RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9159
(259 letters)
>gnl|CDD|179448 PRK02603, PRK02603, photosystem I assembly protein Ycf3;
Provisional.
Length = 172
Score = 33.9 bits (78), Expect = 0.038
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 39 LYYGKKDDKAKA---YNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYI 95
+ Y + KA Y+ +ELN P P L +A H + D++ +E
Sbjct: 80 IIYASNGEHDKALEYYHQALELN---PKQPSALNNIAVIYHKRGEKAEEAGDQDEAEALF 136
Query: 96 LQGIEYAKKAMELAPNN-SNTQKW 118
+ EY K+A+ LAPNN Q W
Sbjct: 137 DKAAEYWKQAIRLAPNNYIEAQNW 160
>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 = 33.5 bits (77), Expect = 0.10
Identities = 22/91 (24%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 41 YGKKDDKAKAYNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYILQGIE 100
Y + D KA + K P++ VL LA L D + +E
Sbjct: 780 YLAQKDYDKAIKHYQTVVKKAPDNAVVLNNLAWLYLELKDPR---------------ALE 824
Query: 101 YAKKAMELAPNNSNTQKWYGICVGANGQFQS 131
YA++A++LAPN G + G+
Sbjct: 825 YAERALKLAPNIPAILDTLGWLLVEKGEADR 855
>gnl|CDD|176974 CHL00033, ycf3, photosystem I assembly protein Ycf3.
Length = 168
Score = 31.9 bits (73), Expect = 0.17
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 39 LYYGKKDDKAKA---YNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYI 95
L + + KA Y +E N P P L +A CH + + D E +E +
Sbjct: 80 LIHTSNGEHTKALEYYFQALERN---PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWF 136
Query: 96 LQGIEYAKKAMELAPNN 112
Q EY K+A+ LAP N
Sbjct: 137 DQAAEYWKQAIALAPGN 153
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 31.7 bits (73), Expect = 0.23
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 11/59 (18%)
Query: 143 RDQMNKAIQMAPKDFTLYSLKGRYQYEISKLSFFERK---IAVLIVSD-----LDEPTA 193
+++ + ++ A + L L+ R LS +++ IA ++ D LDEPTA
Sbjct: 108 EEEIEERVEEALELVGLEGLRDR---SPFTLSGGQKQRVAIAGVLAMDPDILLLDEPTA 163
>gnl|CDD|226414 COG3898, COG3898, Uncharacterized membrane-bound protein [Function
unknown].
Length = 531
Score = 31.7 bits (72), Expect = 0.42
Identities = 48/227 (21%), Positives = 80/227 (35%), Gaps = 63/227 (27%)
Query: 42 GKKDDKAKAYNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYILQGIEY 101
G +D K + ++ DP+ RL LY +R +EA+ Y
Sbjct: 134 GDYEDARKKFEAMLD-------DPET--RLL-GLRGLYLEAQRLGAREAA-------RHY 176
Query: 102 AKKAMELAPNNSNTQKWYGICVGANGQFQSLKEKIKCGVVFRDQMNKAIQMAPKDFTLYS 161
A++A E AP W L+ + G + A+++
Sbjct: 177 AERAAEKAP----QLPWAARAT--------LEARCAAG-----DWDGALKL--------- 210
Query: 162 LKGRYQYEISKLSFFERKIAVLIVS------DLDEPTAEDAIANCLK-AEELAPAPWKEN 214
+ + ++ + ER AVL+ + D D +A D K A +L PA
Sbjct: 211 VDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPA----- 265
Query: 215 QLLIAKCYIEAGEYAKAVQWLDKA-KAIPVVSYESH-DLSTTYSYKR 259
++ A+ G K + L+ A KA P H D++ Y R
Sbjct: 266 AVVAARALFRDGNLRKGSKILETAWKAEP------HPDIALLYVRAR 306
>gnl|CDD|234420 TIGR03967, mycofact_MftB, putative mycofactocin binding protein
MftB. Families TIGR03969 and TIGR03962 describe,
respectively, the putative mycofactocin precursor and
its cognate radical SAM peptide maturase. This small
protein family appears in the same sporadically
distributed cassette and may serve as a scaffolding
protein during mycofactocin maturation or as a carrier
protein for the mature product, a putative novel redox
carrier. A feature of mycofactocin-encoding genomes is
co-clustering with sets of NAD-binding oxidoreductases
in which the NAD is not exchangeable. Therefore it is
proposed that mature mycofactocin, bound by a member of
this family as a carrier protein, docks with the
nicotinoprotein to allow electron transfer. Mediation of
electron transfer through this system would define a
segregated redox pool [Unknown function, General].
