RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2898
(222 letters)
>gnl|CDD|237682 PRK14343, PRK14343, lipoate-protein ligase B; Provisional.
Length = 235
Score = 275 bits (706), Expect = 1e-94
Identities = 101/204 (49%), Positives = 137/204 (67%), Gaps = 8/204 (3%)
Query: 13 LQIIQRGLEPYIVSFNAMLLFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLN 72
+ + RG EPY F+AM F RT T D++W VEH PVYTLG + +H+L++ +
Sbjct: 15 VTVRWRGREPYEACFDAMRAFTDARTADTPDEIWLVEHPPVYTLGQAGDPAHLLVAD--S 72
Query: 73 NIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYN 132
IP+++ DRGG++TYHGPGQ + YLL+DLRRR K+ +++LV IE+AVI T++ YN
Sbjct: 73 GIPLVKVDRGGQITYHGPGQVVAYLLLDLRRR-----KLMVRELVTRIEQAVIDTLAAYN 127
Query: 133 INCKRKKNAPGVYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGY 192
+ +RK APG+Y+A+GP GAKIA++GLKI G YHG+S+NV MDL PF INPCGY
Sbjct: 128 LASERKAGAPGIYVASGPHQGAKIAALGLKIR-NGCSYHGLSLNVKMDLRPFLAINPCGY 186
Query: 193 PGLVIVDMKKLGINTTISKVQHLF 216
GL VDM LG+ + V
Sbjct: 187 AGLETVDMASLGVAADWADVAQTL 210
>gnl|CDD|237681 PRK14342, PRK14342, lipoate-protein ligase B; Provisional.
Length = 213
Score = 244 bits (624), Expect = 2e-82
Identities = 88/209 (42%), Positives = 128/209 (61%), Gaps = 14/209 (6%)
Query: 12 NLQIIQRGLEPYIVSFNAMLLFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKL 71
L + Q GL+PY + AM F R T D++W VEH PV+T G HIL
Sbjct: 5 KLIVRQLGLQPYEPVWQAMQEFTDTRDEETPDEIWLVEHPPVFTQGQAGKPEHILNP--- 61
Query: 72 NNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQY 131
+IP++++DRGG+VTYHGPGQ ++Y+L+DL+R K+ +++LV IE+ VI T+++Y
Sbjct: 62 GDIPVVQSDRGGQVTYHGPGQLVMYVLLDLKRL-----KLGVRQLVTAIEQTVINTLAEY 116
Query: 132 NINCKRKKNAPGVYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCG 191
I K +APGVY+ G KIAS+GL+I +G +HG+++NV+MDL PF INPCG
Sbjct: 117 GIEAHAKPDAPGVYVD-----GKKIASLGLRIR-RGCSFHGLALNVNMDLSPFLRINPCG 170
Query: 192 YPGLVIVDMKKLGINTTISKVQHLFIKNF 220
Y GL + + LG T+ +V +
Sbjct: 171 YAGLEMTQLSDLGGPATVDEVAPRLLAEL 199
>gnl|CDD|223398 COG0321, LipB, Lipoate-protein ligase B [Coenzyme metabolism].
Length = 221
Score = 219 bits (561), Expect = 1e-72
Identities = 80/217 (36%), Positives = 129/217 (59%), Gaps = 14/217 (6%)
Query: 5 SISSTYSNLQIIQRGLEPYIVSFNAMLLFNSNRTNYTI-DQLWFVEHFPVYTLGLKSNFS 63
S S + + + GL Y ++ M F R + D++W VEH PVYT G
Sbjct: 3 SPRSKPKIILVRELGLVDYQEAWQLMETFTDARADGGTPDEIWLVEHPPVYTAGQAGKAE 62
Query: 64 HILISKKLNNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEA 123
H+L+ ++IP+++TDRGG+VTYHGPGQ + Y ++DL+R K+ +++ V +E+A
Sbjct: 63 HLLMP---DDIPVVQTDRGGQVTYHGPGQLVAYPILDLKRP-----KLDVREYVRALEQA 114
Query: 124 VILTMSQYNINCKRKKNAPGVYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEP 183
VI T+++Y I +R+ + PGV++ KIA+IG++I +G +HG+++NV+MDL P
Sbjct: 115 VINTLAEYGIEAERRPDRPGVWVEEE----RKIAAIGIRIR-RGVTFHGLALNVNMDLSP 169
Query: 184 FNNINPCGYPGLVIVDMKKLGINTTISKVQHLFIKNF 220
FN I PCGY G+ + + LG T+ +V + F
Sbjct: 170 FNRIVPCGYAGMEVTSLSDLGPPVTVDEVAKALVAAF 206
>gnl|CDD|237684 PRK14346, PRK14346, lipoate-protein ligase B; Provisional.
