RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18158
(654 letters)
>gnl|CDD|203124 pfam04928, PAP_central, Poly(A) polymerase central domain. The
central domain of Poly(A) polymerase shares structural
similarity with the allosteric activity domain of
ribonucleotide reductase R1, which comprises a
four-helix bundle and a three-stranded mixed beta-
sheet. Even though the two enzymes bind ATP, the
ATP-recognition motifs are different.
Length = 349
Score = 579 bits (1494), Expect = 0.0
Identities = 219/345 (63%), Positives = 261/345 (75%)
Query: 28 TYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKE 87
YG+T ++ + P DL+ T L E LK + E++EE R EVL KLN LVKEW+K+
Sbjct: 3 QYGVTKPISTAGPTPADLELTDSLIEFLKEEGLFESEEESKKREEVLEKLNKLVKEWVKK 62
Query: 88 VSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLK 147
VS K +P AE GGKI+TFGSYRLGVH G+DID LCVAP+HV R D+FSSF+E LK
Sbjct: 63 VSEQKGMPERAAEAAGGKIFTFGSYRLGVHGPGSDIDTLCVAPKHVTREDFFSSFYEILK 122
Query: 148 TVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPDDMDLRDDMLLKNLDQKCV 207
EVT+L VE+AFVP+IK FDGIEID+LFA LAL +PDD+DL DD LL+NLD+K V
Sbjct: 123 LRPEVTELVPVEDAFVPIIKFKFDGIEIDLLFASLALPRVPDDLDLLDDSLLRNLDEKSV 182
Query: 208 RSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQ 267
RSLNGCRVTDEILRLVPN + FR ALR IKLWAK+ GIYSNVLG+LGGV+WA+LVAR+CQ
Sbjct: 183 RSLNGCRVTDEILRLVPNKDVFRTALRAIKLWAKRRGIYSNVLGFLGGVAWAILVARVCQ 242
Query: 268 LYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITP 327
LYPNA+ STLV KFF +FSQW+WP PVLLK + L F VWDPR+ +DRYHLMPIITP
Sbjct: 243 LYPNASPSTLVRKFFRIFSQWQWPNPVLLKPIEEGPLNFRVWDPRLYPSDRYHLMPIITP 302
Query: 328 AYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFE 372
AYP NST NV+ ST ++ EEFK+G I+ +I GK W LFE
Sbjct: 303 AYPSMNSTHNVTRSTLKVITEEFKRGLEITSEILLGKAPWSDLFE 347
>gnl|CDD|240410 PTZ00418, PTZ00418, Poly(A) polymerase; Provisional.
Length = 593
Score = 536 bits (1382), Expect = 0.0
Identities = 245/608 (40%), Positives = 349/608 (57%), Gaps = 56/608 (9%)
Query: 3 FTQHSNSMQTSKPHQDGKPQSQAPVTYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSE 62
F+Q S+S ++ ++YG+T ++L+ P + DL+ + EL LK YN+ E
Sbjct: 27 FSQLSSSKSENEETYLSYSIEC-ALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYE 85
Query: 63 TDEELSSRMEVLSKLNNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGAD 122
T+E R VL LN LV+E++ E SI + I A ++ GK++TFGSYRLGV G+D
Sbjct: 86 TEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQISGKLFTFGSYRLGVVAPGSD 145
Query: 123 IDALCVAPRHVDRADYFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARL 182
ID LC+APRH+ R +FS F+ KL+ +T L+ V +A+ PVIK +DGI+ID+LFA L
Sbjct: 146 IDTLCLAPRHITRESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANL 205
Query: 183 ALKEIPDDM-DLRDDMLLKNLDQKCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWAK 241
L IPD + L DD +L+N+D+K VRSLNGCRV D IL VPN + FR LR IKLWAK
Sbjct: 206 PLPTIPDCLNSLDDDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAK 265
Query: 242 KHGIYSNVLGYLGGVSWAMLVARICQLYPNAAASTLVCKFFLVFSQWKWPQPVLL---KK 298
+ GIYSNVLGYLGGVSWA+L ARICQLYPN A S L+ KFF V+S W W PVLL K+
Sbjct: 266 RRGIYSNVLGYLGGVSWAILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKE 325
Query: 299 PDNVN--LGFPVWDPRVNVADRYHLMPIITPAYPQQNSTFNVSISTRTIMQEEFKQGKTI 356
N+ + F VWDPRVN DR HLMPIITPA+P NST NV+ +T+ ++ EEFK+ I