Length = 81
Score = 28.9 bits (65), Expect = 0.57
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 166 YQYEISKLSFFERKIAVLIVSDL-DEPTAEDAIA 198
Y + +LSF + + V +V L D P AE A+A
Sbjct: 22 YDFGTRRLSFLKDRTLVEVVESLGDAPVAEAALA 55
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit 3.
Apc3, otherwise known as Cdc27, is one of the subunits
of the anaphase-promoting complex or cyclosome. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. The
protein members of this family contain TPR repeats just
as those of Apc7 do, and it appears that these TPR units
bind the C-termini of the APC co-activators CDH1 and
CDC20.
Length = 80
Score = 28.4 bits (64), Expect = 1.0
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 194 EDAIANCLKAEELAPAPWKENQLLIAKCYIEAGEYAKAVQWLDKAKAIP 242
E+AI K L P+ E+ L+A+CY G+Y +A + L K K
Sbjct: 6 ENAIFLAEKLLALTPSN--EDAYLLAQCYFLQGQYKRAYELLRKLKLDN 52
>gnl|CDD|214844 smart00833, CobW_C, Cobalamin synthesis protein cobW C-terminal
domain. CobW proteins are generally found proximal to
the trimeric cobaltochelatase subunit CobN, which is
essential for vitamin B12 (cobalamin) biosynthesis. They
contain a P-loop nucleotide-binding loop in the
N-terminal domain and a histidine-rich region in the
C-terminal portion suggesting a role in metal binding,
possibly as an intermediary between the cobalt transport
and chelation systems. CobW might be involved in cobalt
reduction leading to cobalt(I) corrinoids. This entry
represents the C-terminal domain found in CobW, as well
as in P47K, a Pseudomonas chlororaphis protein needed
for nitrile hydratase expression.
Length = 92
Score = 28.3 bits (64), Expect = 1.1
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 182 VLIVSDLDEPTAEDAIANCL 201
V I DLDE A+ CL
Sbjct: 73 VFIGRDLDEEAIRAALDACL 92
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 27.7 bits (62), Expect = 1.6
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 17/75 (22%)
Query: 37 RLLYYGKKDDKA-KAYNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYI 95
L+ D+A +AY +EL+ P++ + Y LA A +K ++ +EA
Sbjct: 11 NALFKLGDYDEAIEAYEKALELD---PDNAEAYYNLALAY-----LKLGKDYEEA----- 57
Query: 96 LQGIEYAKKAMELAP 110
+E +KA+EL P
Sbjct: 58 ---LEDLEKALELDP 69
>gnl|CDD|218234 pfam04733, Coatomer_E, Coatomer epsilon subunit. This family
represents the epsilon subunit of the coatomer complex,
which is involved in the regulation of intracellular
protein trafficking between the endoplasmic reticulum
and the Golgi complex.
