RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1740
(505 letters)
>gnl|CDD|217170 pfam02661, Fic, Fic/DOC family. This family consists of the Fic
(filamentation induced by cAMP) protein and doc (death
on curing). The Fic protein is involved in cell division
and is suggested to be involved in the synthesis of PAB
or folate, indicating that the Fic protein and cAMP are
involved in a regulatory mechanism of cell division via
folate metabolism. This family contains a central
conserved motif HPFXXGNG in most members. The exact
molecular function of these proteins is uncertain. P1
lysogens of Escherichia coli carry the prophage as a
stable low copy number plasmid. The frequency with which
viable cells cured of prophage are produced is about
10(-5) per cell per generation. A significant part of
this remarkable stability can be attributed to a
plasmid-encoded mechanism that causes death of cells
that have lost P1. In other words, the lysogenic cells
appear to be addicted to the presence of the prophage.
The plasmid withdrawal response depends on a gene named
doc (death on curing) that is represented by this
family. Doc induces a reversible growth arrest of E.
coli cells by targetting the protein synthesis
machinery. Doc hosts the C-terminal domain of its
antitoxin partner Phd (prevents host death) through fold
complementation, a domain that is intrinsically
disordered in solution but that folds into an
alpha-helix on binding to Doc.This domain forms
complexes with Phd antitoxins containing pfam02604.
Length = 94
Score = 96.3 bits (240), Expect = 3e-24
Identities = 41/98 (41%), Positives = 52/98 (53%), Gaps = 4/98 (4%)
Query: 137 DITVADLLEIHKRVLGFADPLASGMFRRTQVFVGGHIPPTPPHIIPLMDEFIAWLNSDVA 196
+T+ DLLEIH+ +L P A G FR V + P I +DE + + D
Sbjct: 1 YLTLEDLLEIHRILLEDIGPWA-GEFRDVDVGLLESALARPEQIPAGLDELELYPDLD-- 57
Query: 197 LRMHPVRFAAIAHYKLVHIHPFIDGNGRTSRLLMNLIL 234
R HP+ AA H+ IHPF DGNGRT+RLL NL L
Sbjct: 58 -REHPLEKAAALHFGFAKIHPFRDGNGRTARLLANLFL 94
>gnl|CDD|225718 COG3177, COG3177, Fic family protein [Function unknown].
Length = 348
Score = 102 bits (257), Expect = 4e-24
Identities = 69/297 (23%), Positives = 115/297 (38%), Gaps = 42/297 (14%)
Query: 86 IEGNSMSLAQTRSIVETRMAIGGKSIAEHNEILGLDLALKYI-NNTLVNRVGDITVADLL 144
IEGN+++L RS +E + GK + E+L + A Y + + D+L
Sbjct: 62 IEGNTLTLEDLRSSLEG-ITGAGKPTDDIKEVLNYERADFYGLEHLDAGEP--FSWLDIL 118
Query: 145 EIHKRVLGFADPLASGMFRRTQVFVG-----GHIPPTPPHIIP-LMDEFIAWLNSDVALR 198
++H + L G R+ V + P ++ LM+E I +L S+ +
Sbjct: 119 KLHAILTSGL-LLEKGKGRQDVVGIIDSGGVHFHAPPSSQLVEELMEELIGFLQSNKKI- 176
Query: 199 MHPVRFAAIAHYKLVHIHPFIDGNGRTSRLLMNLILMQAGFPPVIIPKHERHTIKS---- 254
P+ AAIAH++ +IHPF DGNGRT RLL+ L+L QAG P++I R+ +
Sbjct: 177 -DPLVKAAIAHFRFEYIHPFEDGNGRTGRLLIFLLLAQAGLAPLVILYDSRYIYNNRADY 235
Query: 255 -------------TPGTNIEALGTISAAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNA 301
T I LG A+E K + + +
Sbjct: 236 YRALEAVEEEGVDTTFILIFILGLAETALEYGL--KEIDKIDSLSQLDTEINEWAERIGQ 293
Query: 302 YGEFIEETQSDIITADKMYFKALISYPEHGQALVNRQRTALVVEELDRDFLRKIDEK 358
+ Q +TA ++ +S R L+ + L ++ +
Sbjct: 294 LNVLLFG-QEGYLTAAEIEAILGVSKAT-----ATRDLKELL----ELGILEEVKGR 340
>gnl|CDD|131662 TIGR02613, mob_myst_B, mobile mystery protein B. Members of this
protein family, which we designate mobile mystery
protein B, are found in mobization-related contexts more
often than not, including within a CRISPR-associated
gene region in Geobacter sulfurreducens PCA, and on
plasmids in Agrobacterium tumefaciens and Coxiella
burnetii, always together with mobile mystery protein A
(TIGR02612), a member of the family of helix-turn-helix
DNA binding proteins (pfam01381). This protein is
encoded by the downstream member of the gene pair and
belongs to the Fic protein family (pfam02661), where Fic
(filamentation induced by cAMP) is a regulator of cell
division. The characteristics of having a two-gene
operon in a varied context and often on plasmids, with
one member affecting cell division and the other able to
bind DNA, suggests similarity to addiction modules.
