RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1128
(337 letters)
>gnl|CDD|223579 COG0505, CarA, Carbamoylphosphate synthase small subunit [Amino
acid transport and metabolism / Nucleotide transport and
metabolism].
Length = 368
Score = 225 bits (576), Expect = 2e-71
Identities = 78/190 (41%), Positives = 109/190 (57%), Gaps = 15/190 (7%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF T M GY E +TDPSY QI+ TYPLIGNYGV +D FES RI +GL+
Sbjct: 30 VFNTSMTGYQEILTDPSYKGQIVTFTYPLIGNYGVNDED---------FESDRIHAAGLV 80
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIVHGSVAPLA 123
V ++ + PS+W + +L E+L+ IP +A +DTR LT+ IRE G + G I G A
Sbjct: 81 VRELSERPSNWRATESLDEYLKEEGIPGIAGIDTRALTRKIREKGAMKGVIATGPELDPA 140
Query: 124 VTVEDLV-FVDPNRGNLVDQVSTKEVVTYNPTGSV-----HLCVVDCGLKYNQLRCLIQR 177
+E F +LV +VSTKE T+ H+ V+D G+K N LR L++R
Sbjct: 141 KLLERARAFPGILGTDLVKEVSTKEPYTWPGLNGGGEPGKHVVVIDFGVKRNILRELVKR 200
Query: 178 GAKLSVIPWN 187
G +++V+P +
Sbjct: 201 GCRVTVVPAD 210
Score = 81.9 bits (203), Expect = 2e-17
Identities = 27/59 (45%), Positives = 35/59 (59%)
Query: 192 VPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIFINAVRDSKT 250
+ + + N NDGT EGI H+ LP FSVQ+HPE + GP D LFD FI + +K
Sbjct: 309 LVETLKVTHVNLNDGTVEGIRHKDLPAFSVQYHPEASPGPHDTRYLFDEFIELMEAAKK 367
>gnl|CDD|237139 PRK12564, PRK12564, carbamoyl phosphate synthase small subunit;
Reviewed.
Length = 360
Score = 223 bits (571), Expect = 1e-70
Identities = 73/188 (38%), Positives = 102/188 (54%), Gaps = 14/188 (7%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF T M GY E +TDPSY QI+ TYPLIGNYGV +D FES R GLI
Sbjct: 31 VFNTSMTGYQEILTDPSYAGQIVTFTYPLIGNYGVNRED---------FESDRPHAKGLI 81
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIVHGSVAPLA 123
V ++ D PS+W S +L E+L+ + IP ++ +DTR LT+ +RE G + G I
Sbjct: 82 VRELSDIPSNWRSEMSLDEYLKENGIPGISGIDTRALTRKLREKGAMKGVIATEDFDAEE 141
Query: 124 VTVEDLV-FVDPNRGNLVDQVSTKEVVTY---NPTGSVHLCVVDCGLKYNQLRCLIQRGA 179
+ +E F +LV +VSTKE + + +D G+K N LR L +RG
Sbjct: 142 L-LEKARAFPGLLGLDLVKEVSTKEPYPWPGPGGELKYKVVAIDFGVKRNILRELAERGC 200
Query: 180 KLSVIPWN 187
+++V+P
Sbjct: 201 RVTVVPAT 208
Score = 75.9 bits (188), Expect = 2e-15
Identities = 32/91 (35%), Positives = 41/91 (45%), Gaps = 29/91 (31%)
Query: 177 RGAKLSVIPWNHPIK----------------------VPQGWQPLFTNANDGTNEGIVHE 214
RGA NHP+K +P + N NDGT EG+ H+
Sbjct: 277 RGA-------NHPVKDLETGKVEITSQNHGFAVDEDSLPANLEVTHVNLNDGTVEGLRHK 329
Query: 215 SLPFFSVQFHPEHTAGPADLELLFDIFINAV 245
LP FSVQ+HPE + GP D LFD F+ +
Sbjct: 330 DLPAFSVQYHPEASPGPHDSAYLFDEFVELM 360
>gnl|CDD|233378 TIGR01368, CPSaseIIsmall, carbamoyl-phosphate synthase, small
subunit. This model represents the whole of the small
chain of the glutamine-dependent form (EC 6.3.5.5) of
carbamoyl phosphate synthase, CPSase II. The C-terminal
domain has glutamine amidotransferase activity. Note
that the sequence from the mammalian urea cycle form has
lost the active site Cys, resulting in an
ammonia-dependent form, CPSase I (EC 6.3.4.16). CPSases
of pyrimidine biosynthesis, arginine biosynthesis, and
the urea cycle may be encoded by one or by several
genes, depending on the species [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 358
Score = 219 bits (559), Expect = 6e-69
Identities = 76/191 (39%), Positives = 108/191 (56%), Gaps = 12/191 (6%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF TGM GY E +TDPSY QI+V TYPLIGNYG+ +D ES I +SGL+
Sbjct: 27 VFNTGMTGYQEILTDPSYKGQIVVFTYPLIGNYGINDED---------AESKGIHVSGLV 77
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIVHGSVAPLA 123
V ++ D S+W + +L ++L+ H IP + VDTR L K IRE G + G I
Sbjct: 78 VRELSDRYSNWRATESLDQFLKRHGIPGIYGVDTRALVKKIREKGTMKGVISTEDSNDEE 137
Query: 124 VTVEDLVFVDPNRGNLVDQVSTKEVVTYNPT---GSVHLCVVDCGLKYNQLRCLIQRGAK 180
+ + V D NLV +VSTKE T+ + V+D G+K N LR L++RG +
Sbjct: 138 LVQKASVSPDITGINLVAEVSTKEPYTWGQKRGGKKRRVVVIDFGVKQNILRRLVKRGCE 197
Query: 181 LSVIPWNHPIK 191
++V+P++ +
Sbjct: 198 VTVVPYDTDAE 208
Score = 82.3 bits (204), Expect = 1e-17
Identities = 27/55 (49%), Positives = 35/55 (63%)
Query: 193 PQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIFINAVRD 247
+ N NDGT EGI H+ LP FSVQ+HPE + GP D E LFD FI+ +++
Sbjct: 304 AGDLEVTHVNLNDGTVEGIRHKDLPVFSVQYHPEASPGPHDTEYLFDEFIDLMKE 358
>gnl|CDD|198165 smart01097, CPSase_sm_chain, Carbamoyl-phosphate synthase small
chain, CPSase domain. The carbamoyl-phosphate synthase
domain is in the amino terminus of protein.
Carbamoyl-phosphate synthase catalyses the ATP-dependent
synthesis of carbamyl-phosphate from glutamine or
ammonia and bicarbonate. This important enzyme initiates
both the urea cycle and the biosynthesis of arginine
and/or pyrimidines. The carbamoyl-phosphate synthase
(CPS) enzyme in prokaryotes is a heterodimer of a small
and large chain. The small chain promotes the hydrolysis
of glutamine to ammonia, which is used by the large
chain to synthesise carbamoyl phosphate. The small chain
has a GATase domain in the carboxyl terminus.
