RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013510
(441 letters)
>gnl|CDD|215402 PLN02754, PLN02754, chorismate synthase.
Length = 413
Score = 809 bits (2092), Expect = 0.0
Identities = 351/407 (86%), Positives = 373/407 (91%)
Query: 29 RQLPSPNVQILIRSRTPKKLQVKAAGSAFGTYFRVTTFGESHGGGVGCIIDGCPPRIPLS 88
R+L S +VQI +RSRT K LQ++AAGS FGTYFRVTTFGESHGGGVGC+IDGCPPRIPL+
Sbjct: 1 RRLSSASVQISLRSRTRKNLQIQAAGSTFGTYFRVTTFGESHGGGVGCVIDGCPPRIPLT 60
Query: 89 EADMQVDLDRRRPGQSRITTPRKETDTCKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSE 148
E DMQ DLDRRRPGQSRITTPRKETDTC+I SGVSEG+T GTPI VFVPNTDQRG DYSE
Sbjct: 61 EEDMQFDLDRRRPGQSRITTPRKETDTCEILSGVSEGMTLGTPIAVFVPNTDQRGQDYSE 120
Query: 149 MSVAYRPSHADATYDMKYGVRSVQGGGRSSARETIGRVAPGAVAKKILKQFAGTEILAYV 208
MSVAYRPSHADATYD KYGVR+VQGGGRSSARETIGRVA GAVAKKILKQFAGTEILAYV
Sbjct: 121 MSVAYRPSHADATYDFKYGVRAVQGGGRSSARETIGRVAAGAVAKKILKQFAGTEILAYV 180
Query: 209 SQAHNVVLPEDVVDHEMLTLDQVESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCI 268
SQ H+VVLPED+VDHE LTL+Q+ESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCI
Sbjct: 181 SQVHDVVLPEDLVDHETLTLEQIESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCI 240
Query: 269 VRNCPRGLGSPVFDKLEAELAKAMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGN 328
VRN PRGLGSPVFDKLEAELAKAMMSLPATKGFE+GSGFAGT LTGSEHNDEFY DE G
Sbjct: 241 VRNVPRGLGSPVFDKLEAELAKAMMSLPATKGFEIGSGFAGTLLTGSEHNDEFYMDEHGR 300
Query: 329 IRTRTNRSGGIQGGISNGEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRHDPCVV 388
IRTRTNRSGGIQGGISNGEII MRIAFKPTSTIG+KQNTVTR+ +ETEL ARGRHDPCVV
Sbjct: 301 IRTRTNRSGGIQGGISNGEIIVMRIAFKPTSTIGKKQNTVTRDGQETELRARGRHDPCVV 360
Query: 389 PRAVPMVEAMVALVLMDQLMAQHAQCHLFPINPDLQGTMKLPELEPA 435
PRAVPMVEAMVALVL+DQLMAQ+AQC LFPINP LQ + + A
Sbjct: 361 PRAVPMVEAMVALVLVDQLMAQYAQCELFPINPVLQEPLGIASPAAA 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 = 576 bits (1487), Expect = 0.0
Identities = 203/346 (58%), Positives = 241/346 (69%), Gaps = 4/346 (1%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYS 120
FRVTTFGESHG +G +IDGCP +PL E D+Q +LDRRRPGQ R TTPR E D +I S
Sbjct: 1 FRVTTFGESHGPALGVVIDGCPAGLPLDEEDIQKELDRRRPGQGRGTTPRIEKDEVEILS 60
Query: 121 GVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGV-RSVQGGGRSSA 179
GV EG TTGTPI + + N DQR DYS + RP HAD T +KYG +GGGRSSA
Sbjct: 61 GVFEGKTTGTPIALLIRNKDQRSWDYSMLKTLPRPGHADYTGFLKYGGFDDRRGGGRSSA 120
Query: 180 RETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNIVRCP 239
RET RVA GAVAKK+LK+F G E++A+V + +D E L L++ E + VRCP
Sbjct: 121 RETAARVAAGAVAKKLLKEF-GIEVVAHVKSIGGIEDEPFDLDEEEL-LEEAEESPVRCP 178
Query: 240 DPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSLPATK 299
DPE EKM ID + GDSVGGVV + P GLGSPVFDKL+A LA+A+MS+PA K
Sbjct: 179 DPEAEEKMKELIDEAKKEGDSVGGVVEVVATGVPAGLGSPVFDKLDARLAQALMSIPAVK 238
Query: 300 GFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAFKPTS 359
G E+GSGF + GSE NDE Y DE G I+T+TN +GGI GGISNGE I R+AFKPT
Sbjct: 239 GVEIGSGFEAARMRGSEVNDEIYYDE-GGIKTKTNNAGGILGGISNGEPIVFRVAFKPTP 297
Query: 360 TIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVEAMVALVLMD 405
+I + Q TV +ETEL +GRHDPC VPRAVP+VEAMVALVL D
Sbjct: 298 SIAKPQKTVDLTGEETELAVKGRHDPCAVPRAVPVVEAMVALVLAD 343
>gnl|CDD|216398 pfam01264, Chorismate_synt, Chorismate synthase.