Length = 186
Score = 61.0 bits (148), Expect = 8e-11
Identities = 37/105 (35%), Positives = 55/105 (52%), Gaps = 6/105 (5%)
Query: 138 ITVADLLEIHKRVLGFADPLASGMFRRTQVFVGGHIPPTPPHIIPLMDEFIAWL-NSDVA 196
++ L +H+R+ G A G FR TQ +G P + L+D+ WL N +
Sbjct: 49 LSETFLRRLHRRMFGDVWRWA-GDFRTTQKNIGVSPLQIPSELAILLDDVRYWLQNGTFS 107
Query: 197 LRMHPVRFAAIAHYKLVHIHPFIDGNGRTSRLLMNLILMQAGFPP 241
+RF H++LV IHPF +GNGR +RL +L+L Q G+ P
Sbjct: 108 PDEIAIRF----HHRLVAIHPFPNGNGRHARLATDLLLEQQGYSP 148
>gnl|CDD|225095 COG2184, Fic, Protein involved in cell division [Cell division and
chromosome partitioning].
Length = 201
Score = 47.4 bits (113), Expect = 3e-06
Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 8/109 (7%)
Query: 134 RVGDITVADLLEIHKRVLGFADPLASGMFRRTQVFVGGHIPPTPPHIIPLMDEFIAWLNS 193
R G + +A L IH+++ A G FR + G P +I +D W+
Sbjct: 52 RKGGLDLAHLRAIHRQLFQDIYEWA-GQFRTVGISKGDTRFANPSYIERALDYAEQWM-P 109
Query: 194 DVALRMHPVRFAAIAHY--KLVHIHPFIDGNGRTSRLLMNLILMQAGFP 240
AH ++ HPF +GNGR++R+ ++L+L + G
Sbjct: 110 QETYDF----VERAAHKYVEINIAHPFREGNGRSTRIFLDLLLKELGKA 154
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 39.6 bits (93), Expect = 1e-04
Identities = 13/58 (22%), Positives = 24/58 (41%)
Query: 267 SAAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKAL 324
+ + K+G D+A++ +E A + P N + + D A + KAL
Sbjct: 8 NLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDLEKAL 65
>gnl|CDD|225605 COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 250
Score = 43.2 bits (102), Expect = 2e-04
Identities = 34/134 (25%), Positives = 54/134 (40%), Gaps = 10/134 (7%)
Query: 274 KMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALIS--YPEHG 331
K+G+ D A + + A ++AP+N DVLN YG F+ Q A + + +AL Y E
Sbjct: 81 KLGENDLADESYRKALSLAPNNGDVLNNYGAFLCA-QGRPEEAMQQFERALADPAYGEPS 139
Query: 332 QALVNRQRTALVVEELDR---DFLRKIDEKRDQVSSIPESDPALCKAKK----ESYFQHI 384
L N AL + D+ R ++ ++ E KA Y +
Sbjct: 140 DTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERY 199
Query: 385 YHTVGIEGNSMSLA 398
G + S+ L
Sbjct: 200 QQRGGAQAESLLLG 213
Score = 32.8 bits (75), Expect = 0.36
Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 280 KALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPEHGQALVN 336
+A K E A P + + AD+ Y KAL P +G L N
Sbjct: 53 QAKKNLEKALEHDPSYYLAHLVRA-HYYQKLGENDLADESYRKALSLAPNNGDVLNN 108
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 38.5 bits (90), Expect = 7e-04
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 273 KKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPEHGQ 332
K+G D+AL+ +E A + P N D A + Y KAL P++ +
Sbjct: 11 YKLGDYDEALEYYEKALELDPDNADAYYNLAA-AYYKLGKYEEALEDYEKALELDPDNAK 69
Query: 333 ALVNR 337
A N
Sbjct: 70 AYYNL 74
Score = 35.0 bits (81), Expect = 0.013
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 274 KMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPE 329
K+GK ++AL+ +E A + P N G A + Y KAL P
Sbjct: 46 KLGKYEEALEDYEKALELDPDNAKAYYNLG-LAYYKLGKYEEALEAYEKALELDPN 100
>gnl|CDD|131573 TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein
PilW. Members of this family are designated PilF in ref
(PMID:8973346) and PilW in ref (PMID:15612916). This
outer membrane protein is required both for pilus
stability and for pilus function such as adherence to
human cells. Members of this family contain copies of
the TPR (tetratricopeptide repeat) domain.
