RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15804
(193 letters)
>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
subunit.
Length = 813
Score = 254 bits (650), Expect = 2e-80
Identities = 106/185 (57%), Positives = 143/185 (77%), Gaps = 4/185 (2%)
Query: 1 VEITLKVIKGLYPGVTTVQLDNLAAETAAFYEPLKHPDYAVLWLPELLCPNLHKETKKTW 60
V + KV G+Y GVTT QLD LAAETAA HPDYA+L + NLHK TKK++
Sbjct: 37 VLVAQKVCAGVYKGVTTSQLDELAAETAAAMTT-NHPDYAIL-AARIAVSNLHKNTKKSF 94
Query: 61 SEVIEELYNMVNKETGTRTPMISDKHYEIIMKNADRLNSAIIYDRDFNYNFFGFKTLERS 120
SE ++++YN VN+ +G + P+I+D Y+IIMKNA RL+S IIYDRDF+Y++FGFKTLERS
Sbjct: 95 SETVKDMYNHVNERSGLKAPLIADDVYDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERS 154
Query: 121 YLMKNNGRVVERPQHMLMRVAVGIHGEDIDAAIETYNLLSEKYFTHAADVMLRTHAMSRS 180
YL+K NG+VVERPQHMLMRV+VGIH +DI++AI+TY+L+S+++FTHA+ + +A +
Sbjct: 155 YLLKVNGKVVERPQHMLMRVSVGIHKDDIESAIKTYHLMSQRWFTHASPTLF--NAGTPR 212
Query: 181 PRFSS 185
P+ SS
Sbjct: 213 PQLSS 217
>gnl|CDD|215855 pfam00317, Ribonuc_red_lgN, Ribonucleotide reductase, all-alpha
domain.
Length = 79
Score = 67.7 bits (166), Expect = 2e-15
Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 107 FNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVAVGIHG-----EDIDAAIETYNLLS 160
+ K LE YL+K+ +G V+E PQ M MRVA+ + G + ++ A E Y+LLS
Sbjct: 1 RFLTYLAAKVLEDRYLLKDEDGEVLETPQDMFMRVALALAGAEPPEDRLELAEEFYDLLS 60
Query: 161 EKYFTHA 167
F A
Sbjct: 61 SLKFLPA 67
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 72.8 bits (179), Expect = 3e-15
Identities = 42/173 (24%), Positives = 70/173 (40%), Gaps = 15/173 (8%)
Query: 3 ITLKVIKGLYPGVTTVQLDNLAAETAAFYEPLKHPDYAVLWLPELLCPNLHKETKKTWSE 62
L+ + G Y G+T + LAA T PD L +L KE + +
Sbjct: 1 RELRTVIGFYDGITIAENLILAALTV---IEEDDPDVQRLAARLAG-SDLRKEAVRQF-G 55
Query: 63 VIEELYNMVNKETGTRTPMISDKHYEIIMKN-ADRLNSAIIYDRDFNYNFFGFKTLERSY 121
+ L V + + + D LN I+ +RD +++ K L Y
Sbjct: 56 RFDVLDEKVFALV--ANGYYDQRLLRLYSREDLDDLNKKILLERDRQFSYAAAKVLYSRY 113
Query: 122 LMKNN--GRVVERPQHMLMRVAVGIHGED-----IDAAIETYNLLSEKYFTHA 167
L+K+ ++E PQ + MRVA+ + + ++ A E Y+L+S F A
Sbjct: 114 LLKDEDGSEILELPQDLFMRVALLLAQNEAPERRLEWAKEFYDLMSSLRFMPA 166
>gnl|CDD|153088 cd01679, RNR_I, Class I ribonucleotide reductase. Ribonucleotide
reductase (RNR) catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and many viruses, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophages, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class I RNR is oxygen-dependent and can
be subdivided into classes Ia (eukaryotes, prokaryotes,
viruses and phages) and Ib (which is found in
prokaryotes only). It is a tetrameric enzyme of two
alpha and two beta subunits; this model covers the major
part of the alpha or large subunit, called R1 in class
Ia and R1E in class Ib.