Length = 346
Score = 575 bits (1485), Expect = 0.0
Identities = 202/349 (57%), Positives = 241/349 (69%), Gaps = 5/349 (1%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYS 120
FRVTTFGESHG +G +IDGCP +PL E D+Q +LDRRRPG R TT R E D +I S
Sbjct: 1 FRVTTFGESHGPALGAVIDGCPAGLPLDEEDIQRELDRRRPGYGRGTTQRIEKDEVEILS 60
Query: 121 GVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGGRSSAR 180
GV EG TTGTPI + + N DQR DYSE+ RP HAD TY +KYG R +GGGRSSAR
Sbjct: 61 GVFEGKTTGTPIALLIRNKDQRSWDYSEIKTRPRPGHADLTYFLKYGFRDYRGGGRSSAR 120
Query: 181 ETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNIVRCPD 240
ET RVA GAVAKK+LK+ G E+ +YVS + E E ++VE + VRCPD
Sbjct: 121 ETAARVAAGAVAKKLLKEL-GIEVRSYVSSIGGIEADEADPAEE--DFEEVEKSPVRCPD 177
Query: 241 PEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSLPATKG 300
PE AE+M ID + GDS+GGVV + R P GLG PVFDKL+A+LAKA+MS+PA KG
Sbjct: 178 PEAAERMEELIDEAKKEGDSLGGVVEVVARGVPAGLGEPVFDKLDADLAKALMSIPAVKG 237
Query: 301 FEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAFKPTST 360
E+G GFA + GSE NDE Y D G IR +TN +GGI GGISNGE I +R+AFKPT +
Sbjct: 238 VEIGDGFAAARMRGSEVNDEIYYDG-GRIRRKTNHAGGILGGISNGEPIVVRVAFKPTPS 296
Query: 361 IGRKQNTVTREKKE-TELIARGRHDPCVVPRAVPMVEAMVALVLMDQLM 408
I + Q TV E E E+ +GRHDPCVVPRAVP+ EAMVALVL D L+
Sbjct: 297 IAKPQRTVDLETGEEAEIEVKGRHDPCVVPRAVPVAEAMVALVLADALL 345
>gnl|CDD|235438 PRK05382, PRK05382, chorismate synthase; Validated.