Length = 230
Score = 193 bits (493), Expect = 2e-62
Identities = 90/219 (41%), Positives = 123/219 (56%), Gaps = 32/219 (14%)
Query: 13 LQIIQRGLEPYIVSFNAMLLFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLN 72
+ G Y+ + AM F + RT T D+LW EH PVYT GL H+L
Sbjct: 3 MDRRMLGRVDYLATVQAMQAFTAERTPETPDELWICEHPPVYTQGLAGKADHVLNP---G 59
Query: 73 NIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYN 132
+IP++ T+RGG+VTYHGPGQ + Y LIDLRR ++K+ V IEEAVI T++ +
Sbjct: 60 DIPVVATNRGGQVTYHGPGQVVAYPLIDLRR-----AGYFVKEYVYRIEEAVIRTLAHFG 114
Query: 133 INCKRKKNAPGVYI----------------------ANGPFSG-AKIASIGLKISAKGYV 169
+ R APG+Y+ PF G KIA++G+K+S +
Sbjct: 115 VTGHRVAGAPGIYVRLDDPFSHAALPQRPQKRGGGAPQPPFRGLGKIAALGIKVS-RHCT 173
Query: 170 YHGVSINVSMDLEPFNNINPCGYPGLVIVDMKKLGINTT 208
YHGV++NV+MDLEPF+ INPCGY GL VD+ +G+ TT
Sbjct: 174 YHGVALNVAMDLEPFSRINPCGYAGLQTVDLSTIGVQTT 212
>gnl|CDD|172825 PRK14349, PRK14349, lipoate-protein ligase B; Provisional.
Length = 220
Score = 186 bits (473), Expect = 1e-59
Identities = 78/191 (40%), Positives = 114/191 (59%), Gaps = 10/191 (5%)
Query: 23 YIVSFNAMLLFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLNNIPIIRTDRG 82
Y ++AM F + R T D++W EH PVYTLG H+L IP++ DRG
Sbjct: 11 YASVWDAMKAFTAARGPGTADEIWLCEHAPVYTLGQAGRPEHLL---NPGLIPVVHCDRG 67
Query: 83 GEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYNI-NCKRKKNA 141
G+VTYHGPGQ + Y L DLRR +Y+++ V+ +E+A + T+ + + RK A
Sbjct: 68 GQVTYHGPGQVLAYTLFDLRR-----AGLYVREYVDMLEQATLATLRELGLEQACRKPGA 122
Query: 142 PGVYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGYPGLVIVDMK 201
PG+Y+ AKIA++G+K+ GY YHG+++N+ MDL PF INPCGY GL VD+
Sbjct: 123 PGIYVPQPGGELAKIAALGVKVR-NGYAYHGLALNIDMDLSPFLGINPCGYEGLRTVDLA 181
Query: 202 KLGINTTISKV 212
G+ T++ +
Sbjct: 182 ACGVRTSVERA 192
>gnl|CDD|232877 TIGR00214, lipB, lipoate-protein ligase B. Involved in lipoate
biosynthesis as the main determinant of the
lipoyl-protein ligase activity required for lipoylation
of enzymes such as alpha-ketoacid dehydrogenases.
Involved in activation and re-activation (following
denaturation) of lipoyl-protein ligases (calcium
ion-dependant process) [Protein fate, Protein
modification and repair].