Length = 288
Score = 29.4 bits (66), Expect = 1.6
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 48 AKAYNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEASEKYILQ 97
+A +L E +K DP+ L L L E S + + Q
Sbjct: 216 EEAESLLKEALDKDAKDPETLINLVVCALHL------GKPAEVSNRNLSQ 259
>gnl|CDD|176757 cd08779, Death_PIDD, Death Domain of p53-induced protein with a
death domain. Death domain (DD) found in PIDD
(p53-induced protein with a death domain) and similar
proteins. PIDD is a component of the PIDDosome complex,
which is an oligomeric caspase-activating complex
involved in caspase-2 activation and plays a role in
mediating stress-induced apoptosis. The PIDDosome
complex is composed of three components, PIDD, RAIDD
and caspase-2, which interact through their DDs and
DD-like domains. The DD of PIDD interacts with the DD
of RAIDD, which also contains a Caspase Activation and
Recruitment Domain (CARD) that interacts with the
caspase-2 CARD. Autoproteolysis of PIDD determines the
downstream signaling event, between pro-survival NF-kB
or pro-death caspase-2 activation. In general, DDs are
protein-protein interaction domains found in a variety
of domain architectures. Their common feature is that
they form homodimers by self-association or
heterodimers by associating with other members of the
DD superfamily including CARD, DED (Death Effector
Domain), and PYRIN. They serve as adaptors in signaling
pathways and can recruit other proteins into signaling
complexes.
Length = 86
Score = 27.4 bits (61), Expect = 2.2
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 31 KYPEIDRLLYYGKKDDKAKAYNLTMELNNKQPNDPDVLYRLAKA 74
Y E+ R+ Y + D + +++ +Q DPD + +L A
Sbjct: 26 SYRELQRIKYNNRDDLDEQIFDMLFSWAQRQAGDPDAVGKLVTA 69
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 26.9 bits (60), Expect = 3.2
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 194 EDAIANCLKAEELAPA-----PWK-ENQLLIAKCYIEAGEYAKAVQWLDKAKAI 241
++A+ KA ELA P +A+ Y+ G+Y +A+++L+KA A+
Sbjct: 22 DEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLEKALAL 75
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 26.1 bits (58), Expect = 4.5
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 194 EDAIANCLKAEELAPAPWKENQLLIAKCYIEAGEYAKAVQWLDKAKAI 241
++A+A A P E LL+ + + G A+A L A A
Sbjct: 14 DEALAALEAALARYPLAA-EALLLLGEALLRQGRLAEAAALLRAALAA 60
>gnl|CDD|130116 TIGR01044, rplV_bact, ribosomal protein L22, bacterial type. This
model decribes bacterial and chloroplast ribosomal
protein L22 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 103
Score = 27.1 bits (60), Expect = 4.6
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 170 ISKLSFFERKIAVLIVSDLDEPTAEDAIANCLKAEELAPAPWKENQLLIAKCYIEAGEYA 229
+ L F +K A LI + AIAN L + L++ +++ G
Sbjct: 29 LDILRFTPKKAAPLI-----KKVLASAIANAEHNYGLDA-----DNLVVVTIFVDEGPTL 78
Query: 230 KAVQWLDKAKAIPVVSYESH 249
K ++ K +A + SH
Sbjct: 79 KRIRPRAKGRASRIRKRTSH 98
>gnl|CDD|227122 COG4783, COG4783, Putative Zn-dependent protease, contains TPR
repeats [General function prediction only].
Length = 484
Score = 28.1 bits (63), Expect = 4.7
Identities = 16/82 (19%), Positives = 25/82 (30%), Gaps = 9/82 (10%)
Query: 41 YGKKDDKAKAYNLTMELNNKQPNDPDVLYRLAKACHCLYDIKRRENDKEA-SEKYILQG- 98
K +A + P DP+ LA+A L + A +E Y L G
Sbjct: 384 LLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAE---ALLARAEGYALAGR 440
Query: 99 ----IEYAKKAMELAPNNSNTQ 116
I + +A +
Sbjct: 441 LEQAIIFLMRASQQVKLGFPDW 462
>gnl|CDD|236624 PRK09782, PRK09782, bacteriophage N4 receptor, outer membrane
subunit; Provisional.