Length = 359
Score = 568 bits (1467), Expect = 0.0
Identities = 198/355 (55%), Positives = 240/355 (67%), Gaps = 9/355 (2%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYS 120
FRVTTFGESHG +G +IDGCP +PL+E D+Q +LDRRRPG SR TT R E D +I S
Sbjct: 3 FRVTTFGESHGPALGAVIDGCPAGLPLTEEDIQKELDRRRPGYSRGTTMRIEPDEVEILS 62
Query: 121 GVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGGRSSAR 180
GV EG TTGTPI + + NTDQR DYSE+ RP HAD TY +KYG R +GGGRSSAR
Sbjct: 63 GVFEGKTTGTPIALLIRNTDQRSKDYSEIKTRPRPGHADYTYFLKYGFRDYRGGGRSSAR 122
Query: 181 ETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNIVRCPD 240
ET RVA GAVAKK+LK+ G E+ +V Q + D + E ++ ++N VRCPD
Sbjct: 123 ETAARVAAGAVAKKLLKEL-GIEVRGHVVQIGGIEADLDWEEVE----ERADANPVRCPD 177
Query: 241 PEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSLPATKG 300
PE E+M ID + GDS+GGVV + P GLG PVFDKL+A+LA A+MS+ A KG
Sbjct: 178 PEAEEEMEELIDEAKKEGDSLGGVVEVVAEGVPAGLGEPVFDKLDADLAHALMSINAVKG 237
Query: 301 FEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAFKPTST 360
E+G GFA L GSE NDE Y + I TN +GGI GGISNGE I +R+AFKPT +
Sbjct: 238 VEIGDGFAAARLRGSEVNDEIY---YTGIGRLTNHAGGILGGISNGEPIVVRVAFKPTPS 294
Query: 361 IGRKQNTVT-REKKETELIARGRHDPCVVPRAVPMVEAMVALVLMDQLMAQHAQC 414
I + Q TV R + TEL +GRHDPCVVPRAVP+ EAMVALVL D L+ + Q
Sbjct: 295 IRKPQRTVDIRTGEPTELATKGRHDPCVVPRAVPVAEAMVALVLADHLLRKRDQL 349
>gnl|CDD|223160 COG0082, AroC, Chorismate synthase [Amino acid transport and
metabolism].
Length = 369
Score = 529 bits (1364), Expect = 0.0
Identities = 199/367 (54%), Positives = 242/367 (65%), Gaps = 12/367 (3%)
Query: 53 AGSAFGTYFRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKE 112
G+ FG FRVTTFGESHG +G +IDGCP + LSE D+Q +LDRRRPG SR TT RKE
Sbjct: 1 MGNTFGRLFRVTTFGESHGPALGAVIDGCPAGLELSEEDIQKELDRRRPGYSRGTTMRKE 60
Query: 113 TDTCKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQ 172
D +I SGV EG TTGTPI + + NTDQR DYS + RP HAD TY +KYG R +
Sbjct: 61 KDEVEILSGVFEGKTTGTPIALLIENTDQRSKDYSMIKDPPRPGHADYTYGIKYGFRDYR 120
Query: 173 GGGRSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVE 232
GGGRSSARET RVA GAVAKK+L++ G E+L +V + + L ++VE
Sbjct: 121 GGGRSSARETAARVAAGAVAKKLLREL-GIEVLGHVVSIGGIEADDS------LDFEEVE 173
Query: 233 SNI--VRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAK 290
VRCPDPE E+M ID + GDS+GGVV + P GLG PVFDKL+A+LA
Sbjct: 174 QRASPVRCPDPEAEEEMEELIDKAKKEGDSIGGVVEVVAEGVPAGLGEPVFDKLDAKLAH 233
Query: 291 AMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIIN 350
A+MS+PA KG E+G GF + GSE NDE D G I +TN +GGI GGI+NGE I
Sbjct: 234 ALMSIPAVKGVEIGDGFEAARMRGSEANDEITLD--GGIVRKTNNAGGILGGITNGEPIV 291
Query: 351 MRIAFKPTSTIGRKQNTVTRE-KKETELIARGRHDPCVVPRAVPMVEAMVALVLMDQLMA 409
+R+AFKPT +I + Q TV E +E E +GRHDPCVVPRAVP+VEAMVALVL D L+
Sbjct: 292 VRVAFKPTPSIYKPQRTVDLETGEEVEASTKGRHDPCVVPRAVPVVEAMVALVLADHLLR 351
Query: 410 QHAQCHL 416
+ Q
Sbjct: 352 KFGQDPD 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 = 463 bits (1194), Expect = e-163
Identities = 207/353 (58%), Positives = 250/353 (70%), Gaps = 3/353 (0%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYS 120