Sbjct: 326 VPNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEFKRAHEI 385
Query: 357 SEDI-YNGKTMWDKLFETPNFFTKYRHYLVLIASSVSAEDQLEWCGLIESKVRHLIGNLE 415
+ I N + W + E +FFT Y+H+LV+ + + +W G IESK+R LI LE
Sbjct: 386 IKYIEKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKKLE 445
Query: 416 RNPHINLAHVNPECYTDTTGVIANGSGSPEITAEGKEEGGENTSPPVSGVASMWFIGLDF 475
++ + P+ + +++G + AS +FIGL F
Sbjct: 446 TLNNLKIRPY-PKFFKY------------------QDDGWD--------YASSFFIGLVF 478
Query: 476 IAANV----ILNLTYDIQHFTNAV-HWQATQSKMMKDGMKIEVRHVKKKQLSEYLPAHML 530
+ NV +L Y I+ F + + +W + + D + I ++++KK QL ++ +
Sbjct: 479 FSKNVYNNSTFDLRYAIRDFVDIINNW--PEMEKYPDQIDINIKYLKKSQLPAFVLSQTP 536
Query: 531 KKDKKTKSGDQNTSAKKRKSDQALDELGDKSRPRLDSDSNSLSDKVNNISNNGDQSSSEC 590
++ KTK+ + ++ S Q S S S+ +N S+ SS+E
Sbjct: 537 EEPVKTKANTKTNTSSATTSGQ-------------SGSSGSTSNSNSNESSP-TMSSTEL 582
Query: 591 TEDNSLSQ 598
+S S
Sbjct: 583 LNVSSTST 590
>gnl|CDD|227513 COG5186, PAP1, Poly(A) polymerase [RNA processing and
modification].
Length = 552
Score = 485 bits (1250), Expect = e-166
Identities = 211/549 (38%), Positives = 313/549 (57%), Gaps = 30/549 (5%)
Query: 29 YGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKEV 88
YG+T L+ + + + EL + LK E D+E +R+ VL KL +V+E++ V
Sbjct: 7 YGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARV 66
Query: 89 SIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLKT 148
S K + +A GGKI+T+GSYRLGVH G+DID L V P+HV R+D+F+ F+E+L+
Sbjct: 67 SRNKGMGDGMARPAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRE 126
Query: 149 VDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPDDMDLRDDMLLKNLDQKCVR 208
E+ ++ V +AFVP+IK+ F GI ID++FARL++ +PD ++L DD LLK++D+KC+
Sbjct: 127 RPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSIPVVPDGLNLSDDNLLKSMDEKCIL 186
Query: 209 SLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQL 268
SLNG RVTDEIL LVP+++ F ALR IK WA++ +Y+N G+ GGV+WAM VARICQL
Sbjct: 187 SLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQL 246
Query: 269 YPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITPA 328
YPNA++ +VCKFF + S W WPQPV+LK ++ L VW+P+V +D+YH MP+ITPA
Sbjct: 247 YPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPA 306
Query: 329 YPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTKYRHYLVLIA 388
YP +T N++ ST+ ++ EF + I DI W +LFE +FF++Y+ YL + A
Sbjct: 307 YPSMCATHNITNSTQHVILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITA 366
Query: 389 SSVSAEDQLEWCGLIESKVRHLIGNLERNPHINLAHVNPECY--------TDTTGVIANG 440
S ED L+W GL+ESK+R L+ LE I AH P+ + ++ I +G
Sbjct: 367 MSSCEEDFLKWEGLVESKIRILVSKLEAVDDILYAHPFPKAFRKVYNCVAEESIEKIGSG 426
Query: 441 SGSPE----------ITAEGKEEGGENTSPPVSGVASMWFIGLDFIAANVI--LNLTYDI 488
EE V + ++IGLD I +++ +
Sbjct: 427 VTLEVAYESTDHEKLANDTVPEEESMEDGMKVY--CTTFYIGLDVIPVKPGKKVDIEQPV 484
Query: 489 QHFTNAVH-WQATQSKMMKDGMKIEVRHVKKKQLSE---YLPAHMLKKDKKTKSGDQNTS 544
+ F + + GM IEV +K+K L + Y K + D S
Sbjct: 485 KEFIELCREYDEGDAS----GMNIEVNSLKRKDLPDEVFYPGEERPSNSSKRRRVDTAHS 540
Query: 545 AKKRKSDQA 553
++ K +
Sbjct: 541 TEQLKRQKV 549
>gnl|CDD|218331 pfam04926, PAP_RNA-bind, Poly(A) polymerase predicted RNA binding
domain. Based on its similarity structurally to the RNA
recognition motif this domain is thought to be RNA
binding.