Length = 184
Score = 163 bits (414), Expect = 5e-51
Identities = 65/185 (35%), Positives = 115/185 (62%), Gaps = 11/185 (5%)
Query: 36 NRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLNNIPIIRTDRGGEVTYHGPGQAII 95
R T+D++ VEH+PVYT G H+L + +++++RGG+VTYHGPGQ ++
Sbjct: 6 QRDRQTLDEIMLVEHYPVYTQGQAGKTEHLLFDPDIPPAEVVQSERGGQVTYHGPGQQVM 65
Query: 96 YLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYNINCKRKKNAPGVYIANGPFSGAK 155
Y+++DL+R ++ ++ LV +E+ VI+T+++ I + +A GV++ G K
Sbjct: 66 YVILDLKRF-----QLDVRWLVTQLEQTVIITLAELGIEGEPIADATGVWV-----EGKK 115
Query: 156 IASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGYPGLVIVDMKKLGINTTISKVQHL 215
+AS+G+++ +G +HG+++N++MDL PF++INPCGY G + + + T+ V L
Sbjct: 116 VASLGIRVR-RGCTFHGLALNINMDLSPFSHINPCGYAGREMGSLNQFLPGATVENVAPL 174
Query: 216 FIKNF 220
IK F
Sbjct: 175 LIKAF 179
>gnl|CDD|237680 PRK14341, PRK14341, lipoate-protein ligase B; Provisional.
Length = 213
Score = 138 bits (349), Expect = 9e-41
Identities = 59/172 (34%), Positives = 98/172 (56%), Gaps = 12/172 (6%)
Query: 44 QLWFVEHFPVYTLGLKSNFSHILISKKLNNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRR 103
+W +EH P+YT G + +L + P+ T RGG+ TYHGPGQ + Y+++DL+R
Sbjct: 37 LVWLLEHPPLYTAGTSAKAEDLLDP---DRFPVYETGRGGQYTYHGPGQRVAYVMLDLKR 93
Query: 104 RYSDNIKIYIKKLVENIEEAVILTMSQYNINCKRKKNAPGVYIAN---GPFSGAKIASIG 160
R D ++ V +EE +I T++ +NI +R+++ GV++ G + KIA+IG
Sbjct: 94 RRRD-----VRAFVAALEEWIIATLAAFNIRGERREDRVGVWVRRPDKGSGAEDKIAAIG 148
Query: 161 LKISAKGYVYHGVSINVSMDLEPFNNINPCGYPGLVIVDMKKLGINTTISKV 212
+++ + +HG+SINV DL F+ I PCG + + LG+ T+ V
Sbjct: 149 VRLR-RWVSFHGISINVEPDLSHFSGIVPCGISEHGVTSLVDLGLPVTMDDV 199
>gnl|CDD|237683 PRK14344, PRK14344, lipoate-protein ligase B; Provisional.
Length = 223
Score = 128 bits (324), Expect = 5e-37
Identities = 62/178 (34%), Positives = 93/178 (52%), Gaps = 13/178 (7%)
Query: 39 NYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLNNIPIIRTDRGGEVTYHGPGQAIIYLL 98
+W +EH YTLG ++ ++L S + R DRGGEVT+H PGQ + YL+
Sbjct: 47 PSNPQAVWLLEHQLCYTLGRGASEDNLLFSLNNPPADVFRIDRGGEVTHHMPGQLVTYLV 106
Query: 99 IDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYNINCKRKKNAPGVYIANGPFSGAKIAS 158
+DLRR D + Y+++L E+ +I ++ I+ +R GV+I N K+AS
Sbjct: 107 LDLRRFNKD-LNWYLRQL----EQVLIDVLADLGIDGERLDGLTGVWIGN-----KKVAS 156
Query: 159 IGLKISAKGYV-YHGVSINVSMDLEPFNNINPCGYPGLVIVDMKKLGINTTISKVQHL 215
IG I + ++ HG S+NV DLE FN I PCG G + + I +V+ L
Sbjct: 157 IG--IGCRRWITQHGFSLNVDCDLEGFNKIVPCGLEGCQVGRLSDWIPGLNIKEVKPL 212
>gnl|CDD|184638 PRK14345, PRK14345, lipoate-protein ligase B; Provisional.