Length = 234
Score = 37.7 bits (88), Expect = 0.007
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 274 KMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALIS--YPEHG 331
++G+++KA F A + P+N DVLN YG F+ + Q A + + +A+ YP+
Sbjct: 77 QLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQ-QGKYEQAMQQFEQAIEDPLYPQPA 135
Query: 332 QALVNRQRTAL 342
++L N AL
Sbjct: 136 RSLENAGLCAL 146
Score = 31.2 bits (71), Expect = 0.96
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 276 GKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPEHGQALV 335
G ++ A + + A P + A + ++ A+ + +AL P +G L
Sbjct: 45 GDLEVAKENLDKALEHDPDDYLAYLALA-LYYQQLGELEKAEDSFRRALTLNPNNGDVLN 103
Query: 336 N 336
N
Sbjct: 104 N 104
>gnl|CDD|188156 TIGR01550, DOC_P1, death-on-curing family protein. The
characterized member of this family is the
death-on-curing (DOC) protein of phage P1. It is part of
a two protein operon with prevents-host-death (phd) that
forms an addiction module. DOC lacks homology to
analogous addiction module post-segregational killing
proteins involved in plasmid maintenance. These modules
work as a combination of a long lived poison (e.g. this
protein) and a more abundant but shorter lived antidote.
Members of this family have a well-conserved central
motif HxFx[ND][AG]NKR. A similar region, with K replaced
by G, is found in the huntingtin interacting protein
(HYPE) family [Unknown function, General].
Length = 121
Score = 34.8 bits (80), Expect = 0.027
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 203 RFAAIAHYKLVHIHPFIDGNGRTSRLLMNLILMQAGF 239
+A+ Y L+ HPF + N RT+ + L L G+
Sbjct: 52 EVSAVLLYALIRSHPFNNANKRTALNALLLFLELNGY 88
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 29.3 bits (67), Expect = 0.27
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 274 KMGKIDKALKLFEHAFAIAPHN 295
K+G D+AL+ +E A + P+N
Sbjct: 13 KLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|222121 pfam13428, TPR_14, Tetratricopeptide repeat.
Length = 44
Score = 29.4 bits (66), Expect = 0.34
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 268 AAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEF 305
A + +G +D+AL L A A+ P +P+ L
Sbjct: 7 LARALLALGDLDEALALLRRALALDPDDPEALLLLARL 44
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 29.0 bits (66), Expect = 0.36
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 274 KMGKIDKALKLFEHAFAIAPHN 295
K+G ++AL+ +E A + P+N
Sbjct: 13 KLGDYEEALEAYEKALELDPNN 34
>gnl|CDD|226687 COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 287
Score = 32.3 bits (74), Expect = 0.48
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 274 KMGKIDKALKLFEHAFAIAPHNPDVLNAYGE--FIEETQSDIITADKMYFKALISYPEHG 331
+G+ AL + +A +A NP++L E + + Q A + +AL P +
Sbjct: 168 ALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANI 227
Query: 332 QAL 334
+AL
Sbjct: 228 RAL 230
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 29.6 bits (67), Expect = 0.51
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 274 KMGKIDKALKLFEHAFAIAPHNPDVLNAYGEF 305
+ G D+AL E A A P + L GE
Sbjct: 9 RAGDYDEALAALEAALARYPLAAEALLLLGEA 40
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 28.5 bits (65), Expect = 0.53
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 274 KMGKIDKALKLFEHAFAIAPHN 295
K+GK D+AL+ +E A + P+N
Sbjct: 13 KLGKYDEALEYYEKALELNPNN 34
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 32.4 bits (74), Expect = 0.72