Length = 130
Score = 184 bits (470), Expect = 2e-58
Identities = 54/111 (48%), Positives = 73/111 (65%), Gaps = 9/111 (8%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF TGM GY E +TDPSY QI+V TYPLIGNYGV +D FES +I + GL+
Sbjct: 29 VFNTGMTGYQEILTDPSYAGQIVVFTYPLIGNYGVNDED---------FESDKIQVKGLV 79
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKI 114
V ++ D PS+W S +L E+L+ + IP ++ +DTR LT+ +RE G + G I
Sbjct: 80 VRELSDEPSNWRSEQSLDEFLKENGIPGISGIDTRALTRKLREKGAMKGVI 130
>gnl|CDD|183784 PRK12838, PRK12838, carbamoyl phosphate synthase small subunit;
Reviewed.
Length = 354
Score = 191 bits (488), Expect = 3e-58
Identities = 76/184 (41%), Positives = 107/184 (58%), Gaps = 14/184 (7%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF TGM GY E +TDPSY QI+V TYPLIGNYG+ D +ES + + G+I
Sbjct: 29 VFNTGMTGYQEVLTDPSYKGQIVVFTYPLIGNYGINADD---------YESKQPQVKGVI 79
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIVHGSVAPLA 123
V ++ SH+ + +L ++L+ NIP ++ VDTR L KHIRE G + I A
Sbjct: 80 VYELSREGSHYRAKQSLDDFLKEWNIPGISGVDTRALVKHIREKGTMKASITTTDDAHAF 139
Query: 124 VTVEDLVFVDPNRGNLVDQVSTKEVVTYNPTGSVHLCVVDCGLKYNQLRCLIQRGAKLSV 183
++ LV N+V QVSTKE TY G H+ ++D G K + LR L +RG K++V
Sbjct: 140 DQIKALVLP----KNVVAQVSTKEPYTY-GNGGKHVALIDFGYKKSILRSLSKRGCKVTV 194
Query: 184 IPWN 187
+P++
Sbjct: 195 LPYD 198
Score = 68.4 bits (168), Expect = 7e-13
Identities = 23/51 (45%), Positives = 29/51 (56%)
Query: 195 GWQPLFTNANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIFINAV 245
F N NDG+ EG+ H+ P SVQFHPE GP D E +FD F+ +
Sbjct: 300 PLSVRFFNVNDGSIEGLRHKKKPVLSVQFHPEAHPGPHDAEYIFDEFLEMM 350
>gnl|CDD|144543 pfam00988, CPSase_sm_chain, Carbamoyl-phosphate synthase small
chain, CPSase domain. The carbamoyl-phosphate synthase
domain is in the amino terminus of protein.
Carbamoyl-phosphate synthase catalyzes the ATP-dependent
synthesis of carbamyl-phosphate from glutamine or
ammonia and bicarbonate. This important enzyme initiates
both the urea cycle and the biosynthesis of arginine
and/or pyrimidines. The carbamoyl-phosphate synthase
(CPS) enzyme in prokaryotes is a heterodimer of a small
and large chain. The small chain promotes the hydrolysis
of glutamine to ammonia, which is used by the large
chain to synthesise carbamoyl phosphate. See pfam00289.
The small chain has a GATase domain in the carboxyl
terminus. See pfam00117.
Length = 131
Score = 178 bits (455), Expect = 2e-56
Identities = 56/112 (50%), Positives = 72/112 (64%), Gaps = 9/112 (8%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF TGM GY E +TDPSY QI+V TYPLIGNYG+ P+D FES + GLI
Sbjct: 29 VFNTGMTGYQEILTDPSYAGQIVVFTYPLIGNYGINPED---------FESDKPHAKGLI 79
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIV 115
V ++ D PS+W S +L E+L+ H IP ++ VDTR LT+ +RE G + G I
Sbjct: 80 VRELSDIPSNWRSEESLDEFLKEHGIPGISGVDTRALTRKLREKGAMKGVIS 131
>gnl|CDD|214392 CHL00197, carA, carbamoyl-phosphate synthase arginine-specific
small subunit; Provisional.
Length = 382
Score = 127 bits (320), Expect = 1e-33
Identities = 65/215 (30%), Positives = 103/215 (47%), Gaps = 33/215 (15%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF TGM GY E +TDPSY +QI+ TYP IGN G+ +D ES +I + G+I
Sbjct: 33 VFNTGMTGYQEIITDPSYFEQIVTFTYPEIGNTGINLED---------IESVKIQVKGII 83
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSG----------- 112
++C + S+W +L +L+ H IP + +DTR LT+H+R G ++G
Sbjct: 84 AKNICKSSSNWRQQESLVSYLQRHKIPFIFGIDTRALTQHLRRFGTMNGCISNQNLNLSY 143
Query: 113 ---KIVHG------SVAPLAVTVEDLVFVDPNRGNLVDQVSTKEVVTYNPTGSVHLCVVD 163
KI + P T + + + + + + +Y + + V+D
Sbjct: 144 LRAKIKESPHMPSSDLIPRVTTSSYYEWDEKSHPSFYLADNKRPHSSY----QLKIIVID 199
Query: 164 CGLKYNQLRCLIQRGAKLSVIPWNHPIKVPQGWQP 198
G+KYN LR L G ++V+P P + +QP
Sbjct: 200 FGVKYNILRRLKSFGCSITVVPATSPYQDILSYQP 234
Score = 55.6 bits (134), Expect = 1e-08
Identities = 25/48 (52%), Positives = 32/48 (66%)
Query: 202 NANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIFINAVRDSK 249
N NDGT GI H P+FSVQ+HPE + GP D + LF+ FI ++ SK
Sbjct: 331 NLNDGTVAGISHSPKPYFSVQYHPEASPGPHDADYLFEYFIEIIKHSK 378
>gnl|CDD|153215 cd01744, GATase1_CPSase, Small chain of the glutamine-dependent
form of carbamoyl phosphate synthase, CPSase II. This
group of sequences represents the small chain of the
glutamine-dependent form of carbamoyl phosphate
synthase, CPSase II. CPSase II catalyzes the production
of carbomyl phosphate (CP) from bicarbonate, glutamine
and two molecules of MgATP. The reaction is believed to
proceed by a series of four biochemical reactions
involving a minimum of three discrete highly reactive
intermediates. The synthesis of CP is critical for the
initiation of two separate biosynthetic pathways. In one
CP is coupled to aspartate, its carbon and nitrogen
nuclei ultimately incorporated into the aromatic
moieties of pyrimidine nucleotides. In the second
pathway CP is condensed with ornithine at the start of
the urea cycle and is utilized for the detoxification of
ammonia and biosynthesis of arginine. CPSases may be
encoded by one or by several genes, depending on the
species. The E.coli enzyme is a heterodimer consisting
of two polypeptide chains referred to as the small and
large subunit. Ammonia an intermediate during the
biosynthesis of carbomyl phosphate produced by the
hydrolysis of glutamine in the small subunit of the
enzyme is delivered via a molecular tunnel between the
remotely located carboxyphosphate active site in the
large subunit. CPSase IIs belong to the triad family of
amidotransferases having a conserved Cys-His-Glu
catalytic triad in the glutaminase active site. This
group also contains the sequence from the mammalian urea
cycle form which has lost the active site Cys, resulting
in an ammonia-dependent form, CPSase I.