Length = 234
Score = 116 bits (292), Expect = 5e-32
Identities = 59/189 (31%), Positives = 94/189 (49%), Gaps = 13/189 (6%)
Query: 5 SISSTYSNLQIIQRGLEPYIVSFNAMLLFNSNRTNYTI-DQLWFVEHFPVYTLGLKSNFS 63
SI S+ +++ + GL Y +++ R D L +EH VYT G K
Sbjct: 4 SIRSSTMPIEVRRLGLVDYQEAWDLQRELADARVAGEGPDTLLLLEHPAVYTAG-KRTEP 62
Query: 64 HILISKKLNNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEA 123
H + + P++ DRGG++T+HGPGQ + Y +I L + + V +EEA
Sbjct: 63 H---ERPTDGTPVVDVDRGGKITWHGPGQLVGYPIIKLAEP------LDVVDYVRRLEEA 113
Query: 124 VILTMSQYNINCKRKKNAPGVYI-ANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLE 182
+I + +N R GV++ A+G KIA+IG+++S +G HG ++N DL
Sbjct: 114 LIAVCADLGLNAGRVDGRSGVWVPADGGRPDRKIAAIGIRVS-RGVTMHGFALNCDNDLA 172
Query: 183 PFNNINPCG 191
F+ I PCG
Sbjct: 173 AFDAIVPCG 181
>gnl|CDD|172823 PRK14347, PRK14347, lipoate-protein ligase B; Provisional.
Length = 209
Score = 103 bits (259), Expect = 1e-27
Identities = 70/210 (33%), Positives = 108/210 (51%), Gaps = 20/210 (9%)
Query: 22 PYIVSFNAMLLFNSNRTNYTIDQ-----LWFVEHFPVYTLGLKSNFSHILISKKLNNIPI 76
P + L + N I ++ VEH VYT G +L +IP+
Sbjct: 8 PDFADYQVTLKLMEDYVNKVISDHEPEIVYLVEHSEVYTAGTNYKQEELL---NYGDIPV 64
Query: 77 IRTDRGGEVTYHGPGQAIIY--LLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYNIN 134
I T RGG+ T+HGPGQ +IY L + R+ D +K+YIK L EE +I +++ + I
Sbjct: 65 IYTGRGGKFTFHGPGQRVIYPILNLASPNRHKD-LKLYIKML----EEWIINSLNYFGIK 119
Query: 135 CKRKKNAPGVYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGYPG 194
K+ G+++ AKIA+IG+++ K YHGV+IN+S DL F+ I PCG
Sbjct: 120 AYIIKDKVGIWVKVRKDEFAKIAAIGVRVR-KWVTYHGVAINISTDLSKFSGIIPCGLEN 178
Query: 195 LVIVDMKKLGINTTISK----VQHLFIKNF 220
++ + +LGI+ +S+ +Q F K F
Sbjct: 179 SLVTSLNQLGIHVEMSEFDKIIQTEFNKIF 208
>gnl|CDD|172824 PRK14348, PRK14348, lipoate-protein ligase B; Provisional.
Length = 221
Score = 94.3 bits (234), Expect = 7e-24
Identities = 56/169 (33%), Positives = 97/169 (57%), Gaps = 10/169 (5%)
Query: 27 FNAMLLFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISK-KLNNI--PIIRTDRGG 83
F+A++ N +Y +++ F EH VYTLG +++L+ + +L I + DRGG
Sbjct: 24 FDALVHAKQNGESYE-NRIIFCEHPHVYTLGRSGKENNMLLGEEQLKTIGATLYHIDRGG 82
Query: 84 EVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQYNINCKRKKNAPG 143
++TYHGPGQ + Y +++L + + +K+ V +EEAVI + Y + R + A G
Sbjct: 83 DITYHGPGQLVCYPILNL-----EEFGLGLKEYVHLLEEAVIRVCASYGVVAGRLEKATG 137
Query: 144 VYIANGPFSGAKIASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGY 192
V++ KI +IG++ S+ HG+++NV+ DL F+ I+PCG+
Sbjct: 138 VWLEGDTSRARKICAIGVR-SSHYVTMHGLALNVNTDLRYFSYIHPCGF 185
>gnl|CDD|217367 pfam03099, BPL_LplA_LipB, Biotin/lipoate A/B protein ligase family.