Length = 141
Score = 145 bits (369), Expect = 4e-41
Identities = 54/166 (32%), Positives = 84/166 (50%), Gaps = 29/166 (17%)
Query: 375 NFFTKYRHYLVLIASSVSAEDQLEWCGLIESKVRHLIGNLERNPHINLAHVNPECYTDTT 434
+FFTKY+HYL + AS+ + ED L+W G +ESK+R L+ LER I LAH P+ + +
Sbjct: 1 DFFTKYKHYLQITASAKNEEDHLKWSGWVESKLRLLVLKLERVEGIKLAHPFPKGFEE-- 58
Query: 435 GVIANGSGSPEITAEGKEEGGENTSPPVSGVASMWFIGLDFI----AANVILNLTYDIQH 490
E EE E + +FIGL+ + L++TY IQ
Sbjct: 59 -------------DESDEESKEIY-------TTSFFIGLELKKKKEEGSKKLDITYAIQE 98
Query: 491 FTNAVHWQATQSKMMKDGMKIEVRHVKKKQLSEYLPAHMLKKDKKT 536
F + V + + GM IE++HVK+K L +++ ++ KK+
Sbjct: 99 FKDIVR---SWPQYRPPGMDIEIKHVKRKDLPDFVFPEGEQRPKKS 141
>gnl|CDD|143392 cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT) domain of
poly(A) polymerases and terminal uridylyl transferases.
Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail
synthesis, and terminal uridylyl transferases (TUTases)
uridylate RNA. PAPs in this subgroup include human PAP
alpha, mouse testis-specific cytoplasmic PAP beta, human
nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4
and-5, Schizosaccharomyces pombe caffeine-induced death
proteins -1, and -14, Caenorhabditis elegans Germ Line
Development-2, and Chlamydomonas reinhardtii MUT68. This
family also includes human U6 snRNA-specific TUTase1,
and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This
family belongs to the Pol beta-like NT superfamily. In
the majority of enzymes in this superfamily, two
carboxylates, Dx[D/E], together with a third more distal
carboxylate, coordinate two divalent metal cations
involved in a two-metal ion mechanism of nucleotide
addition. For the majority of proteins in this family,
these carboxylate residues are conserved.
Length = 114
Score = 100 bits (251), Expect = 3e-25
Identities = 47/157 (29%), Positives = 62/157 (39%), Gaps = 47/157 (29%)
Query: 70 RMEVLSKLNNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVA 129
R EVL +L L+KEW G K+Y FGSY G+ G+DID +
Sbjct: 2 REEVLDRLQELIKEWFP----------------GAKLYPFGSYVTGLGLPGSDIDLCLLG 45
Query: 130 PRH-VDRADYFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFD--GIEIDMLFARLALKE 186
P H VDR D+ + LK EV ++ + A VP+IK GIE+D+ F
Sbjct: 46 PNHRVDREDFLRKLAKLLKKSGEVVEVEPIINARVPIIKFVDKPTGIEVDISFNN----- 100
Query: 187 IPDDMDLRDDMLLKNLDQKCVRSLNGCRVTDEILRLV 223
LNG R T + V
Sbjct: 101 -----------------------LNGIRNTKLLRAYV 114
>gnl|CDD|216779 pfam01909, NTP_transf_2, Nucleotidyltransferase domain. Members of
this family belong to a large family of
nucleotidyltransferases. This family includes kanamycin
nucleotidyltransferase (KNTase) which is a plasmid-coded
enzyme responsible for some types of bacterial
resistance to aminoglycosides. KNTase in-activates
antibiotics by catalyzing the addition of a nucleotidyl
group onto the drug.