Length = 460
Score = 62.9 bits (154), Expect = 6e-12
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 133 PQHMLMRVAVGIHGEDIDAAIETYNLLSEKYFTHAADVMLRTHAMSRSPRFSS 185
PQ LMRVA+G+ D++ A E Y+LLS++ FT A + +A + + SS
Sbjct: 1 PQDRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLF--NAGTPRGQLSS 51
>gnl|CDD|236266 PRK08447, PRK08447, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 789
Score = 59.4 bits (144), Expect = 1e-10
Identities = 36/101 (35%), Positives = 56/101 (55%), Gaps = 12/101 (11%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVAVGIHGEDIDA-- 151
D LN+ I +RD +N+ G KTL YL+K+ N +E PQHM M +A+ + ++D
Sbjct: 123 DDLNAYIKPERDLQFNYLGIKTLYDRYLIKDRNNNPIELPQHMFMAIAMFLAQNELDPQK 182
Query: 152 -AIETYNLLSEKYFTHAADVMLRTHAMS--RSPRFSSFSLY 189
A + Y+++S K+ +VML T +S R+ R S Y
Sbjct: 183 WAKKFYDVIS-KF-----EVMLATPTLSNARTTRHQLSSCY 217
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 58.4 bits (142), Expect = 2e-10
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMKNNGRVVERPQHMLMRVAVGIHGEDIDA--- 151
+RL +A+ +RD + + G +TL Y + +G +E PQ MRVA+G+ +ID
Sbjct: 282 ERLGAALDPERDLQFTYLGLQTLYDRYFLHVDGTRIELPQAFFMRVAMGLALNEIDREAR 341
Query: 152 AIETYNLLS 160
AIE YNLLS
Sbjct: 342 AIEFYNLLS 350
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 54.6 bits (131), Expect = 6e-09
Identities = 53/169 (31%), Positives = 81/169 (47%), Gaps = 21/169 (12%)
Query: 11 LYPGVTTVQLDNLAAETAAFYEPLKHPDYAVLWLPELLCPNLHKET--KKTWSEVIEELY 68
Y G+ ++ LA AA K PDYA + ELL ++KE K + E +EE +
Sbjct: 281 FYSGIKESEV-VLACIMAARANIEKEPDYAFV-AAELLLDVVYKEALGKSKYDEDLEEAH 338
Query: 69 N------MVNKETGTRTPMISDKHYEIIMKNADRLNSAIIYDRDFNYNFFGFKTLERSYL 122
++ +T P + KHY++ D L A+ RD +++ G + L Y
Sbjct: 339 KDHFKRYILEGDTYRLNPEL--KHYDL-----DALAEALDLSRDLQFSYMGVQNLYDRYF 391
Query: 123 MKNNGRVVERPQHMLMRVAVGI---HGEDIDA-AIETYNLLSEKYFTHA 167
+ GR +E PQ MRV++G+ G+D + AI YNLLS +T A
Sbjct: 392 NHHEGRRLETPQIFWMRVSMGLALNEGQDKTSWAITFYNLLSTFRYTPA 440
>gnl|CDD|233902 TIGR02506, NrdE_NrdA, ribonucleoside-diphosphate reductase, alpha
subunit. This model represents the alpha (large) chain
of the class I ribonucleotide reductase (RNR). RNR's are
responsible for the conversion of the ribose sugar of
RNA into the deoxyribose sugar of DNA. This is the
rate-limiting step of DNA biosynthesis. Class I RNR's
generate the required radical (on tyrosine) via a
"non-heme" iron cofactor which resides in the beta
(small) subunit. The alpha subunit contains the
catalytic and allosteric regulatory sites. The mechanism
of this enzyme requires molecular oxygen. E. Coli
contains two versions of this enzyme which are regulated
independently (NrdAB and NrdEF, where NrdA and NrdE are
the large chains ). Most organisms contain only one, but
the application of the gene symbols NrdA and NrdE are
somewhat arbitrary. This model identifies RNR's in
diverse clades of bacteria, eukaryotes as well as
numerous DNA viruses and phage [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 617
Score = 52.0 bits (125), Expect = 4e-08
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 111 FFGFKTLERSYLMKNN--GRVVERPQHMLMRVAVGIHG-----EDIDAAIETYNLLSEKY 163