Length = 178
Score = 91.4 bits (228), Expect = 3e-22
Identities = 32/61 (52%), Positives = 37/61 (60%), Gaps = 5/61 (8%)
Query: 187 NH-----PIKVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIF 241
NH P +P G + N NDGT EGI H+ LP FSVQFHPE + GP D E LFD F
Sbjct: 118 NHGYAVDPDSLPGGLEVTHVNLNDGTVEGIRHKDLPVFSVQFHPEASPGPHDTEYLFDEF 177
Query: 242 I 242
+
Sbjct: 178 L 178
Score = 52.5 bits (127), Expect = 3e-08
Identities = 13/30 (43%), Positives = 23/30 (76%)
Query: 161 VVDCGLKYNQLRCLIQRGAKLSVIPWNHPI 190
V+D G+K+N LR L++RG +++V+P+N
Sbjct: 3 VIDFGVKHNILRELLKRGCEVTVVPYNTDA 32
>gnl|CDD|178370 PLN02771, PLN02771, carbamoyl-phosphate synthase
(glutamine-hydrolyzing).
Length = 415
Score = 91.2 bits (226), Expect = 2e-20
Identities = 69/224 (30%), Positives = 106/224 (47%), Gaps = 42/224 (18%)
Query: 4 VFQTGMVGYPEAMTDPSYHQQILVLTYPLIGNYGVPPQDKDEHGILKYFESHRIWISGLI 63
VF T + GY E +TDPSY Q +++T P IGN GV D+ ES + +++GL+
Sbjct: 83 VFNTSLTGYQEILTDPSYAGQFVLMTNPHIGNTGVNFDDE---------ESRQCFLAGLV 133
Query: 64 VGDMCDTPSHWNSASTLGEWLRAHNIPALANVDTRRLTKHIRECGVVSGKIVHGSVAPLA 123
+ + + S+W TLG++L NI + +VDTR +T+ +RE G + G + S
Sbjct: 134 IRSLSISTSNWRCTKTLGDYLAERNIMGIYDVDTRAITRRLREDGSLIGVL---STEDSK 190
Query: 124 VTVE--------DLVFVDPNRGNLVDQVSTKEVVTY-NPTG-------------SVHLCV 161
E D+V +D L+ VS K + + T S H+
Sbjct: 191 TDEELLKMSRSWDIVGID-----LISGVSCKSPYEWVDKTNPEWDFNTNSRDGESYHVIA 245
Query: 162 VDCGLKYNQLRCLIQRGAKLSVIPWNHPIKVPQGWQP---LFTN 202
D G+K+N LR L G K++V+P P +P LF+N
Sbjct: 246 YDFGIKHNILRRLASYGCKITVVPSTWPASEALKMKPDGVLFSN 289
Score = 40.3 bits (94), Expect = 0.001
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 177 RGAKLSVIPWNH-----PIKVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPEHTAGP 231
R ++ + NH P +P+G + N NDG+ G+ +L S+Q+HPE + GP
Sbjct: 349 RTGRVEISAQNHNYAVDPASLPEGVEVTHVNLNDGSCAGLAFPALNVMSLQYHPEASPGP 408
Query: 232 ADLELLF 238
D + F
Sbjct: 409 HDSDNAF 415
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 75.8 bits (187), Expect = 5e-15
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 271 ALIAKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTYNATAHDLAVKE 330
A IA+ + VRK+R++ GI P K++DT AAE AQT YLY TY D+ +
Sbjct: 495 AQIARLIGVTEAE-VRKLRKELGIMPVYKRVDTCAAEFEAQTPYLYSTYEGERDDVPFTD 553
Query: 331 TVSII 335
++
Sbjct: 554 KKKVL 558
>gnl|CDD|198164 smart01096, CPSase_L_D3, Carbamoyl-phosphate synthetase large
chain, oligomerisation domain. Carbamoyl-phosphate
synthase catalyses the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 124
Score = 68.6 bits (169), Expect = 2e-14
Identities = 23/49 (46%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 271 ALIAKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTY 319
IAK + VR +R++ GIRP K++DT AAE PA T Y Y TY
Sbjct: 77 RQIAKLLGVTEAE-VRALRKELGIRPVYKRVDTCAAEFPANTPYYYSTY 124
>gnl|CDD|215729 pfam00117, GATase, Glutamine amidotransferase class-I.
Length = 186
Score = 70.0 bits (172), Expect = 3e-14
Identities = 30/95 (31%), Positives = 36/95 (37%), Gaps = 14/95 (14%)
Query: 155 GSVHLCVVDCGLKYNQLRCLIQRGAKLSVIPWNH-----PIKVPQGWQPLFTNANDGTNE 209
G D GL Y I R H P +P G + + N G
Sbjct: 101 GKNSPVGHDKGLFYGLPNVFIVR--------RYHSYAVDPDTLPDGLEVTAASENGG-IM 151
Query: 210 GIVHESLPFFSVQFHPEHTAGPADLELLFDIFINA 244
I H+ P F VQFHPE + P ELLF+ FI
Sbjct: 152 AIRHKENPIFGVQFHPESSLTPGGPELLFNFFIKL 186
Score = 34.2 bits (79), Expect = 0.045
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 161 VVDCG--LKYNQLRCLIQRGAKLSVIPWNHPIKV 192
++D G YN R L + G ++ V+P + P +
Sbjct: 2 LIDNGDSFTYNLARALRELGVEVEVVPNDTPAEE 35
>gnl|CDD|217231 pfam02787, CPSase_L_D3, Carbamoyl-phosphate synthetase large chain,
oligomerisation domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 122
Score = 67.2 bits (165), Expect = 6e-14
Identities = 23/49 (46%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 271 ALIAKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTY 319
A IAK ++ VRK+R++ GI+P K +DT AAE A+T Y Y TY
Sbjct: 75 AQIAKLLGVTEE-EVRKLRKELGIKPVYKMVDTCAAEFEAKTPYYYSTY 122
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 62.8 bits (154), Expect = 1e-10
Identities = 19/37 (51%), Positives = 23/37 (62%)
Query: 285 VRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTYNA 321
VRK+R+ GI P K++DT AAE A T Y Y TY
Sbjct: 509 VRKLRKALGIHPVYKRVDTCAAEFEADTPYYYSTYEE 545
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 45.7 bits (109), Expect = 2e-05
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 271 ALIAKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTYN 320
AL+A+ ++ VR +R+ GIRP K +DT AAE A+T Y Y TY
Sbjct: 496 ALLAELTGVTEE-EVRALRKKLGIRPSYKMVDTCAAEFEAKTPYYYSTYF 544
>gnl|CDD|153213 cd01742, GATase1_GMP_Synthase, Type 1 glutamine amidotransferase
(GATase1) domain found in GMP synthetase. Type 1
glutamine amidotransferase (GATase1) domain found in GMP
synthetase. GMP synthetase is a glutamine
amidotransferase from the de novo purine biosynthetic
pathway. Glutamine amidotransferase (GATase) activity
catalyse the transfer of ammonia from the amide side
chain of glutamine to an acceptor substrate. GMP
synthetase catalyses the amination of the nucleotide
precursor xanthosine 5'-monophospahte to form GMP. GMP
synthetase belongs to the triad family of
amidotransferases having a conserved Cys-His-Glu
catalytic triad in the glutaminase active site.