Length = 92
Score = 58.3 bits (141), Expect = 9e-11
Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 4/95 (4%)
Query: 91 AKNIPPTVAEKVGG-KIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLKTV 149
I + E G ++ FGSY G + G+DID L V+P +D + E ++ +
Sbjct: 1 LSKIKEILKELYGVAEVVLFGSYARGTYLPGSDIDLLVVSPDPLDEEEELEELAEIIEEL 60
Query: 150 DEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLAL 184
+E L +E V K+ + ID+L R+ L
Sbjct: 61 EE---LLGLEVDLVTREKLEIPLVRIDILEERVLL 92
>gnl|CDD|143387 cd05397, NT_Pol-beta-like, Nucleotidyltransferase (NT) domain of
DNA polymerase beta and similar proteins. This
superfamily includes the NT domains of DNA polymerase
beta and other family X DNA polymerases, as well as the
NT domains of Class I and Class II CCA-adding enzymes,
RelA- and SpoT-like ppGpp synthetases and hydrolases,
2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli
adenylyltransferase (GlnE), Escherichia coli uridylyl
transferase (GlnD), poly (A) polymerases, terminal
uridylyl transferases, and Staphylococcus aureus
kanamycin nucleotidyltransferase, and similar proteins.
The Escherichia coli CCA-adding enzyme belongs to this
superfamily but is not included as this enzyme lacks the
N-terminal helix conserved in the remainder of the
superfamily. In the majority of the Pol beta-like
superfamily NTs, two carboxylates, Dx[D/E], together
with a third more distal carboxylate coordinate two
divalent metal cations that are essential for catalysis.
These divalent metal ions are involved in a two-metal
ion mechanism of nucleotide addition. Two of the three
catalytic carboxylates are found in Rel-Spo enzymes,
with the second carboxylate of the DXD motif missing.
Evidence supports a single-cation synthetase mechanism
for Rel-Spo enzymes.
Length = 49
Score = 35.0 bits (81), Expect = 0.006
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 12/48 (25%)
Query: 81 VKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCV 128
+KE +K+ G +I +GS G+ K +DID CV
Sbjct: 7 IKERLKK------------LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42
>gnl|CDD|227585 COG5260, TRF4, DNA polymerase sigma [DNA replication,
recombination, and repair].
Length = 482
Score = 37.1 bits (86), Expect = 0.029
Identities = 36/158 (22%), Positives = 60/158 (37%), Gaps = 32/158 (20%)
Query: 34 ALNLSPPNQLDLQRTRELAECLKPYN-VSETDEELSSRMEVLSKLNNLVKEWIKEVSIAK 92
L LS + + + +E L+ Y+ ++ +DEEL R +L KL L+K+ +
Sbjct: 41 LLELSIDSVFNEESDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDAD--- 97
Query: 93 NIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRAD------YFSSFFEKL 146
+ FGS G+ +DID ++ + F + L
Sbjct: 98 -------------LKVFGSTETGLALPKSDIDLCIISDPRGYKETRNAGSLASHLFKKNL 144
Query: 147 KTVDEVTDLRAVEEAFVPVIKMNFD---GIEIDMLFAR 181
V V A VP+IK+ D G+ D+ F
Sbjct: 145 AKEVVV-----VSTARVPIIKL-VDPQSGLHCDISFNN 176
>gnl|CDD|143393 cd05403, NT_KNTase_like, Nucleotidyltransferase (NT) domain of
Staphylococcus aureus kanamycin nucleotidyltransferase,
and similar proteins. S. aureus KNTase is a plasmid
encoded enzyme which confers resistance to a wide range
of aminoglycoside antibiotics which have a 4'- or
4''-hydroxyl group in the equatorial position, such as
kanamycin A. This enzyme transfers a nucleoside
monophosphate group from a nucleotide (ATP,GTP, or UTP)
to the 4'-hydroxyl group of kanamycin A. This enzyme is
a homodimer, having two NT active sites. The nucleotide
and antibiotic binding sites of each active site include
residues from each monomer. Included in this subgroup is
Escherichia coli AadA5 which confers resistance to the
antibiotic spectinomycin and is a putative
aminoglycoside-3'-adenylyltransferase. It is part of the
aadA5 cassette of a class 1 integron. This subgroup also
includes Haemophilus influenzae HI0073 which forms a 2:2
heterotetramer with an unrelated protein HI0074.