+ G K L YL++N G + E PQ MRVA+G+ + AI Y+LLS
Sbjct: 1 YMGLKELYNRYLLRNAATGAIYESPQEAYMRVAMGLASLEPKDTRLADAIRFYDLLSRLK 60
Query: 164 FTHAADVMLRTHAMSRSPRFSS 185
+ A + +A + + SS
Sbjct: 61 ISPATPTLF--NAGTPRGQLSS 80
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 50.1 bits (120), Expect = 2e-07
Identities = 49/186 (26%), Positives = 85/186 (45%), Gaps = 21/186 (11%)
Query: 11 LYPGVTTVQLDNLAAETAAFYEPLKHPDYAVLWLPELLCPNLHKETKKTWS--EVIEELY 68
L G+TT + + ++AA ++ PDY + LL L K+ + I+ +
Sbjct: 47 LRDGMTTKDIQEILIKSAADLISVEEPDYQYV-AARLLMFALRKQVYGQFEPPSFIDHIS 105
Query: 69 NMVNKETGTRTPMISDKHYEIIMKNADRLNSAIIYDRDFNYNFFGFKTLERSYLMKN--N 126
VN+ G P I K+ + L S I +DRDF + + G L+ YL+++
Sbjct: 106 KCVNE--GKYDPEILSKYSA---EEITYLESFIDHDRDFEFTYAGAMQLKEKYLVQDRST 160
Query: 127 GRVVERPQHMLMRVAVGIHGED-----IDAAIETYNLLSEKYFTHAADVMLRTHAMSRSP 181
G + E PQ M +A+ +H ++ ++ I YN +S + + +M A R+P
Sbjct: 161 GEIYETPQFAYMLIAMALHQDEPKEDRLEHVIRFYNAVSTRKISLPTPIM----AGVRTP 216
Query: 182 --RFSS 185
+FSS
Sbjct: 217 TRQFSS 222
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 43.3 bits (102), Expect = 4e-05
Identities = 38/140 (27%), Positives = 63/140 (45%), Gaps = 22/140 (15%)
Query: 47 LLCPNLHKETKKTW---SEVIEELYNMVNKETGTRTPMISDKHY-EIIMKNADR-----L 97
L +L+KE + S + Y +V K ++ +K Y E +++N + L
Sbjct: 94 LYVFDLYKEARINRHYNSFGYGDYYELVKK-------LVEEKLYGEYLLQNYSKEEIKEL 146
Query: 98 NSAIIYDRDFNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVAVGIHGEDIDA----- 151
I +RDF +N+ G K L YL+K N ++E PQ M +A+ + +
Sbjct: 147 EKYIKPERDFLFNYEGLKLLADRYLVKGFNREILELPQERFMGIAMHLAIPEGKEKRVYY 206
Query: 152 AIETYNLLSEKYFTHAADVM 171
A + Y+LLSE T A +
Sbjct: 207 AKKFYDLLSELKATVATPTL 226
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 39.5 bits (93), Expect = 6e-04
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 10/58 (17%)
Query: 117 LERSYLMKN-NGRVVERPQHMLMRVAVGI--------HGEDIDA-AIETYNLLSEKYF 164
LE+ YL K+ +G+ +E P+ M RVA I D++A A Y+L++ F
Sbjct: 20 LEKRYLKKDEDGKPIETPEDMFRRVARTIAAAELIYDSKADVEALADRFYDLMTSLEF 77
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 38.4 bits (89), Expect = 0.002
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVAVGIHGEDID--- 150
+RL +A+ RD + G TL Y ++ NG +E PQ+ MR+A+G+ + D
Sbjct: 134 ERLAAALDPTRDELLKYIGVVTLNNRYGIRARNGDALEVPQYFWMRIAMGLSLNEDDPTS 193
Query: 151 AAIETYNLLSE 161
+A+ Y +S+
Sbjct: 194 SALAFYEKMSK 204
>gnl|CDD|236378 PRK09102, PRK09102, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 601
Score = 35.3 bits (82), Expect = 0.013
Identities = 23/83 (27%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 91 MKNADRLNSAIIYDRDFNYNFFGFKTLERSYLMKNNGRVVERPQHMLMRVAVGIHGEDID 150
M+N I RD FG TL YL++ E Q + R+A DID
Sbjct: 3 MQNKLVFQINIDRSRDAWLTEFGKATLRDRYLLEG-----ESYQDLFARIAE--AYADID 55
Query: 151 AAIET--YNLLSEKYFTHAADVM 171
Y+ +S +F A V+
Sbjct: 56 PEHAQRFYDYMSRGWFMPATPVL 78
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 34.2 bits (79), Expect = 0.031
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMKN--NGRVVERPQHMLMRVA 141
D++++ I + RD N+++ K LE YL++N G + E Q + + VA