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 268 AAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEF 305
A I++++ G D A++ FE I P N + A
Sbjct: 506 ARIDIQE-GNPDDAIQRFEKVLTIDPKNLRAILALAGL 542
Score = 30.8 bits (70), Expect = 2.2
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 268 AAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISY 327
AI + K G + KA + FE A +I P A I+ + + A + + K L
Sbjct: 472 GAIYLGK-GDLAKAREAFEKALSIEPDFFPAA-ANLARIDIQEGNPDDAIQRFEKVLTID 529
Query: 328 PEHGQAL 334
P++ +A+
Sbjct: 530 PKNLRAI 536
Score = 29.7 bits (67), Expect = 4.8
Identities = 23/109 (21%), Positives = 39/109 (35%), Gaps = 7/109 (6%)
Query: 228 LLMNLILMQAGFPPVIIPKHERHTIKSTPGTNIEALGTISAAIEMKKMGKIDKALKLFEH 287
L +L L Q +P I + + I+ + A+ G +A+K E
Sbjct: 708 LEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLAS------GNTAEAVKTLEA 761
Query: 288 AFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPEHGQALVN 336
P++ + A E + Q D A K Y + P++ L N
Sbjct: 762 WLKTHPNDAVLRTALAE-LYLAQKDYDKAIKHYQTVVKKAPDNAVVLNN 809
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 31.9 bits (72), Expect = 0.83
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 266 ISAAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKAL 324
I + K G I ++ F P PDV N YGE + + Q+ A + + A+
Sbjct: 437 IQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLD-QNKFDEAIEKFDTAI 494
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 29.3 bits (66), Expect = 1.1
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 273 KKMGKIDKALKLFEHAFAIA----PHNPDVLNAYGEF--IEETQSDIITADKMYFKAL 324
+++G D+AL+L E A +A +P+ A + D A + KAL
Sbjct: 16 RRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLEKAL 73
>gnl|CDD|173038 PRK14574, hmsH, outer membrane protein; Provisional.
Length = 822
Score = 31.6 bits (71), Expect = 1.2
Identities = 45/206 (21%), Positives = 82/206 (39%), Gaps = 28/206 (13%)
Query: 237 AGFPPVIIPKHERHTIKSTPGTNIEALGTISAAIEMKKMGKIDKALKLFEHAFAIAPHNP 296
AG +I +ER+ NI + G SAA + + D+AL L++ + P NP
Sbjct: 81 AGRDQEVIDVYERYQ----SSMNISSRGLASAARAYRNEKRWDQALALWQSSLKKDPTNP 136
Query: 297 DVLN--------------AYGEFIEETQSDIITADKMYFKALISYPEHG----QALVNRQ 338
D+++ + E + D + M L + QA
Sbjct: 137 DLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAV 196
Query: 339 RTALVVEELDRDFLRKIDEKR--DQVSSIPESDPALCKAKKESYFQHIYHTVGIEGNSMS 396
R A EE+ ++ L + R + + + +P L A+ +++ + E M+
Sbjct: 197 RLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAE---HYRQLERDAAAEQVRMA 253
Query: 397 LAQTRSIVETRMAIGGKSIAEHNEIL 422
+ TRS E R I K++A++ +L
Sbjct: 254 VLPTRSETE-RFDIADKALADYQNLL 278
>gnl|CDD|219180 pfam06798, PrkA, PrkA serine protein kinase C-terminal domain.
This is a family of PrkA bacterial and archaeal serine
kinases approximately 630 residues long. This family
corresponds to the C-terminal domain.
Length = 254
Score = 31.0 bits (71), Expect = 1.2
Identities = 29/128 (22%), Positives = 44/128 (34%), Gaps = 29/128 (22%)
Query: 266 ISAAIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNA----YGEFIEETQS---DIITADK 318
+S A+ + L + E + + Y EF++ + + I K
Sbjct: 46 LSNALVSDSEERCINPLDVLEELEQGIKDHESIPEEDRDKYLEFLKVVRKEYNERI--KK 103
Query: 319 MYFKALI-SYPEHGQALVNRQ-------------RTALVVEELDRD--FLRKIDEKRDQV 362
KA I SY E Q L + + L EEL+ D FLR I+E+
Sbjct: 104 EVQKAYIESYEEAAQNLFDNYLDNVEAYINDEKVKDPLTGEELEPDERFLRSIEEQIG-- 161
Query: 363 SSIPESDP 370
I E
Sbjct: 162 --ISEERK 167
>gnl|CDD|226180 COG3654, Doc, Prophage maintenance system killer protein [General
function prediction only].