Length = 181
Score = 42.1 bits (100), Expect = 9e-05
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 190 IKVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPE--HT 228
+K+P+G++ + ++ N I +E + VQFHPE HT
Sbjct: 131 VKLPEGFKVIASSDNCP-VAAIANEEKKIYGVQFHPEVTHT 170
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 42.5 bits (100), Expect = 3e-04
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 273 IAKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNYLYLTYNA 321
IA + ++ +K VR R G+ P K++DT AAE A T Y+Y +Y+
Sbjct: 518 IAFATKSTEKE-VRSKRLSLGVTPSYKRVDTCAAEFEANTPYMYSSYDG 565
>gnl|CDD|153216 cd01745, GATase1_2, Subgroup of proteins having the Type 1
glutamine amidotransferase (GATase1) domain. This group
contains a subgroup of proteins having the Type 1
glutamine amidotransferase (GATase1) domain. GATase
activity catalyses the transfer of ammonia from the
amide side chain of glutamine to an acceptor substrate.
Glutamine amidotransferases (GATase) includes the triad
family of amidotransferases which have a conserved
Cys-His-Glu catalytic triad in the glutaminase active
site. In this subgroup this triad is conserved. GATase
activity can be found in a range of biosynthetic
enzymes, including: glutamine amidotransferase,
formylglycinamide ribonucleotide, GMP synthetase ,
anthranilate synthase component II, glutamine-dependent
carbamoyl phosphate synthase, cytidine triphosphate
synthetase, gamma-glutamyl hydrolase, imidazole glycerol
phosphate synthase and, cobyric acid synthase. Glutamine
amidotransferase (GATase) domains can occur either as
single polypeptides, as in glutamine amidotransferases,
or as domains in a much larger multifunctional synthase
protein, such as CPSase.
Length = 189
Score = 40.3 bits (95), Expect = 5e-04
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 191 KVPQGWQPLFTNANDGTNEGIVHESLPF-FSVQFHPE-HTAGPADLELLFDIFI 242
++ G + A DG E I PF VQ+HPE D LF+ F+
Sbjct: 137 RLADGLRVEAR-APDGVIEAIESPDRPFVLGVQWHPEWLADTDPDSLKLFEAFV 189
>gnl|CDD|224982 COG2071, COG2071, Predicted glutamine amidotransferases [General
function prediction only].
Length = 243
Score = 40.4 bits (95), Expect = 6e-04
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 203 ANDGTNEGIVHESLPF-FSVQFHPEHTAG--PADLELLFDIFINAVRDSK 249
A DGT E + ++ F VQ+HPE+ P L LF+ F+NA +
Sbjct: 194 APDGTVEAVEVKNDAFVLGVQWHPEYLVDTNPLSLA-LFEAFVNACKKHA 242
>gnl|CDD|153214 cd01743, GATase1_Anthranilate_Synthase, Type 1 glutamine
amidotransferase (GATase1) domain found in Anthranilate
synthase. Type 1 glutamine amidotransferase (GATase1)
domain found in Anthranilate synthase (ASase). This
group contains proteins similar to para-aminobenzoate
(PABA) synthase and ASase. These enzymes catalyze
similar reactions and produce similar products, PABA and
ortho-aminobenzoate (anthranilate). Each enzyme is
composed of non-identical subunits: a glutamine
amidotransferase subunit (component II) and a subunit
that produces an aminobenzoate products (component I).
ASase catalyses the synthesis of anthranilate from
chorismate and glutamine and is a tetrameric protein
comprising two copies each of components I and II.
Component II of ASase belongs to the family of triad
GTases which hydrolyze glutamine and transfer nascent
ammonia between the active sites. In some bacteria, such
as Escherichia coli, component II can be much larger
than in other organisms, due to the presence of
phosphoribosyl-anthranilate transferase (PRTase)
activity. PRTase catalyses the second step in tryptophan
biosynthesis and results in the addition of
5-phosphoribosyl-1-pyrophosphate to anthranilate to
create N-5'-phosphoribosyl-anthranilate. In E.coli, the
first step in the conversion of chorismate to PABA
involves two proteins: PabA and PabB which co-operate to
transfer the amide nitrogen of glutamine to chorismate
forming 4-amino-4 deoxychorismate (ADC). PabA acts as a
glutamine amidotransferase, supplying an amino group to
PabB, which carries out the amination reaction. A third
protein PabC then mediates elimination of pyruvate and
aromatization to give PABA. Several organisms have
bipartite proteins containing fused domains homologous
to PabA and PabB commonly called PABA synthases. These
hybrid PABA synthases may produce ADC and not PABA.
Length = 184
Score = 36.7 bits (86), Expect = 0.006
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 205 DGTNEGIVHESLPFFSVQFHPE 226
DG + H LP + VQFHPE
Sbjct: 148 DGVIMALRHRDLPIYGVQFHPE 169
>gnl|CDD|129966 TIGR00888, guaA_Nterm, GMP synthase (glutamine-hydrolyzing),
N-terminal domain or A subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains in
most of the Archaea. This N-terminal region would be the
smaller subunit [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 188
Score = 36.5 bits (85), Expect = 0.009
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 190 IKVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPE--HT 228
++P+G++ L T+ N + HE P + VQFHPE HT
Sbjct: 131 KELPEGFKVLATSDN-CPVAAMAHEEKPIYGVQFHPEVTHT 170
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 36.3 bits (85), Expect = 0.011
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 203 ANDGTNEGIVHESLPFFSVQFHPE 226
+DG G+ H+ LP + VQFHPE
Sbjct: 147 TDDGEIMGVRHKELPIYGVQFHPE 170
>gnl|CDD|237429 PRK13566, PRK13566, anthranilate synthase; Provisional.
Length = 720
Score = 37.2 bits (87), Expect = 0.012
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 205 DGTNEGIVHESLPFFSVQFHPE 226
DG I H++LP +VQFHPE
Sbjct: 676 DGVIMAIEHKTLPVAAVQFHPE 697
>gnl|CDD|179112 PRK00758, PRK00758, GMP synthase subunit A; Validated.
Length = 184
Score = 35.2 bits (82), Expect = 0.020
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 209 EGIVHESLPFFSVQFHPE--HT 228
E + H+ P + VQFHPE HT
Sbjct: 146 EAMKHKEKPIYGVQFHPEVAHT 167
>gnl|CDD|237764 PRK14607, PRK14607, bifunctional glutamine
amidotransferase/anthranilate phosphoribosyltransferase;
Provisional.