Sbjct: 126 DQMDTFIDHWRDMNFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVA 174
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 32.5 bits (74), Expect = 0.14
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 115 KTLERSYLMKN-NGRVVERPQHMLMRVAVGI 144
K LE YL+K+ +G+++E P+ M RVA I
Sbjct: 119 KVLEARYLLKDEDGKIIETPRQMFRRVARHI 149
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 32.0 bits (73), Expect = 0.18
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVA 141
+ I +RD + + G L + Y+++ + +E PQ M + +A
Sbjct: 222 EEAAGFIDPERDKLFTYSGLDLLLKRYVIRTHSHEPLESPQEMFLGIA 269
>gnl|CDD|233900 TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (Class II RNRs) related to the characterized
species from Pyrococcus , Thermoplasma , Corynebacterium
and Deinococcus. RNR's are responsible for the
conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. This model identifies genes in a
wide range of deeply branching bacteria. All are
structurally related to the class I (non-heme iron
dependent) RNRs. In most species this gene is known as
NrdJ, while in mycobacteria it is called NrdZ [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 589
Score = 29.6 bits (67), Expect = 1.1
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 117 LERSYLMK-NNGRVVERPQHMLMRVAVGIHGEDIDAAIETYNLLSEKYFTHAADVMLRTH 175
L YL K +G ++E P+ + RVA + + + L E+++ D+M+
Sbjct: 2 LAARYLRKDEDGNILESPEDLFRRVARALAAAEDKYNSPVWKQLYERFY----DLMVNLG 57
Query: 176 AMSRSP 181
M SP
Sbjct: 58 FMPNSP 63
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 29.3 bits (66), Expect = 1.5
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 6/79 (7%)
Query: 95 DRLNSAIIYDRDFNYNFFGFKTLERSYLMK-NNGRVVERPQHMLMRVAVGIHGED----- 148
I +RD + + G L YL ++ V E PQ + +A+ + +
Sbjct: 142 IEAGKMIDPERDKLFTYIGLYLLADRYLATDSDRNVYELPQERWLTIALYLMQNEPRERR 201
Query: 149 IDAAIETYNLLSEKYFTHA 167
+ E Y LS Y T A
Sbjct: 202 MQLVKEAYWALSNLYMTVA 220
>gnl|CDD|235592 PRK05756, PRK05756, pyridoxamine kinase; Validated.
Length = 286
Score = 28.7 bits (65), Expect = 2.0
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 130 VERPQHMLMRVAVGIHGEDIDAAIETYNLLS----EKYFTHAA----DVMLRTHAM 177
+ RP MR VG+ G D+ +A+ LL E+ H +VM RT
Sbjct: 206 ISRPLVDFMRQPVGV-G-DLTSALFLARLLQGGSLEEALEHTTAAVYEVMARTKER 259
>gnl|CDD|224867 COG1956, COG1956, GAF domain-containing protein [Signal
transduction mechanisms].
Length = 163
Score = 28.0 bits (63), Expect = 2.1
Identities = 18/88 (20%), Positives = 39/88 (44%), Gaps = 18/88 (20%)
Query: 65 EELYNMVNKETGTRTPMISDKHYEI-IMKNADRLNSAIIYDRDFNYNFFGFKTLERSYLM 123
EE Y ++ K+ +++ + I + NA SA++ +R + N+ GF YL+
Sbjct: 13 EEQYALLLKQLKA---LLAGETNFIANLANA----SALLKERLPDVNWVGF------YLL 59
Query: 124 KNNGRVVE----RPQHMLMRVAVGIHGE 147
+ + V+ + + + G+ G
Sbjct: 60 EGDELVLGPFQGKVACVRIPFGKGVCGT 87
>gnl|CDD|216853 pfam02030, Lipoprotein_8, Hypothetical lipoprotein (MG045 family).
This family includes hypothetical lipoproteins, the
amino terminal part of this protein is related to
pfam01547, a family of solute binding proteins. This
suggests this family also has a solute binding function.