This family includes biotin protein ligase,
lipoate-protein ligase A and B. Biotin is covalently
attached at the active site of certain enzymes that
transfer carbon dioxide from bicarbonate to organic
acids to form cellular metabolites. Biotin protein
ligase (BPL) is the enzyme responsible for attaching
biotin to a specific lysine at the active site of biotin
enzymes. Each organism probably has only one BPL. Biotin
attachment is a two step reaction that results in the
formation of an amide linkage between the carboxyl group
of biotin and the epsilon-amino group of the modified
lysine. Lipoate-protein ligase A (LPLA) catalyzes the
formation of an amide linkage between lipoic acid and a
specific lysine residue in lipoate dependent enzymes.
The unusual biosynthesis pathway of lipoic acid is
mechanistically intertwined with attachment of the
cofactor.
Length = 124
Score = 62.8 bits (153), Expect = 8e-13
Identities = 29/126 (23%), Positives = 51/126 (40%), Gaps = 11/126 (8%)
Query: 59 KSNFSHILISK-KLNNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYS---DNIKIYIK 114
KS + + + + + R GG +H PG + Y L+ L S ++ Y+
Sbjct: 6 KSTKEEVNLEGLEEGGVVVARRQTGGRRVWHSPGGNLAYSLLLLPELKSFKPSDLPAYVL 65
Query: 115 KLVENIEEAVILTMSQYNINCKRKKNAPGVYIANGPFSGAKIASIGLKISAKGYVYHGVS 174
LV + EA+ I + K P + N G KIA I +I +G H +
Sbjct: 66 LLVLAVLEALGPKAGIPGIWVRIKW--PNDLLVN----GKKIAGILQEIR-RGGTLHHGT 118
Query: 175 INVSMD 180
+ + ++
Sbjct: 119 LGIGIN 124
>gnl|CDD|129526 TIGR00434, cysH, phosophoadenylyl-sulfate reductase (thioredoxin).
This enzyme, involved in the assimilation of inorganic
sulfate, is designated cysH in Bacteria and MET16 in
Saccharomyces cerevisiae. Synonyms include
phosphoadenosine phosphosulfate reductase, PAPS
reductase, and PAPS reductase, thioredoxin-dependent. In
a reaction requiring reduced thioredoxin and NADPH, it
converts 3(prime)-phosphoadenylylsulfate (PAPS) to
sulfite and adenosine 3(prime),5(prime) diphosphate
(PAP). A related family of plant enzymes, scoring below
the trusted cutoff, differs in having a thioredoxin-like
C-terminal domain, not requiring thioredoxin, and in
having a preference for 5(prime)-adenylylsulfate (APS)
over PAPS [Central intermediary metabolism, Sulfur
metabolism].
Length = 212
Score = 31.7 bits (72), Expect = 0.24
Identities = 27/73 (36%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 46 WFVEHFP---VYT--LGLKSNFSHILISKKLNNIPIIRTDRGGEVTYHGPGQAIIYLLID 100
W F VY+ G++ L+SK +IP+I D G YH P Y LID
Sbjct: 7 WAYVTFGGHLVYSTSFGIQGAVLLDLVSKISPDIPVIFLDTG----YHFPET---YELID 59
Query: 101 -LRRRYSDNIKIY 112
L RY NIK+Y
Sbjct: 60 ELTERYPLNIKVY 72
>gnl|CDD|162743 TIGR02172, Fb_sc_TIGR02172, Fibrobacter succinogenes paralogous
family TIGR02172. This model describes a paralogous
family of five proteins, likely to be enzymes, in the
rumen bacterium Fibrobacter succinogenes S85. Members
show homology to proteins described by pfam01636, a
phosphotransferase enzyme family associated with
resistance to aminoglycoside antibiotics. However,
members of this family score below the current trusted
and noise cutoffs for pfam01636.