Structurally HI0074 is related to the substrate-binding
domain of S. aureus KNTase. The genes encoding HI0073
and HI0074 form an operon. Little is known about the
substrate specificity or function of two-component NTs.
The characterized members of this subgroup may not be
representive of the function of this subgroup. This
subgroup belongs to the Pol beta-like NT superfamily. In
the majority of enzymes in this superfamily, two
carboxylates, Dx[D/E], together with a third more distal
carboxylate, co-ordinate two divalent metal cations
involved in a two-metal ion mechanism of nucleotide
addition. These carboxylate residues are conserved in
this subgroup.
Length = 93
Score = 33.2 bits (76), Expect = 0.076
Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 9/98 (9%)
Query: 82 KEWIKEV-SIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFS 140
+E ++E+ I + + V K+Y FGSY G +DID L + +D +
Sbjct: 1 EEILEEILEILRELLGGVE-----KVYLFGSYARGDARPDSDIDLLVIFDDPLDPLELAR 55
Query: 141 SFFEKLKTVD---EVTDLRAVEEAFVPVIKMNFDGIEI 175
E + ++ L A+E + I + +GI +
Sbjct: 56 LLEELELLLGRPVDLVVLNALELELLLRILIEGEGIYL 93
>gnl|CDD|237340 PRK13300, PRK13300, tRNA CCA-pyrophosphorylase; Provisional.
Length = 447
Score = 32.6 bits (75), Expect = 0.80
Identities = 31/128 (24%), Positives = 48/128 (37%), Gaps = 16/128 (12%)
Query: 51 LAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFG 110
L E L+ + T+EE +V +L ++E IKE+ + ++ G
Sbjct: 3 LEEVLE--RIKPTEEEREKLKKVAEELIERLEEAIKELGLD------------AEVELVG 48
Query: 111 SYRLGVHHKG-ADIDALCVAPRHVDRADYFSSFFEKLKTVDEVTDLRAVEE-AFVPVIKM 168
S G G DID + P+ R + E K V + E A P +
Sbjct: 49 STARGTWLSGDRDIDIFVLFPKDTSREELEEKGLEIGKEVAKELLGDYEERYAEHPYVTG 108
Query: 169 NFDGIEID 176
DG E+D
Sbjct: 109 EIDGFEVD 116
>gnl|CDD|215331 PLN02613, PLN02613, endoglucanase.
Length = 498
Score = 31.4 bits (71), Expect = 1.9
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 109 FGS-YRLGVHHKGADIDALCVAPRHVDRADYFSSFF 143
FG+ Y +HH+G+ I ++ V P VD FSS++
Sbjct: 392 FGTKYPTQIHHRGSSIPSIQVLPEKVDCNGGFSSYY 427
>gnl|CDD|131968 TIGR02922, TIGR02922, TIGR02922 family protein. Two members of
this family are found in Colwellia psychrerythraea 34H
and one each in various other species of Colwellia and
Shewanella. One member from C. psychrerythraea is of
special interest because it is preceded by the same
cis-regulatory site as a number of genes that have the
PEP-CTERM domain described by TIGR02595 [Hypothetical
proteins, Conserved].
