Proteins in this family are
typically between 265 and 420 amino acids in length. It
appears that these proteins are distantly related to the
PDDEXK superfamily and so these domains are likely to be
nucleases. This family has a C-terminal cysteine cluster
similar to that found in pfam01930.
Length = 237
Score = 30.7 bits (70), Expect = 1.2
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 194 GAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLT---------LDQVESNIVR 242
AV +++L+Q G E Y+ V E D ++T LD+VE NI R
Sbjct: 161 MAVYQELLRQKTGEEFPPYII----AVTKETPPDKAIITIPDDLLDEALDEVEENIER 214
>gnl|CDD|221290 pfam11885, DUF3405, Protein of unknown function (DUF3405). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 636 to 810
amino acids in length.
Length = 483
Score = 30.1 bits (68), Expect = 3.0
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 122 KIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGGR 181
+ ++G G + G VF R H++ S YR A Y G + GGR
Sbjct: 405 RWFNGGPNGASGGARPSVF---GWDREHNFRGTSWYYRAGFARNLYRRWLGYKVDGDGGR 461
Query: 182 SSARETIGRV 191
E GR+
Sbjct: 462 EWELEGEGRM 471
>gnl|CDD|216782 pfam01914, MarC, MarC family integral membrane protein. Integral
membrane protein family that includes the antibiotic
resistance protein MarC. These proteins may be
transporters.
Length = 203
Score = 28.0 bits (63), Expect = 7.3
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 351 GEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVE--AMVALVL 408
G I+ IA K+ T EK+E+E I + VVP A+P++ + +
Sbjct: 76 GGILLFLIAIDMLFGKQSKEKTSKSEKEESEDID----EIAVVPLAIPLIAGPGAITTTM 131
Query: 409 MDQLMAQH 416
+ LMA+H
Sbjct: 132 V--LMAEH 137
>gnl|CDD|200456 cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found
in bacterial and eukaryotic Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes AmyA proteins from bacteria, fungi, mammals,
insects, mollusks, and nematodes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 329
Score = 27.9 bits (63), Expect = 9.8
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 12/47 (25%)
Query: 139 VFVPNTD-QRGHDYSEMSVAYRPSHADATYDMK--------YGVRSV 176
VFV N D QRGH + Y+ Y + YG V
Sbjct: 231 VFVDNHDNQRGHGGGGDMLTYKDGRR---YKLANAFMLAWPYGTPRV 274
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
0.318 0.135 0.393
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,870,664
Number of extensions: 2249826
Number of successful extensions: 1889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1843
Number of HSP's successfully gapped: 21
Length of query: 446
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 346
Effective length of database: 6,502,202
Effective search space: 2249761892
Effective search space used: 2249761892
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: 61 (27.3 bits)