Length = 493
Score = 28.0 bits (62), Expect = 3.2
Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 50 PNLHKETKKTWSEVIEELYNMVNKETGTRTPMISDKH--YEI--IMKNADRLNSAIIYDR 105
P L K+ WS+VI+ + ++ R I D + + I++ ++ N + +
Sbjct: 161 PELEKK-DVYWSDVIKAIVRHKDRFNKNRLIAIDDARTIFSLANIVQLENKNNIIDVNPK 219
Query: 106 DFNYNFFG--FKTLERSYLMKNN 126
+ N+F +++ L NN
Sbjct: 220 ELKTNYFLNVYESFSYLGLKLNN 242
>gnl|CDD|241354 cd13200, FERM_C_KCBP, kinesin-like calmodulin binding protein FERM
domain C-lobe. KCBPs (also called KIPK/Kinesin-like
Calmodulin-Binding Protein-Interacting Protein Kinase),
a member of the Kinesin-14 family, is a C-terminal
microtubule motor with three unique domains including a
myosin tail homology region 4 (MyTH4), a talin-like
domain, and a calmodulin-binding domain (CBD). Binding
of the Ca2+-activated calmodulin to KCBP causes the
motor to dissociate from microtubules. The microtubule
binding of KCBP is controlled by the calcium binding
protein KIC containing a single EF-hand motif. KCBPs
are unique to land plants and green algae. The MyTH4
and talin-like domains are not found in other kinesins,
while the CBD domain is also only found in
Strongylocentrotus purpuratus kinesin-C (SpKinC). The
FERM domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 189
Score = 27.4 bits (61), Expect = 3.4
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 18/51 (35%)
Query: 138 MRVAVGIH--------GEDIDAAIETYNLLSEKYFTHAADVMLRTHAMSRS 180
MRVA +H GE+I A++T H DVM++ ++ +R+
Sbjct: 143 MRVAGVLHIFQFETKQGEEICVALQT----------HINDVMMKRYSKARA 183
>gnl|CDD|214866 smart00862, Trans_reg_C, Transcriptional regulatory protein, C
terminal. This domain is almost always found associated
with the response regulator receiver domain. It may play
a role in DNA binding.
Length = 76
Score = 26.4 bits (59), Expect = 3.5
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 114 FKTLERSYLMKNNGRVVERPQHMLMRVAVGIHGEDIDAAIETY 156
F+ LE L++N GRVV R + L+ G + D ++ +
Sbjct: 11 FRLLE--LLLRNPGRVVSREE--LLEAVWGDDEDVDDNTLDVH 49
>gnl|CDD|233405 TIGR01418, PEP_synth, phosphoenolpyruvate synthase. Also called
pyruvate,water dikinase and PEP synthase. The member
from Methanococcus jannaschii contains a large intein.
This enzyme generates phosphoenolpyruvate (PEP) from
pyruvate, hydrolyzing ATP to AMP and releasing inorganic
phosphate in the process. The enzyme shows extensive
homology to other enzymes that use PEP as substrate or
product. This enzyme may provide PEP for
gluconeogenesis, for PTS-type carbohydrate transport
systems, or for other processes [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 782
Score = 27.8 bits (62), Expect = 4.0
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 147 EDIDAAI-ETYNLLSEKYFTHAADVMLRTHA 176
D++ AI E Y+ LSE Y ADV +R+ A
Sbjct: 94 PDLEEAIREAYDKLSEDYGKEEADVAVRSSA 124
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 27.8 bits (61), Expect = 4.5
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 104 DRDFNYNFFGFKTLERSYLMKN-NGRVVERPQHMLMRVAV 142
D+ F+ N + L YL K+ NG ++E P+ + RVA+
Sbjct: 112 DKRFSIN--ALRVLASRYLKKDENGNIIESPRELFERVAI 149
>gnl|CDD|222643 pfam14278, TetR_C_8, Transcriptional regulator C-terminal region.
This domain is a tetracycline repressor, domain 2, or
C-terminus.