Length = 67
Score = 28.2 bits (63), Expect = 2.0
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 336 FNVSISTRTIMQEEFKQGKTI 356
F V+ S R ++ +EFK+GK+I
Sbjct: 27 FPVNESGRVMIPQEFKRGKSI 47
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 31.0 bits (71), Expect = 2.4
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 27 VTYGMTTALNLSPPNQLDLQRT-RELAECLKPYNVSETDEELSSRM 71
TY +TT SP ++ + T + A+ + + S+ D E M
Sbjct: 208 PTYNITTDFWESPNDEDLFEMTAKYGAKYGQNFFNSDLDPEDVRSM 253
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 30.9 bits (70), Expect = 2.7
Identities = 23/94 (24%), Positives = 31/94 (32%), Gaps = 5/94 (5%)
Query: 531 KKDKKTKSGDQNTSAKKRKSDQALDELGDKS-----RPRLDSDSNSLSDKVNNISNNGDQ 585
DKK + D +TS D L + D+ SL+ + N+ N
Sbjct: 73 NNDKKFSTIDSSTSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSD 132
Query: 586 SSSECTEDNSLSQVYGLNDSVADSIDNSLDDLSS 619
S NS N + SI N D SS
Sbjct: 133 ISDYEQPRNSEKSTNDSNKNSDSSIKNDTDTQSS 166
Score = 30.1 bits (68), Expect = 4.6
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 12/95 (12%)
Query: 530 LKKDKKTKSGDQNTSAKKRKS---DQALDELGDKSRPRLDSDSNSLSDKVNNISNNGDQS 586
+K D T+S Q+ + ++ + + + N + + + +S
Sbjct: 157 IKNDTDTQSSKQDKADNQKAPSSNNTKPSTSNKQPNSPKPTQPNQSNSQPASDDTANQKS 216
Query: 587 SSECTEDNSLSQVYGLNDSVADSI-DNSLDDLSST 620
SS+ + S DS DSI D +D T
Sbjct: 217 SSKDNQSMS--------DSALDSILDQYSEDAKKT 243
>gnl|CDD|118094 pfam09558, DUF2375, Protein of unknown function (DUF2375). Two
members of this family are found in Colwellia
psychrerythraea (strain 34H / ATCC BAA-681) and one each
in various other species of Colwellia and Shewanella.
One member from C. psychrerythraea is of special
interest because it is preceded by the same
cis-regulatory site as a number of genes that have the
PEP-CTERM domain described by PEP_anchor (IPR013424).
Length = 71
Score = 27.8 bits (62), Expect = 3.2
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 336 FNVSISTRTIMQEEFKQGKTI 356
VS + R ++ +EF++GK+I
Sbjct: 29 LPVSETGRVMIPQEFRRGKSI 49
>gnl|CDD|238281 cd00504, GXGXG, GXGXG domain. This domain of unknown function is
found at the C-terminus of the large subunit (gltB) of
glutamate synthase (GltS), in subunit C of tungsten
formylmethanofuran dehydrogenase (FwdC) and in subunit C
of molybdenum formylmethanofuran dehydrogenase (FmdC).
It is also found in a primarily archeal group of
proteins predicted to encode part of the large subunit
of GltS. It is characterized by a repeated GXXGXXXG
motif. GltS is a complex iron-sulfur flavoprotein that
catalyzes the synthesis of L-glutamate from L-glutamine
and 2-oxoglutarate. It requires the transfer of ammonia
and electrons among three distinct active centers that
carry out L-Gln hydrolysis, conversion of 2-oxoglutarate
into L-Glu, and electron uptake from a donor. These
catalytic sites occur in other domains within the
protein or or encoded by separate genes, and are not
present in the domain in this CD. FwdC and FmdC are
reversible ion pumps that catalyze the formylation and
deformylation of methanofuran in hyperthermophiles and
bacteria. They require the presence of either tungstun
(FwdC) or molybdenum (FmdC). The specific function of
this domain also remains unidentified in the
formylmethanofuran dehydrogenases.