Length = 226
Score = 29.7 bits (67), Expect = 1.0
Identities = 16/43 (37%), Positives = 19/43 (44%)
Query: 32 LFNSNRTNYTIDQLWFVEHFPVYTLGLKSNFSHILISKKLNNI 74
L S + Y ID F P++ LGL F H L KL I
Sbjct: 165 LITSGKGTYWIDLGDFGYGNPLFDLGLLFMFCHYLDDDKLQAI 207
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.7 bits (67), Expect = 1.2
Identities = 19/75 (25%), Positives = 22/75 (29%), Gaps = 7/75 (9%)
Query: 72 NNIPIIRTDRGGEVTYHGPGQA------IIYLLIDLRRRYSDNIKIYIKKLVENIEEAVI 125
N P + EV Q I LL LR R N KI + V E
Sbjct: 526 NCRPKLLNGTTFEVAVDNELQEKELTNLIPDLLGFLRGRL-KNSKITMTVRVSEPTEVNR 584
Query: 126 LTMSQYNINCKRKKN 140
S +KN
Sbjct: 585 AYSSVEKFQYLAQKN 599
>gnl|CDD|220732 pfam10401, IRF-3, Interferon-regulatory factor 3. This is the
interferon-regulatory factor 3 chain of the
hetero-dimeric structure which also contains the shorter
chain CREB-binding protein. These two subunits make up
the DRAF1 (double-stranded RNA-activated factor 1).
Viral dsRNA produced during viral transcription or
replication leads to the activation of DRAF1. The
DNA-binding specificity of DRAF1 correlates with
transcriptional induction of ISG
(interferon-alpha,beta-stimulated gene). IRF-3 preexists
in the cytoplasm of uninfected cells and translocates to
the nucleus following viral infection. Translocation of
IRF-3 is accompanied by an increase in serine and
threonine phosphorylation, and association with the CREB
coactivator occurs only after infection.
Length = 180
Score = 28.8 bits (65), Expect = 1.8
Identities = 7/26 (26%), Positives = 17/26 (65%)
Query: 112 YIKKLVENIEEAVILTMSQYNINCKR 137
Y ++L++++E ++L ++ I KR
Sbjct: 64 YTRRLLKHLERGLLLEVNGQGIYAKR 89
>gnl|CDD|153405 cd08036, LARP_5, La RNA-binding domain of La-related protein 5.
This domain is found in vertebrate La-related protein 5
(LARP5). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 26.9 bits (59), Expect = 2.3
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 27 FNAMLLFNSNRTN-----YTIDQLWFVEHFPVYTLGLKSNFSHI--------LISKKLNN 73
L F +R N Y I Q+ ++ P+ T+ +N HI LI L +
Sbjct: 4 LKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTV---ANLDHIKKLSTDVDLIVDVLRS 60
Query: 74 IPIIRTDRGGE 84
+P+++ D GE
Sbjct: 61 LPLVQVDEKGE 71
>gnl|CDD|128929 smart00686, DM13, Domain present in fly proteins (CG14681, CG12492,
CG6217), worm H06A10.1 and Arabidopsis thaliana MBG8.9.
Length = 108
Score = 27.3 bits (61), Expect = 3.3
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 43 DQLWF-VEHFPVYTLGLKSNFSHILISKKLN 72
++ F V+ L NF H+L + LN
Sbjct: 76 SLTIDDIKWFSVWCLKTAHNFGHVLFPENLN 106
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 509
Score = 27.8 bits (63), Expect = 4.6
Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 92 QAIIYLLIDLRRRYSDNIKI--YIKKL----VENIEE 122
A+ LL +L+ +Y+D K+ Y+ + +EN++
Sbjct: 219 FAVGPLLDELKEKYADLPKVLAYLDAVQEDILENLDL 255
>gnl|CDD|153282 cd07598, BAR_FAM92, The Bin/Amphiphysin/Rvs (BAR) domain of Family
with sequence similarity 92 (FAM92). BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. This group is composed of proteins from the
family with sequence similarity 92 (FAM92), which were
originally identified by the presence of the unknown
domain DUF1208. This domain shows similarity to the BAR
domains of sorting nexins. Mammals contain at least two
member types, FAM92A and FAM92B, which may exist in many
variants. The Xenopus homolog of FAM92A1, xVAP019, is
essential for embryo survival and cell differentiation.
FAM92A1 may be involved in regulating cell proliferation
and apoptosis. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 211
Score = 27.7 bits (62), Expect = 4.9
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 112 YIKKLVENIEEAVILTMSQYNINCKRKKN 140
Y + VE +E V+ ++ Y CK ++
Sbjct: 76 YRQAEVERLEAKVVQPLALYGTICKHARD 104
>gnl|CDD|218382 pfam05013, FGase, N-formylglutamate amidohydrolase.