FRVTTFGESHG VG IIDGCP +PL+E D+Q DLDRRRPG SR T RKE D +I S
Sbjct: 1 FRVTTFGESHGKAVGAIIDGCPAGLPLTEEDIQPDLDRRRPGYSRGTRMRKENDEVEILS 60
Query: 121 GVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGGRSSAR 180
GV EG TTG PI + + N D R DYS++ RP HAD TY +KYG+ +GGGRSSAR
Sbjct: 61 GVFEGKTTGAPIALMIRNKDVRSSDYSDIRTFPRPGHADYTYWLKYGIDDYRGGGRSSAR 120
Query: 181 ETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLTLDQVESNIVRCPD 240
ET RVA GAVAKK+L + +G EI+AYV+Q V +P D E ++V+S+ VRCPD
Sbjct: 121 ETAARVAAGAVAKKLLAETSGIEIVAYVTQIGEVEIPRVYYDPE--EKERVDSSPVRCPD 178
Query: 241 PEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPVFDKLEAELAKAMMSLPATKG 300
PE ++M+A ID + GDS+GGVV C+ RN P GLG P+FDKL+A LA AMMS+PA KG
Sbjct: 179 PEAEKEMVAEIDKAKKDGDSIGGVVECVARNVPVGLGEPLFDKLDARLAHAMMSIPAVKG 238
Query: 301 FEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGGIQGGISNGEIINMRIAFKPTST 360
E+G GF + GSE NDEF ++ G IR +TN SGGI GGI+NGE I +RIAFKPT T
Sbjct: 239 VEIGDGFELASMRGSEANDEFVFED-GGIRRKTNNSGGILGGITNGEPIRVRIAFKPTPT 297
Query: 361 IGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVEAMVALVLMDQLMAQHAQ 413
IG+ Q TV + +E L +GRHDPCVVPRAVP+VEAM ALVL D L+ Q A
Sbjct: 298 IGKPQKTVDLDTEEPALATKGRHDPCVVPRAVPVVEAMTALVLADALLEQRAS 350
>gnl|CDD|171518 PRK12463, PRK12463, chorismate synthase; Reviewed.
Length = 390
Score = 185 bits (470), Expect = 3e-54
Identities = 135/375 (36%), Positives = 196/375 (52%), Gaps = 27/375 (7%)
Query: 61 FRVTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYS 120
R T GESHG + I++G P + L+ + +L RR+ G R + ETDT +I S
Sbjct: 1 MRYITAGESHGPQLTVILEGVPAGLTLAAEHINKELLRRQKGHGRGRRMQIETDTVEIVS 60
Query: 121 GVSEGVTTGTPIHVFVPNTD---------------QRGHDYSEMSVAYRPSHADATYDMK 165
GV G+T G+PI + V N D + + RP HAD +K
Sbjct: 61 GVRHGMTLGSPITLIVKNDDFKHWTKVMGAEPISEKESKEMKRTITKPRPGHADLNGAIK 120
Query: 166 YGVRSVQGG-GRSSARETIGRVAPGAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHE 224
YG R ++ RSSARET RVA GAVAK+ILK+ G EI +V + V
Sbjct: 121 YGHRDIRNVLERSSARETTVRVAAGAVAKQILKEL-GVEIAGHVLEIGGV----KAKHIS 175
Query: 225 MLTLDQV----ESNIVRCPDPEYAEKMIAAIDAVRVRGDSVGGVVTCIVRNCPRGLGSPV 280
L+++++ E++ VRC D ++M+ AID + GDS+GG+V I P G+GS V
Sbjct: 176 NLSIEEIQTITENSPVRCLDKTVEQEMMDAIDNAKSSGDSIGGIVEVIAEGMPIGVGSYV 235
Query: 281 -FD-KLEAELAKAMMSLPATKGFEVGSGFAGTFLTGSEHNDEFYTDEFGNIRTRTNRSGG 338
+D KL+A+LA A+MS+ A KG E+G GF GS+ +DE DE +TN +GG
Sbjct: 236 HYDRKLDAKLAGAIMSINAFKGAEIGVGFEAARQPGSKVHDEILWDEEQGYTRKTNNAGG 295
Query: 339 IQGGISNGEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVEAM 398
++GG++ G I +R KP T+ + +V + KE + R D C VP A + E++
Sbjct: 296 LEGGMTTGMPIVVRGVMKPIPTLYKPLASVDIDTKEAFQASIERSDSCAVPAAGVVAESV 355
Query: 399 VALVLMDQLMAQHAQ 413
VA L L+ Q +
Sbjct: 356 VAWELAHALVEQFGK 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 = 0.012
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|217553 pfam03430, TATR, Trans-activating transcriptional regulator. This
family of trans-activating transcriptional regulator
(TATR), also known as intermediate early protein 1, are
common to the Nucleopolyhedroviruses.