Length = 987
Score = 28.3 bits (63), Expect = 5.1
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 97 QGIEYAKKAMELAPNNSNTQKWYGICVGANG 127
+ + A+EL PNNSN Q G + +G
Sbjct: 627 AAVSDLRAALELEPNNSNYQAALGYALWDSG 657
>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 = 26.6 bits (59), Expect = 6.1
Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 21/95 (22%)
Query: 147 NKAIQMAPKDFTLYSLKGRYQYEISKLSFFERKIAVLIVSDLDEPTAEDAIANCLKAEEL 206
KA+++ P + Y Y++ K E+A+ + KA EL
Sbjct: 24 EKALELDPDNADAYYNLAAAYYKLGKY--------------------EEALEDYEKALEL 63
Query: 207 APAPWKENQLLIAKCYIEAGEYAKAVQWLDKAKAI 241
P + + Y + G+Y +A++ +KA +
Sbjct: 64 DPD-NAKAYYNLGLAYYKLGKYEEALEAYEKALEL 97
>gnl|CDD|163532 TIGR03820, lys_2_3_AblA, lysine-2,3-aminomutase. This model
describes lysine-2,3-aminomutase as found along with
beta-lysine acetyltransferase in a two-enzyme pathway
for making the compatible solute
N-epsilon-acetyl-beta-lysine. This compatible solute, or
osmolyte, is known to protect a number of methanogenic
archaea against salt stress. The trusted cutoff
distinguishes a tight clade with essentially full-length
homology from additional homologs that are shorter or
highly diverged in the C-terminal region. All members of
this family have the radical SAM motif CXXXCXXC, while
some but not all have a second copy of the motif in the
C-terminal region.
Length = 417
Score = 27.4 bits (61), Expect = 7.8
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 10/47 (21%)
Query: 65 PD-VLYRLAKAC-----HCLYDIKRRENDKEA--SEKYILQGIEYAK 103
PD VL+ ++ C HC KR+ D+++ S++ IL+GIEY +
Sbjct: 107 PDRVLFLVSNTCAMYCRHCTR--KRKVGDRDSIPSKEQILEGIEYIR 151
>gnl|CDD|199906 cd10318, RGL11, Rhamnogalacturonan lyase of the polysaccharide
lyase family 11. The rhamnogalacturonan lyase of the
polysaccharide lyase family 11 (RGL11) cleaves glycoside
bonds in polygalacturonan as well as RG
(rhamnogalacturonan) type-I through a beta-elimination
reaction. Functionally characterized members of this
family, YesW and YesX from Bacillus subtilis, cleave
glycoside bonds between rhamnose and galacturonic acid
residues in the RG-I region of plant cell wall pectin.
YesW and YesX work synergistically, with YesW cleaving
the glycoside bond of the RG chain endolytically, and
YesX converting the resultant oligosaccharides through
an exotype reaction. This domain is sometimes found in
architectures with non-catalytic carbohydrate-binding
modules (CBMs). There are two types of RG lyases, which
both cleave the alpha-1,4 bonds of the RG-I main chain
through a beta-elimination reaction, but belong to two
structurally unrelated polysaccharide lyase (PL)
families, 4 and 11.
Length = 564
Score = 27.6 bits (62), Expect = 8.7
Identities = 9/21 (42%), Positives = 9/21 (42%)
Query: 81 IKRRENDKEASEKYILQGIEY 101
I D S YIL G EY
Sbjct: 207 IGDASADYRNSSGYILSGPEY 227
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 27.3 bits (61), Expect = 9.3
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 62 PNDPDVLYRLAKACHCLYDIKRRENDKE 89
+D VL + A A + R+ND +
Sbjct: 289 SSDSAVL-KKAGAARARAILALRDNDAD 315
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
0.318 0.133 0.393
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,967,544
Number of extensions: 1214113
Number of successful extensions: 1221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1212
Number of HSP's successfully gapped: 56
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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 (21.7 bits)
S2: 58 (26.0 bits)