Length = 97
Score = 26.1 bits (58), Expect = 5.1
Identities = 11/66 (16%), Positives = 20/66 (30%), Gaps = 3/66 (4%)
Query: 61 SEVIEELYNMVNKETGTRTPMISDKHYEIIMKNADRLNSAIIYDRDFNYNFFGF-KTLER 119
EV E L ++ K + ++ D L I+ + F K L +
Sbjct: 2 QEVSEALDEYSIEQDNLNPLTFLTKLLPYLYEHRDELR--ILLSTYGDLGFIEKLKKLYK 59
Query: 120 SYLMKN 125
+
Sbjct: 60 DLIENY 65
>gnl|CDD|223839 COG0768, FtsI, Cell division protein FtsI/penicillin-binding
protein 2 [Cell envelope biogenesis, outer membrane].
Length = 599
Score = 27.4 bits (61), Expect = 5.8
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 56 TKKTWSEVIEELYNMVNKETGTRTPMISDKHYEIIMK 92
+ +T +V E + +VN G + Y I K
Sbjct: 489 SPETAEKVREGMRAVVNDGGGGTGKAAAVPGYRIAGK 525
>gnl|CDD|235454 PRK05421, PRK05421, hypothetical protein; Provisional.
Length = 263
Score = 27.2 bits (61), Expect = 5.9
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 47 LLCPNLHKETKKTWSEVIEEL 67
LL N++K+ + W V++ L
Sbjct: 46 LLVWNIYKQQRAGWLSVLKNL 66
>gnl|CDD|233627 TIGR01899, cas_TM1807_csm5, CRISPR type III-A/MTUBE-associated RAMP
protein Csm5. CRISPR is a term for Clustered Regularly
Interspaced Short Palidromic Repeats. A number of
protein families appear only in association with these
repeats and are designated Cas (CRISPR associated)
proteins. Members of this cas gene family are found in
the mtube subtype of CRISPR/cas locus and designated
Csm5, for CRISPR/cas Subtype Mtube, protein 5 [Mobile
and extrachromosomal element functions, Other].
Length = 365
Score = 27.0 bits (60), Expect = 6.3
Identities = 20/117 (17%), Positives = 37/117 (31%), Gaps = 23/117 (19%)
Query: 26 ETAAFYEPLKHPDYAVLWLPELLCPNLHKETKKTWSEVIEELYNMVNKE--TGT------ 77
+P K+ DY+ + E ++ I+E + + G+
Sbjct: 70 LEEVKLDPAKYRDYSS--------KIISGEPRREKKLTIKEFHKINGDPYIPGSSIKGAI 121
Query: 78 RTPMISDKHYEIIMKNADRLNSAIIYDRDFNYNFFGFKTLERSYLMKNNGRVVERPQ 134
RT ++ + + KN D L I D + +K NG P+
Sbjct: 122 RTALL----WNYLKKNPDLL---EIVDDHLQKELRQYGRAFERKELKKNGISNTIPK 171
>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional.
Length = 1060
Score = 27.1 bits (60), Expect = 6.8
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 134 QHMLMRVAVGIHGEDIDAAIETYNLLSEKYFTHAADVMLRTHAMS 178
M ++V +DID A+ L+ E AD L T +S
Sbjct: 438 STFNMLMSVCASSQDIDGALRVLRLVQEAGLK--ADCKLYTTLIS 480
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 26.8 bits (59), Expect = 8.2
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 71 VNKETGTRTPMISDKHYEIIMKNADRLNSAIIYD 104
V+KE R + Y M + DRL YD
Sbjct: 904 VDKENSLRNSELKCCVYPSAMGSNDRLFHYCFYD 937
>gnl|CDD|106304 PRK13346, PRK13346, superantigen-like protein 7; Reviewed.
Length = 231
Score = 26.5 bits (58), Expect = 8.3
Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 124 KNNGRVVERPQHMLMRVAVGIHGEDIDAAIETYNLLSEKYFTHAADVMLRTHAMSRSPRF 183
K N + E H+ + ++G ++DA+I+++ + E+ D +R + +
Sbjct: 124 KKNNKSSETNTHLFVN---KVYGGNLDASIDSFLINKEEVSLKELDFKIRQQLVENYGLY 180
Query: 184 SSFSLYG 190
+ YG
Sbjct: 181 KGTTKYG 187
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
0.321 0.135 0.400
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,035,345
Number of extensions: 943042
Number of successful extensions: 929
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 47
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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 (21.9 bits)
S2: 56 (25.2 bits)