Length = 534
Score = 35.8 bits (83), Expect = 0.030
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 203 ANDGTNEGIVHESLPFFSVQFHPEHTAGPADLELLFDIFINAVRDS 248
++DG GI H+ P F VQFHPE + + + + F+N R+
Sbjct: 148 SDDGEIMGIRHKEHPIFGVQFHPE-SILTEEGKRILKNFLNYQREE 192
>gnl|CDD|223586 COG0512, PabA, Anthranilate/para-aminobenzoate synthases component
II [Amino acid transport and metabolism / Coenzyme
metabolism].
Length = 191
Score = 34.1 bits (79), Expect = 0.057
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 210 GIVHESLPFFSVQFHPE 226
+ H+ LP + VQFHPE
Sbjct: 157 AVRHKKLPIYGVQFHPE 173
>gnl|CDD|223578 COG0504, PyrG, CTP synthase (UTP-ammonia lyase) [Nucleotide
transport and metabolism].
Length = 533
Score = 34.8 bits (81), Expect = 0.059
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 209 EGIVHESLPFF-SVQFHPEHTAGPADLELLFDIFINAVRDSK 249
E + PFF + QFHPE + P LF F+ A + K
Sbjct: 489 EIVELPDHPFFVATQFHPEFKSRPLRPHPLFVGFVKAALEYK 530
>gnl|CDD|130874 TIGR01815, TrpE-clade3, anthranilate synthase, alpha
proteobacterial clade. This model represents a small
clade of anthranilate synthases from alpha
proteobacteria and Nostoc (a cyanobacterium). This
enzyme is the first step in the pathway for the
biosynthesis of tryprophan from chorismate [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 717
Score = 34.9 bits (80), Expect = 0.065
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 205 DGTNEGIVHESLPFFSVQFHPEHT---AGPADLELLFDIFINAVRDSKTRTP 253
DG I H LP +VQFHPE G A L ++ ++ + T
Sbjct: 666 DGLIMAIEHRRLPLAAVQFHPESIMTLDGGAGLAMIGNVVDRLAAGALTDAA 717
>gnl|CDD|223592 COG0518, GuaA, GMP synthase - Glutamine amidotransferase domain
[Nucleotide transport and metabolism].
Length = 198
Score = 33.4 bits (77), Expect = 0.091
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 191 KVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPE 226
++P+G L ++ N+ + + VQFHPE
Sbjct: 143 ELPEGAVVLASSETCP-NQAFRYG-KRAYGVQFHPE 176
>gnl|CDD|215481 PLN02889, PLN02889, oxo-acid-lyase/anthranilate synthase.
Length = 918
Score = 32.9 bits (75), Expect = 0.30
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 176 QRGAKLSVIPWNHPIKVPQGWQPLFTNANDGTN--EGIVHESLPFFSVQFHPEHTA 229
Q G S P++ +K W + GI+H + P + +QFHPE A
Sbjct: 265 QIGQSGSSDPFSSKLKNGTSWPSSHSERMQNGKILMGIMHSTRPHYGLQFHPESIA 320
>gnl|CDD|153217 cd01746, GATase1_CTP_Synthase, Type 1 glutamine amidotransferase
(GATase1) domain found in Cytidine Triphosphate
Synthetase. Type 1 glutamine amidotransferase (GATase1)
domain found in Cytidine Triphosphate Synthetase (CTP).
CTP is involved in pyrimidine
ribonucleotide/ribonucleoside metabolism. CTPs produce
CTP from UTP and glutamine and regulate intracellular
CTP levels through interactions with four ribonucleotide
triphosphates. The enzyme exists as a dimer of identical
chains that aggregates as a tetramer. CTP is derived
form UTP in three separate steps involving two active
sites. In one active site, the UTP O4 oxygen is
activated by Mg-ATP-dependent phosphorylation, followed
by displacement of the resulting 4-phosphate moiety by
ammonia. At a separate site, ammonia is generated via
rate limiting glutamine hydrolysis (glutaminase)
activity. A gated channel that spans between the
glutamine hydrolysis and amidoligase active sites
provides a path for ammonia diffusion. CTPs belong to
the triad family of amidotransferases having a conserved
Cys-His-Glu catalytic triad in the glutaminase active
site.
Length = 235
Score = 32.1 bits (74), Expect = 0.31
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 201 TNANDGTNEGIVHESLPFF-SVQFHPEHTAGPADLELLFDIFI 242
T+ + G E + PFF QFHPE + P LF F+
Sbjct: 193 TDPDGGLVEIVELPDHPFFVGTQFHPEFKSRPLKPHPLFVGFV 235
>gnl|CDD|232926 TIGR00337, PyrG, CTP synthase. CTP synthase is involved in
pyrimidine ribonucleotide/ribonucleoside metabolism. The
enzyme catalyzes the reaction L-glutamine + H2O + UTP +
ATP = CTP + phosphate + ADP + L-glutamate. The enzyme
exists as a dimer of identical chains that aggregates as
a tetramer. This gene has been found circa 500 bp 5'
upstream of enolase in both beta (Nitrosomonas europaea)
and gamma (E.coli) subdivisions of proteobacterium (FEMS
Microbiol Lett 1998 Aug 1;165(1):153-7) [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 525
Score = 32.3 bits (74), Expect = 0.41
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 218 FFSVQFHPEHTAGPADLELLFDIFINA 244
F + QFHPE T+ P LF F+ A
Sbjct: 499 FVACQFHPEFTSRPNRPHPLFLGFVKA 525
>gnl|CDD|235882 PRK06895, PRK06895, putative anthranilate synthase component II;
Provisional.
Length = 190
Score = 31.2 bits (71), Expect = 0.48
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 213 HESLPFFSVQFHPE 226
H++LP + VQFHPE
Sbjct: 158 HKTLPIYGVQFHPE 171
>gnl|CDD|234614 PRK00074, guaA, GMP synthase; Reviewed.
Length = 511
Score = 31.6 bits (73), Expect = 0.57
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 191 KVPQGWQPLFTNANDGTNEGIVHESLPFFSVQFHPE--HT 228
++P+G++ + + N I +E F+ VQFHPE HT
Sbjct: 137 ELPEGFKVIASTEN-CPIAAIANEERKFYGVQFHPEVTHT 175
>gnl|CDD|181066 PRK07649, PRK07649, para-aminobenzoate/anthranilate synthase
glutamine amidotransferase component II; Validated.
Length = 195
Score = 30.5 bits (69), Expect = 0.78
Identities = 19/46 (41%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 207 TNEG----IVHESLPFFSVQFHPEHTAGPADLELLFDIFINAVRDS 248
T EG I H++LP VQFHPE ELL + FI S
Sbjct: 147 TEEGEIMAIRHKTLPIEGVQFHPESIMTSHGKELLQN-FIRKYSPS 191
>gnl|CDD|235437 PRK05380, pyrG, CTP synthetase; Validated.
Length = 533
Score = 31.1 bits (72), Expect = 0.80
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 217 PFF-SVQFHPEHTAGPADLELLFDIFINAVRDSK 249
P+F VQFHPE + P LF F+ A ++K
Sbjct: 497 PWFVGVQFHPEFKSRPRRPHPLFAGFVKAALENK 530
>gnl|CDD|233027 TIGR00566, trpG_papA, glutamine amidotransferase of anthranilate
synthase or aminodeoxychorismate synthase. This model
describes the glutamine amidotransferase domain or
peptide of the tryptophan-biosynthetic pathway enzyme
anthranilate synthase or of the folate biosynthetic
pathway enzyme para-aminobenzoate synthase. In at least
one case, a single polypeptide from Bacillus subtilis
was shown to have both functions. This model covers a
subset of the sequences described by the PFAM model
GATase.