Length = 132
Score = 29.7 bits (67), Expect = 1.7
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 204 FAAIAHYKLVHIHPFIDGNGRTSRLLMNLILMQAGF 239
AA L+ H F DGN RT+ L L+ G+
Sbjct: 56 LAAAYFVALIKNHAFADGNKRTALAAALLFLLLNGY 91
>gnl|CDD|134311 PRK00536, speE, spermidine synthase; Provisional.
Length = 262
Score = 30.2 bits (68), Expect = 2.4
Identities = 13/50 (26%), Positives = 22/50 (44%)
Query: 301 AYGEFIEETQSDIITADKMYFKALISYPEHGQALVNRQRTALVVEELDRD 350
A+ F +T D + AD+ + IS+ H + N + + LD D
Sbjct: 87 AHQLFKYDTHVDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLD 136
>gnl|CDD|184424 PRK13964, coaD, phosphopantetheine adenylyltransferase;
Provisional.
Length = 140
Score = 28.9 bits (65), Expect = 3.5
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 278 IDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYPEHGQALVNR 337
+ KALKLF+ + + NPD NA + + K + ++ + L+N
Sbjct: 21 LKKALKLFDKVYVVVSINPDKSNASD----------LDSRFKNVKNKLKDFKNVEVLINE 70
Query: 338 QR-TALVVEELDRDFL 352
+ TA + ++L +FL
Sbjct: 71 NKLTAEIAKKLGANFL 86
>gnl|CDD|221433 pfam12130, DUF3585, Protein of unknown function (DUF3585). This
domain is found in eukaryotes. This domain is typically
between 135 and 149 amino acids in length and is found
associated with pfam00307.
Length = 142
Score = 28.8 bits (65), Expect = 3.6
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 12 CLEEDLLALISYPEHGQALVNRQRTALVVEELDRDFLRKIDEKRDQVSSIPESD 65
LE++L AL+S PEH + +RQR +++E L K+ +KRD + E D
Sbjct: 81 DLEQELRALLSKPEHLKTEEDRQREEELLQE-----LVKLVQKRDALVDDLEED 129
>gnl|CDD|182396 PRK10347, PRK10347, cell filamentation protein Fic; Provisional.
Length = 200
Score = 28.6 bits (64), Expect = 6.6
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 207 IAHY--KLVHIHPFIDGNGRTSRLLMNLILMQAGF 239
+AHY ++ +HPF G+G R+ + + AG+
Sbjct: 124 LAHYYCEINVLHPFRVGSGLAQRIFFEQLAIHAGY 158
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit 4.
Members of this family function as part of the Mediator
(Med) complex, which links DNA-bound transcriptional
regulators and the general transcription machinery,
particularly the RNA polymerase II enzyme. They play a
role in basal transcription by mediating activation or
repression according to the specific complement of
transcriptional regulators bound to the promoter.
Length = 176
Score = 28.1 bits (63), Expect = 7.4
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 311 SDIITADKMYFKALISYPEHGQALVNRQRTALVVEELD---RDFLRKIDEKRDQVSSIP 366
D+I+AD AL EH + VE LD +D L+++ E ++ ++P
Sbjct: 5 EDLISADDELKSALKELEEHQENQQRILELRAEVESLDEKIKDILKELKEAEKELRTLP 63
>gnl|CDD|227122 COG4783, COG4783, Putative Zn-dependent protease, contains TPR
repeats [General function prediction only].
Length = 484
Score = 28.5 bits (64), Expect = 9.6
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 269 AIEMKKMGKIDKALKLFEHAFAIAPHNPDVLNAYGEFIEETQSDIITADKMYFKALISYP 328
A++ G+ D+ALKL + A P NP L G+ I + A + KAL P
Sbjct: 313 ALQTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGD-ILLEANKAKEAIERLKKALALDP 371
Query: 329 E-------HGQALVNRQRTALVVEELDR 349
QAL+ + + L+R
Sbjct: 372 NSPLLQLNLAQALLKGGKPQEAIRILNR 399
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 0.137 0.396
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,646,688
Number of extensions: 2706109
Number of successful extensions: 2377
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2367
Number of HSP's successfully gapped: 39
Length of query: 505
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 404
Effective length of database: 6,457,848
Effective search space: 2608970592
Effective search space used: 2608970592
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: 61 (27.0 bits)