Length = 149
Score = 29.5 bits (67), Expect = 3.2
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 103 GGKIYTFGS--YRLGVHHKGADI 123
GGKI+ G+ R GV G I
Sbjct: 85 GGKIFVRGNAGERFGVRMSGGTI 107
>gnl|CDD|219615 pfam07876, Dabb, Stress responsive A/B Barrel Domain. The function
of this family is unknown, but it is upregulated in
response to salt stress in Populus balsamifera. It is
also found at the C-terminus of an fructose
1,6-bisphosphate aldolase from Hydrogenophilus
thermoluteolus. Arthrobacter nicotinovorans ORF106 is
found in the pA01 plasmid, which encodes genes for
molybdopterin uptake and degradation of plant alkaloid
nicotine. The structure of one has been solved and the
domain forms an a/b barrel dimer. Although there is a
clear duplication within the domain it is not obviously
detectable in the sequence.
Length = 96
Score = 28.0 bits (63), Expect = 4.6
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 63 TDEELSSRMEVLSKLNNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGAD 122
++EE++ +E L L + IK + + +N+ P G + YT D
Sbjct: 14 SEEEIAEVLEGLEALKGEIPG-IKSIEVGRNVSPE-----GNQGYTHALV--SEFESKED 65
Query: 123 IDALCVAPRHVDRADYFSSFFEKLKTVD 150
+DA P HV + EK VD
Sbjct: 66 LDAYLTHPAHVAFVERVKPLVEKRVVVD 93
>gnl|CDD|224622 COG1708, COG1708, Predicted nucleotidyltransferases [General
function prediction only].
Length = 128
Score = 28.4 bits (63), Expect = 5.0
Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 4/96 (4%)
Query: 105 KIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLKTVDEVTDLRAVEEAFVP 164
IY FGSY G K +DID L V+ D + L +++ A + V
Sbjct: 28 LIYLFGSYARGDFVKESDIDLLVVSD---DNPLLVIERLKILADLEKELGKVADKLLPVD 84
Query: 165 VIKMNFDGIEIDMLFARLALKEIPDDMDLRDDMLLK 200
V ++ + E+ L + +E+ D +L ++ +
Sbjct: 85 VHILDPEEYEVLFLRLVIG-EELDVDRELFREIRRE 119
>gnl|CDD|227925 COG5638, COG5638, Uncharacterized conserved protein [Function
unknown].
Length = 622
Score = 29.8 bits (66), Expect = 5.9
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 12/77 (15%)
Query: 120 GADIDALCVAPRHVDRADYFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLF 179
G + D + + ++R Y+ + E +++ + + DG+E +
Sbjct: 240 GNEFDMVKLRQYQLERLRYYYAVVE----CEDIETSKNIYS--------ACDGVEYENSA 287
Query: 180 ARLALKEIPDDMDLRDD 196
L L+ +PD + DD
Sbjct: 288 NVLDLRFVPDSLTFDDD 304
>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 575
Score = 29.3 bits (66), Expect = 7.3
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 210 LNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAM 260
L GCR EI RL P+++ + + AK H I S+ + GG++ ++
Sbjct: 13 LAGCRAALEIKRLDPSLD--------VAVVAKTHPIRSHSVAAQGGIAASL 55
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 29.0 bits (65), Expect = 8.4
Identities = 20/109 (18%), Positives = 42/109 (38%), Gaps = 10/109 (9%)
Query: 531 KKDKKTKSGDQNTSAKKRK------SDQALDELGDKSRPRLDSDSNSLSDKVNN----IS 580
KK KK+K + S+ K D++ E + + + +S S+ + +
Sbjct: 153 KKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLV 212
Query: 581 NNGDQSSSECTEDNSLSQVYGLNDSVADSIDNSLDDLSSTSPHPTPPVK 629
++ D+ E + ++ ++S + S S S +PP K
Sbjct: 213 DSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSEESSPPSK 261
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 0.133 0.394
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,085,685
Number of extensions: 3259005
Number of successful extensions: 2836
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2825
Number of HSP's successfully gapped: 32
Length of query: 654
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 551
Effective length of database: 6,369,140
Effective search space: 3509396140
Effective search space used: 3509396140
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 (21.6 bits)
S2: 62 (27.5 bits)