Length = 188
Score = 30.5 bits (69), Expect = 0.80
Identities = 10/17 (58%), Positives = 10/17 (58%)
Query: 210 GIVHESLPFFSVQFHPE 226
I H LP VQFHPE
Sbjct: 155 AIRHRDLPLEGVQFHPE 171
>gnl|CDD|239972 cd04599, CBS_pair_GGDEF_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains in
association with the GGDEF (DiGuanylate-Cyclase (DGC))
domain. The GGDEF domain has been suggested to be
homologous to the adenylyl cyclase catalytic domain and
is thought to be involved in regulating cell surface
adhesiveness in bacteria. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 105
Score = 29.3 bits (66), Expect = 0.84
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 124 VTVEDLVFVDPNRGNLVDQVSTKEVVTYNPTGS 156
+T D+ PNR LV T+EVVT +P S
Sbjct: 39 ITSRDVRRAHPNR--LVADAMTREVVTISPEAS 69
>gnl|CDD|226135 COG3608, COG3608, Predicted deacylase [General function prediction
only].
Length = 331
Score = 30.8 bits (70), Expect = 0.91
Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 15/93 (16%)
Query: 14 EAMTDPSYH-----QQILVLTYPLIGNYGVPPQ--DKDEHGILKYFESHRIWISGLIVGD 66
EA D I V+T L G V + + GIL + G++ G+
Sbjct: 187 EADADGMLRTAAERAGIPVITVELGGAGDVDAESIEIAAEGILNFLRHR-----GILAGE 241
Query: 67 MCDTPSHWNSASTLGEWLRAHNIPALANVDTRR 99
+ TP+ + + E +RA PA V+
Sbjct: 242 VEKTPTKGLALPSSDEMIRA---PAGGLVEFLV 271
>gnl|CDD|180689 PRK06774, PRK06774, para-aminobenzoate synthase component II;
Provisional.
Length = 191
Score = 30.2 bits (68), Expect = 0.99
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 210 GIVHESLPFFSVQFHPE 226
GI H +LP VQFHPE
Sbjct: 158 GIRHRTLPLEGVQFHPE 174
>gnl|CDD|216847 pfam02016, Peptidase_S66, LD-carboxypeptidase.
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a
peptide bond between a di-basic amino acid and the
C-terminal D-alanine in the tetrapeptide moiety in
peptidoglycan. This cleaves the bond between an L- and a
D-amino acid. The function of this activity is in murein
recycling. This family also includes the microcin c7
self-immunity protein. This family corresponds to Merops
family S66.
Length = 281
Score = 30.2 bits (69), Expect = 1.2
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 11/56 (19%)
Query: 45 EHGILKYFESHRIWISGLIVGDMCDTPSHWNSAST----LGEWLRAHNIPALANVD 96
GIL ++G+I+G D + T L E L IP L +
Sbjct: 214 LAGILDK-------VAGIILGRFTDCDDDEDYGDTLEEVLEEVLGDLGIPVLYGLP 262
>gnl|CDD|181566 PRK08857, PRK08857, para-aminobenzoate synthase component II;
Provisional.
Length = 193
Score = 29.8 bits (67), Expect = 1.5
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 200 FTNANDGTNE---GIVHESLPFFSVQFHPE 226
+T DG+ + G H++LP +VQFHPE
Sbjct: 146 WTELEDGSMDEIMGFQHKTLPIEAVQFHPE 175
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 30.2 bits (68), Expect = 1.8
Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 19/96 (19%)
Query: 69 DTPSHWNSASTLGEWLRAHNIPALANV---DTRRLTKHIRECGVVSGKIVHGSVAPLAVT 125
+ P W AS++ E LR ++ +L V T L R LA+
Sbjct: 219 EQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKER----------------LALM 262
Query: 126 VEDLVFVDPNRGNLVDQVSTKEVVTYNPTGSVHLCV 161
++ V V+ +RG ++D+V+ E + NP V L V
Sbjct: 263 KKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDV 298
>gnl|CDD|227551 COG5226, CEG1, mRNA capping enzyme, guanylyltransferase (alpha)
subunit [RNA processing and modification].
Length = 404
Score = 29.9 bits (67), Expect = 2.1
Identities = 27/123 (21%), Positives = 39/123 (31%), Gaps = 38/123 (30%)
Query: 212 VHESLPFFSVQFHPE---HTAGPADLELLFDIFINAVRDSKTRTPVPPIRKTIYDTL--- 265
VH S P S D EL+FD VP +R ++D L
Sbjct: 102 VHTSFPPCSTVLKDGEVLLEDTLLDGELVFDCLPY--------EKVPQLRYLLFDCLAYA 153
Query: 266 ------VPKDEAL--IAKSFQTPK----------------KTSVRKMREDNGIRPYNKQI 301
+ K E L + K + P+ SV++M + G K+I
Sbjct: 154 GMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFHFSVKQMLKSYGFWKIYKKI 213
Query: 302 DTL 304
L
Sbjct: 214 PEL 216
>gnl|CDD|181107 PRK07765, PRK07765, para-aminobenzoate synthase component II;
Provisional.
Length = 214
Score = 29.2 bits (66), Expect = 2.4
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 4/24 (16%)
Query: 207 TNEGIV----HESLPFFSVQFHPE 226
T+ G++ H LP VQFHPE
Sbjct: 151 TDSGVIMAVRHRELPIHGVQFHPE 174
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport
and metabolism].
Length = 342
Score = 29.6 bits (67), Expect = 2.4
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 305 AAEHPAQTNYLY 316
AA +PA+T+YLY
Sbjct: 300 AALNPAKTDYLY 311
>gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators, YofA and
SoxR, contains the type 2 periplasmic binding fold.
YofA is a LysR-like transcriptional regulator of cell
growth in Bacillus subtillis. YofA controls cell
viability and the formation of constrictions during cell
division. YofaA positively regulates expression of the
cell division gene ftsW, and thus is essential for cell
viability during stationary-phase growth of Bacillus
substilis. YofA shows significant homology to SoxR from
Arthrobacter sp. TE1826. SoxR is a negative regulator
for the sarcosine oxidase gene soxA. Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine,
which is involved in the metabolism of creatine and
choline. The topology of this substrate-binding domain
is most similar to that of the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 193
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 96 DTRRLTKHIRE----CGVVSGKIVHGSVAPLAVTVEDLVFVDPNRGNLVDQVST 145
T L + + E V+G + H + V E+LV V P V +
Sbjct: 37 TTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPVSRAED 90
>gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease,
includes microcin C7 self immunity protein.