Formylglutamate amidohydrolase (FGase) catalyzes the
terminal reaction in the five-step pathway for histidine
utilisation in Pseudomonas putida. By this action,
N-formyl-L-glutamate (FG) is hydrolysed to produce
L-glutamate plus formate.
Length = 221
Score = 27.5 bits (62), Expect = 5.1
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 81 RGGEVT--YHGPGQAIIYLLIDLRRR-YSD 107
+GG +T Y P + + + I++RR Y D
Sbjct: 192 KGGYITRHYGRPARGLHAVQIEIRRDLYMD 221
>gnl|CDD|237785 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
Length = 621
Score = 27.7 bits (62), Expect = 5.3
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 122 EAVILTMSQ-------YNINCKRKKNAPGVYIANGPF 151
EA+IL + YN+N K K P + I N PF
Sbjct: 82 EALILENNLIKELKPRYNVNLKDDKTYPYLVITNEPF 118
>gnl|CDD|223173 COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
Length = 248
Score = 27.3 bits (61), Expect = 5.4
Identities = 23/115 (20%), Positives = 42/115 (36%), Gaps = 19/115 (16%)
Query: 72 NNIPIIRTDRGGEVTYHGPGQAIIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILTMSQY 131
+ IP++R GG +H G ++ +Y K L++ + +A+
Sbjct: 64 DGIPVVRRPSGGGAVFHDLGNLNYSVITPDEGGLESYETLY-KFLLQPVIDAL------- 115
Query: 132 NINCKRKKNAPGVYIANGP----FSGAKIASIGLKISAKGYVYHGVSINVSMDLE 182
R G G G KI+ + KG + H ++ + +DLE
Sbjct: 116 -----RALGVEGAE-CPGRNDLVVDGKKISGSAQRR-TKGRILHHGTLLLDIDLE 163
>gnl|CDD|216092 pfam00742, Homoserine_dh, Homoserine dehydrogenase.
Length = 178
Score = 27.0 bits (61), Expect = 6.2
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 72 NNIPIIRTDRGGEVTYHGPG 91
+N +I TDR G + +GPG
Sbjct: 145 DNAVLIETDRYGPLVIYGPG 164
>gnl|CDD|236761 PRK10795, PRK10795, penicillin-binding protein 2; Provisional.
Length = 634
Score = 27.4 bits (61), Expect = 7.5
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 87 YHGPGQA--IIYLLIDLRRRYSDNIKIYIKKLVENIEEAVILT 127
+ P QA IYL +DL ++ YI+ L+ AV++T
Sbjct: 241 HEQPPQAGHDIYLTLDL------KLQQYIETLLAGSRAAVVVT 277
>gnl|CDD|240300 PTZ00165, PTZ00165, aspartyl protease; Provisional.
Length = 482
Score = 27.0 bits (60), Expect = 8.1
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 116 LVENIEEAVILTMSQYNINCKRKKNAPG 143
+V+NI++ +L + ++ + N PG
Sbjct: 251 IVDNIKKQNLLKRNIFSFYMSKDLNQPG 278
>gnl|CDD|213916 TIGR04303, GeoRSP_rSAM, GeoRSP system radical SAM/SPASM protein.
Members of this family are radical SAM/SPASM domain
proteins from a cassette restricted to the genus
Geobacter. Genes always found adjacent include a
non-radical SAM protein with a closely related SPASM
domain and a short stretch of N-terminal homology as
well to this family, and also a PqqD-like protein. The
three-gene cassette is designated GeoRSP for the genus
Geobacter, this radical SAM protein, the SPASM domain
protein, and the PqqD family protein.
Length = 325
Score = 26.8 bits (59), Expect = 9.4
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 156 IASIGLKISAKGYVYHGVSINVSMDLEPFNNINPCGYPGLVI 197
IAS+G + A V V +S++++ +I PCG+ +VI
Sbjct: 223 IASLGAR-DAGSLVKGSVCGKLSLNIKSNGDITPCGFIPVVI 263
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
0.323 0.141 0.411
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,432,275
Number of extensions: 1105633
Number of successful extensions: 1048
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1009
Number of HSP's successfully gapped: 40
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.8 bits)