Length = 571
Score = 34.9 bits (80), Expect = 0.087
Identities = 34/155 (21%), Positives = 45/155 (29%), Gaps = 14/155 (9%)
Query: 3 SSVASKTFLAAPRTDGSLGSLLPDLRRQLPSPNVQILIRSRTPKKLQVKAAGSAFGTYFR 62
A KT A T +L L D + LP Q R A S Y +
Sbjct: 54 VENAYKTVENASLTFFALYIPLTDSNKPLPRAVPQDYERES---------AVSPIVEYPQ 104
Query: 63 VTTFGESHGGGVGCIIDGCPPRIPLSEADMQVDLDRRRPGQSRITTPRKETDTCKIYSGV 122
+ GES + + SE D D G+ + P+K K
Sbjct: 105 ALSPGESLPESLSETKQVTVSKRKGSELDSDSDSSDSSKGKKLVNKPKKRQKYKKATIQS 164
Query: 123 SEGVTT----GTPIHVFVPNTDQRGHDYSEMSVAY 153
+T T I P TDQ + Y
Sbjct: 165 PTSLTEEENYNTEICTVAP-TDQIAKYFLMDFSPY 198
>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 = 0.57
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 = 0.91
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 = 1.3
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 189 GAVAKKILKQFAGTEILAYVSQAHNVVLPEDVVDHEMLT---------LDQVESNIVR 237
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 = 29.7 bits (67), Expect = 3.0
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 117 KIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEMSVAYRPSHADATYDMKYGVRSVQGGGR 176
+ ++G G + G VF R H++ S YR A Y G + GGR
Sbjct: 405 RWFNGGPNGASGGARPSVF---GWDREHNFRGTSWYYRAGFARNLYRRWLGYKVDGDGGR 461
Query: 177 SSARETIGRV 186
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 = 28.4 bits (64), Expect = 6.6
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 346 GEIINMRIAFKPTSTIGRKQNTVTREKKETELIARGRHDPCVVPRAVPMVE--AMVALVL 403
G I+ IA K+ T EK+E+E I + VVP A+P++ + +
Sbjct: 76 GGILLFLIAIDMLFGKQSKEKTSKSEKEESEDID----EIAVVPLAIPLIAGPGAITTTM 131
Query: 404 MDQLMAQH 411
+ LMA+H
Sbjct: 132 V--LMAEH 137
>gnl|CDD|227832 COG5545, COG5545, Predicted P-loop ATPase and inactivated
derivatives [General function prediction only].
Length = 517
Score = 28.8 bits (64), Expect = 6.8
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 90 ADMQVDLDRRRPGQSRITTPRKETDTCKIYSGVSEGVTTGTPIHVFVPNTDQRGHDYSEM 149
+ Q ++D R+ G R P++ ++ +G+ TTG F D H S
Sbjct: 379 LEGQKEVDFRKAGDGREIAPQRL----RVTAGLRVLWTTGDEKLEFRIGMDPARHVTSAQ 434
Query: 150 S 150
Sbjct: 435 E 435
>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 = 28.3 bits (64), Expect = 9.5
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 12/47 (25%)
Query: 134 VFVPNTD-QRGHDYSEMSVAYRPSHADATYDMK--------YGVRSV 171
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: 22,605,273
Number of extensions: 2218729
Number of successful extensions: 1848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1810
Number of HSP's successfully gapped: 23
Length of query: 441
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 341
Effective length of database: 6,502,202
Effective search space: 2217250882
Effective search space used: 2217250882
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)