LD-carboxypeptidase (Muramoyltetrapeptide
carboxypeptidase; EC 3.4.17.13; Merops family S66;
initially described as Carboxypeptidase II) family also
includes the microcin c7 self-immunity protein (MccF) as
well as uncharacterized proteins including hypothetical
proteins. LD-carboxypeptidase hydrolyzes the amide bond
that links the dibasic amino acids to C-terminal
D-amino acids. The physiological substrates of
LD-carboxypeptidase are tetrapeptide fragments (such as
UDP-MurNAc-tetrapeptides) that are produced when
bacterial cell walls are degraded; they contain an
L-configured residue (L-lysine or meso-diaminopimelic
acid residue) as the penultimate residue and D-alanine
as the ultimate residue. A possible role of
LD-carboxypeptidase is in peptidoglycan recycling
whereby the resulting tripeptide (precursor for murein
synthesis) can be reconverted into peptidoglycan by
attachment of preformed D-Ala-D-Ala dipeptides. Some
enzymes possessing LD-carboxypeptidase activity also act
as LD-transpeptidase by replacing the terminal D-Ala
with another D-amino acid. MccF contributes to
self-immunity towards microcin C7 (MccC7), a ribosomally
encoded peptide antibiotic that contains a
phosphoramidate linkage to adenosine monophosphate at
its C-terminus. Its possible biological role is to
defend producer cells against exogenous microcin from
re-entering after having been exported. It is suggested
that MccF is involved in microcin degradation or
sequestration in the periplasm.
Length = 282
Score = 29.1 bits (66), Expect = 2.8
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 11/56 (19%)
Query: 45 EHGILKYFESHRIWISGLIVGDMCDTPSHWNSASTLGEWLRAH----NIPALANVD 96
G+L ++G+I+G D + + TL E L+ IP L +
Sbjct: 217 LAGVLDK-------VAGIILGRFTDCEDNDDFGYTLEEVLKEVLGDLGIPVLYGLP 265
>gnl|CDD|153219 cd01748, GATase1_IGP_Synthase, Type 1 glutamine amidotransferase
(GATase1) domain found in imidazole glycerol phosphate
synthase (IGPS). Type 1 glutamine amidotransferase
(GATase1) domain found in imidazole glycerol phosphate
synthase (IGPS). IGPS incorporates ammonia derived from
glutamine into
N1-[(5'-phosphoribulosyl)-formimino]-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to form
5'-(5-aminoimidazole-4-carboxamide) ribonucleotide
(AICAR) and imidazole glycerol phosphate (IGP). The
glutamine amidotransferase domain generates the ammonia
nucleophile which is channeled from the glutaminase
active site to the PRFAR active site. IGPS belong to the
triad family of amidotransferases having a conserved
Cys-His-Glu catalytic triad in the glutaminase active
site.
Length = 198
Score = 28.6 bits (65), Expect = 3.1
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 5/22 (22%)
Query: 218 FFSVQFHPE--HTAGPADLELL 237
F QFHPE AG L+LL
Sbjct: 176 IFGTQFHPEKSGKAG---LKLL 194
>gnl|CDD|217147 pfam02618, YceG, YceG-like family. This family of proteins is
found in bacteria. Proteins in this family are typically
between 332 and 389 amino acids in length. This family
was previously incorrectly annotated and names as
aminodeoxychorismate lyase. The structure of Escherichia
coli yceG was solved by X-ray crystallography.
Length = 291
Score = 29.0 bits (66), Expect = 3.7
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 305 AAEHPAQTNYLY 316
AA +PA+T+YLY
Sbjct: 255 AALNPAKTDYLY 266
>gnl|CDD|182348 PRK10270, PRK10270, putative aminodeoxychorismate lyase;
Provisional.
Length = 340
Score = 28.7 bits (64), Expect = 3.9
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 10/42 (23%)
Query: 305 AAEHPAQTNYLY----------LTYNATAHDLAVKETVSIIK 336
AA HPA+T YLY N +H+ +V++ + ++K
Sbjct: 294 AAAHPAKTPYLYFVADGKGGHTFNTNLASHNRSVQDYLKVLK 335
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 29.1 bits (65), Expect = 4.0
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 10 VGYPEAMTDPSYHQQILVLTYPL 32
+G P+++TDP Y QI+++ +
Sbjct: 261 LGEPDSLTDPGYRGQIILMNWAQ 283
>gnl|CDD|153218 cd01747, GATase1_Glutamyl_Hydrolase, Type 1 glutamine
amidotransferase (GATase1) domain found in
gamma-Glutamyl Hydrolase. Type 1 glutamine
amidotransferase (GATase1) domain found in
gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase
catalyzes the cleavage of the gamma-glutamyl chain of
folylpoly-gamma-glutamyl substrates and is a central
enzyme in folyl and antifolyl poly-gamma-glutamate
metabolism. GATase activity involves the removal of the
ammonia group from a glutamate molecule and its
subsequent transfer to a specific substrate, thus
creating a new carbon-nitrogen group on the substrate.
gamma-Glutamyl hydrolases belong to the triad family of
amidotransferases having a conserved Cys-His-Glu
catalytic triad in the glutaminase active site.
Length = 273
Score = 28.8 bits (65), Expect = 4.3
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 196 WQP-LFTNANDGTNEGIV---HESLPFFSVQFHPEHTA 229
+ L TN + E I P + VQ+HPE A
Sbjct: 179 FFNVLTTNDDWNGVEFISTVEAYKYPIYGVQWHPEKNA 216
>gnl|CDD|227608 COG5283, COG5283, Phage-related tail protein [Function unknown].
Length = 1213
Score = 28.7 bits (64), Expect = 4.9
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 274 AKSFQTPKKTSVRKMREDNGIRPYNKQIDTLAAEHPAQTNY 314
A Q ++ + M D G +P +QI A TN
Sbjct: 949 ALKAQVKRRDLLDDMIGDEGKKPQRQQITLEIA---YDTNG 986
>gnl|CDD|100062 cd05824, LbH_M1P_guanylylT_C, Mannose-1-phosphate
guanylyltransferase, C-terminal Left-handed parallel
beta helix (LbH) domain: Mannose-1-phosphate
guanylyltransferase is also known as GDP-mannose
pyrophosphorylase. It catalyzes the synthesis of
GDP-mannose from GTP and mannose-1-phosphate, and is
involved in the maintenance of cell wall integrity and
glycosylation. Similar to ADP-glucose
pyrophosphorylase, it contains an N-terminal catalytic
domain that resembles a dinucleotide-binding Rossmann
fold and a C-terminal LbH fold domain, presumably with
4 turns, each containing three imperfect tandem repeats
of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity.
Length = 80
Score = 26.7 bits (59), Expect = 4.9
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 58 WISGLIVGDMCDTPSHWNSASTLGEWLRAHNIPALAN 94
W+ IVG WNS T+G W R N+ L +
Sbjct: 48 WVKSSIVG--------WNS--TVGRWTRLENVTVLGD 74
>gnl|CDD|183877 PRK13170, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 196
Score = 27.9 bits (63), Expect = 5.9
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 218 FFSVQFHPE 226
FF VQFHPE
Sbjct: 172 FFGVQFHPE 180
>gnl|CDD|153433 cd08010, yceG_like, proteins similar to Escherichia coli yceG. The
gene product of Escherichia coli yceG has been
erroneously annotated as an aminodeoxychorismate lyase.
Its overexpression has been reported to cause abnormal
biofilm architecture, and it has been reported to be
part of a putative five-gene operon. It might function
as a periplasmic solute-binding protein. The family also
includes Streptomyces caeruleus NovB, an uncharacterized
member of the novobiocin biosynthetic gene cluster.
Length = 245
Score = 27.9 bits (63), Expect = 6.2
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 305 AAEHPAQTNYLY 316
AA +PA+T+YLY
Sbjct: 212 AALNPAKTDYLY 223
>gnl|CDD|219535 pfam07722, Peptidase_C26, Peptidase C26. These peptidases have
gamma-glutamyl hydrolase activity; that is they catalyze
the cleavage of the gamma-glutamyl bond in
poly-gamma-glutamyl substrates. They are structurally
related to pfam00117, but contain extensions in four
loops and at the C terminus.
Length = 219
Score = 27.6 bits (62), Expect = 7.7
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 203 ANDGTNEGIVHESL--PFFSVQFHPE 226
A DGT E I + VQ+HPE
Sbjct: 194 APDGTIEAIESPNAPYFVLGVQWHPE 219
>gnl|CDD|153210 cd01653, GATase1, Type 1 glutamine amidotransferase (GATase1)-like
domain. Type 1 glutamine amidotransferase
(GATase1)-like domain. This group includes proteins
similar to Class I glutamine amidotransferases, the
intracellular PH1704 from Pyrococcus horikoshii, the
C-terminal of the large catalase: Escherichia coli
HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4
beta-galactosidase middle domain. The majority of
proteins in this group have a reactive Cys found in the
sharp turn between a beta strand and an alpha helix
termed the nucleophile elbow. For Class I glutamine
amidotransferases proteins which transfer ammonia from
the amide side chain of glutamine to an acceptor
substrate, this Cys forms a Cys-His-Glu catalytic triad
in the active site. Glutamine amidotransferases
activity can be found in a range of biosynthetic enzymes
included in this cd: glutamine amidotransferase,
formylglycinamide ribonucleotide, GMP synthetase,
anthranilate synthase component II, glutamine-dependent
carbamoyl phosphate synthase, cytidine triphosphate
synthetase, gamma-glutamyl hydrolase, imidazole glycerol
phosphate synthase and, cobyric acid synthase. For
Pyrococcus horikoshii PH1704, the Cys of the nucleophile
elbow together with a different His and, a Glu from an
adjacent monomer form a catalytic triad different from
the typical GATase1 triad. The E. coli HP-II C-terminal
domain, S. meliloti Rm1021 ThuA and the A4
beta-galactosidase middle domain lack the catalytic
triad typical GATaseI domains. GATase1-like domains can
occur either as single polypeptides, as in Class I
glutamine amidotransferases, or as domains in a much
larger multifunctional synthase protein, such as CPSase.
Length = 115
Score = 26.8 bits (59), Expect = 8.0
Identities = 8/21 (38%), Positives = 8/21 (38%)
Query: 218 FFSVQFHPEHTAGPADLELLF 238
VQFHPE G L
Sbjct: 93 VLGVQFHPEAIDGAEAGARLL 113
>gnl|CDD|237288 PRK13141, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 205
Score = 27.4 bits (62), Expect = 8.3
Identities = 21/91 (23%), Positives = 25/91 (27%), Gaps = 40/91 (43%)
Query: 184 IPWNHPIKVPQ-GWQPLFTNANDGTNEGI--------VH-------------------ES 215
P +KVP GW L +GI VH
Sbjct: 108 FPPEEGLKVPHMGWNQLELKKESPLLKGIPDGAYVYFVHSYYADPCDEEYVAATTDYGVE 167
Query: 216 LP-------FFSVQFHPE--HTAGPADLELL 237
P F QFHPE G L++L
Sbjct: 168 FPAAVGKDNVFGAQFHPEKSGDVG---LKIL 195
>gnl|CDD|233837 TIGR02365, dha_L_ycgS, dihydroxyacetone kinase,
phosphoprotein-dependent, L subunit. Two types of
dihydroxyacetone kinase (glycerone kinase) are
described. In yeast and a few bacteria, e.g. Citrobacter
freundii, the enzyme is a single chain that uses ATP as
phosphoryl donor and is designated EC 2.7.1.29. By
contract, E. coli and many other bacterial species have
a multisubunit form (EC 2.7.1.-) with a phosphoprotein
donor related to PTS transport proteins. This family
represents the subunit homologous to the E. coli YcgS
subunit.
Length = 194
Score = 27.3 bits (61), Expect = 8.5
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 231 PADLELLFDIFINAVRDSKTRTPVPPIRKTIYDTLVPKDEAL 272
DL + + + ++R P KT+ D P EAL
Sbjct: 96 AEDLAEILQAGLEGI---QSRGKATPGEKTMVDVWAPVVEAL 134
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 28.1 bits (63), Expect = 8.7
Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 4/63 (6%)
Query: 220 SVQFHPEHTAGPADLELLFDIFINAVRDSKTR-TPVPPIRKTIYDTLVPKDEALIAKSFQ 278
+V+F P L+ D+ I+ + P + D V A +
Sbjct: 743 TVRFVPISEDSARALKDAQDVAISNLDSLSLLSLPDSLALPSYEDPGVL---ARVPADGD 799
Query: 279 TPK 281
+PK
Sbjct: 800 SPK 802
>gnl|CDD|183878 PRK13181, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 199
Score = 27.5 bits (62), Expect = 8.8
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 218 FFSVQFHPE--HTAGPADLE 235
++VQFHPE AG L+
Sbjct: 175 IYAVQFHPEKSGKAGLKLLK 194
>gnl|CDD|146870 pfam04441, Pox_VERT_large, Poxvirus early transcription factor
(VETF), large subunit. The poxvirus early transcription
factor (VETF), in addition to the viral RNA polymerase,
is required for efficient transcription of early genes
in vitro. VETF is a heterodimeric protein that binds
specifically to early gene promoters. The heterodimer is
comprised of an 82 kDa (this family) subunit and a 70
kDa subunit.
Length = 700
Score = 27.8 bits (62), Expect = 9.2
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 7/82 (8%)
Query: 257 IRKTI-YDTLV--PKDEALIAKSFQTPKKTSVRKMREDNGIRPYNKQ--IDTLAAEHPAQ 311
++K + D + P D + F P T++R + +NG+ ID
Sbjct: 576 VKKQLDSDRITFFPPDRNKLKDLF--PYITNIRTIISENGLTLTTDGFYIDGELFTEKLS 633
Query: 312 TNYLYLTYNATAHDLAVKETVS 333
T + T N T ++ + S
Sbjct: 634 TKFTTFTKNITTSPKSISKYFS 655
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
0.319 0.136 0.421
Gapped
Lambda K H
0.267 0.0911 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,336,409
Number of extensions: 1658944
Number of successful extensions: 1428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1405
Number of HSP's successfully gapped: 83
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
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: 59 (26.2 bits)