RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4703
(401 letters)
>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 = 73.6 bits (181), Expect = 3e-16
Identities = 35/94 (37%), Positives = 52/94 (55%), Gaps = 4/94 (4%)
Query: 10 NKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIED 69
L GN +K GDY+ AL++Y KAL++ + A N AA Y K + ++ +ED
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALEL----DPDNADAYYNLAAAYYKLGKYEEALED 56
Query: 70 CSKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTD 103
K+LE+ PD+ KA + AY +GK+EEA
Sbjct: 57 YEKALELDPDNAKAYYNLGLAYYKLGKYEEALEA 90
Score = 45.8 bits (109), Expect = 1e-06
Identities = 22/66 (33%), Positives = 34/66 (51%)
Query: 49 CLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIH 108
L N +Y K D+ +E K+LE+ PD+ A + AY +GK+EEA D +
Sbjct: 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKAL 61
Query: 109 RVEPTN 114
++P N
Sbjct: 62 ELDPDN 67
Score = 38.9 bits (91), Expect = 4e-04
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 20 FKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPD 79
+K G YE AL+ Y KAL++ + A N Y K + ++ +E K+LE+ P+
Sbjct: 45 YKLGKYEEALEDYEKALELDPDN----AKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
>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 = 69.6 bits (170), Expect = 7e-13
Identities = 46/156 (29%), Positives = 71/156 (45%), Gaps = 19/156 (12%)
Query: 11 KLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDC 70
KLKE GN A++ D+ A+ Y+KA+ E NRAA + +KV+ED
Sbjct: 129 KLKEKGNKAYRNKDFNKAIKLYSKAI-----ECKPDPVYYSNRAACHNALGDWEKVVEDT 183
Query: 71 SKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEP-TNKAIQPVLSRLFAIVT 129
+ +LE+ PD KAL RR AY+ +GK+ +A D ++ N+ + RL
Sbjct: 184 TAALELDPDYSKALNRRANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLL---- 239
Query: 130 KRMQENEQLQNKVHNMFKYVFDTSAPMDKRVTAVNN 165
+ ++K K + +T VT V N
Sbjct: 240 -----KKFAESKA----KEILETKPENLPSVTFVGN 266
Score = 33.0 bits (75), Expect = 0.31
Identities = 27/115 (23%), Positives = 49/115 (42%), Gaps = 12/115 (10%)
Query: 8 DYNKLKE--------SGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLK 59
D KL E G +G + AL +K++++ + RA++ L+
Sbjct: 322 DLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYI----KRASMNLE 377
Query: 60 QNQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTN 114
DK ED K+L++ +DP + R Q + G+F +A D + ++P
Sbjct: 378 LGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDF 432
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 51.9 bits (125), Expect = 6e-09
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 5/73 (6%)
Query: 7 NDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQN-DK 65
++ LK GN+ FK GDY+ A++ Y KAL++ + A N A YLK ++ ++
Sbjct: 1 DNAEALKNLGNALFKLGDYDEAIEAYEKALEL----DPDNAEAYYNLALAYLKLGKDYEE 56
Query: 66 VIEDCSKSLEIVP 78
+ED K+LE+ P
Sbjct: 57 ALEDLEKALELDP 69
Score = 51.2 bits (123), Expect = 9e-09
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 45 ERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGK-FEEAYTD 103
+ A LKN K D+ IE K+LE+ PD+ +A + AY +GK +EEA D
Sbjct: 1 DNAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALED 60
Query: 104 AKHIHRVEP 112
+ ++P
Sbjct: 61 LEKALELDP 69
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 42.4 bits (100), Expect = 2e-05
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTA---EESHERATCLKNRAAVYLKQNQNDKVIEDCSK 72
+ GDY+ AL+ KAL++ E+ E A L N A +YL D+ +E K
Sbjct: 12 ALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLEK 71
Query: 73 SLEI 76
+L +
Sbjct: 72 ALAL 75
Score = 30.4 bits (69), Expect = 0.24
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 45 ERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIV----PDDPK---ALFRRCQAYEAIGKF 97
+ A L N A V + D+ +E K+LE+ D P+ AL + Y A+G +
Sbjct: 3 DLAAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDY 62
Query: 98 EEA 100
+EA
Sbjct: 63 DEA 65
>gnl|CDD|179448 PRK02603, PRK02603, photosystem I assembly protein Ycf3;
Provisional.
Length = 172
Score = 44.3 bits (105), Expect = 2e-05
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 15 SGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSL 74
G SA G+Y AL+ Y +ALK+ E+ ++R+ L N +Y ++DK +E ++L
Sbjct: 41 DGMSAQADGEYAEALENYEEALKLE-EDPNDRSYILYNMGIIYASNGEHDKALEYYHQAL 99
Query: 75 EIVPDDPKAL 84
E+ P P AL
Sbjct: 100 ELNPKQPSAL 109
>gnl|CDD|221172 pfam11701, UNC45-central, Myosin-binding striated muscle assembly
central. The UNC-45 or small muscle protein 1 of
C.elegans is expressed in two forms from different
genomic positions in mammals, as a general tissue
protein UNC-45a and a specific form Unc-45b expressed
only in striated and skeletal muscle. All members carry
up to three amino-terminal tetratricopeptide repeat
(TPR) domains towards their N-terminal, a UCS domain at
the C-terminal that contains a number of Arm repeats
pfam00514 and this central region of approximately 400
residues. Both the general form and the muscle form of
UNC-45 function in myotube formation through cell
fusion. Myofibril formation requires both GC and SM
UNC-45, consistent with the fact that the cytoskeleton
is necessary for the development and maintenance of
organised myofibrils. The S. pombe Rng3p, is crucial for
cell shape, normal actin cytoskeleton, and contractile
ring assembly, and is essential for assembly of the
myosin II-containing progenitors of the contractile
ring. Widespread defects in the cytoskeleton are found
in null mutants of all three fungal proteins. Mammalian
Unc45 is found to act as a specific chaperone during the
folding of myosin and the assembly of striated muscle by
forming a stable complex with the general chaperone
Hsp90. The exact function of this central region is not
known.
Length = 155
Score = 42.2 bits (100), Expect = 1e-04
Identities = 17/32 (53%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 211 IIKQGVDILKRLYM-SKNENIRVRALVGLCKL 241
I K G++ LK LY SK++ I+V A V LCKL
Sbjct: 124 ISKNGLEWLKDLYKNSKDDEIKVLAAVVLCKL 155
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 35.5 bits (83), Expect = 0.001
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 47 ATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDD 80
A L N YLK + D+ +E K+LE+ P++
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
Score = 33.5 bits (78), Expect = 0.007
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 16 GNSAFKQGDYETALDFYTKALKV 38
GN+ K G Y+ AL++Y KAL++
Sbjct: 8 GNAYLKLGKYDEALEYYEKALEL 30
Score = 27.0 bits (61), Expect = 1.4
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 81 PKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTN 114
KAL+ AY +GK++EA + + P N
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
>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 = 35.5 bits (83), Expect = 0.002
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 47 ATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDD 80
A L N YLK D+ +E K+LE+ P++
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
Score = 33.6 bits (78), Expect = 0.008
Identities = 12/23 (52%), Positives = 18/23 (78%)
Query: 16 GNSAFKQGDYETALDFYTKALKV 38
GN+ K GDY+ AL++Y KAL++
Sbjct: 8 GNAYLKLGDYDEALEYYEKALEL 30
>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 = 39.7 bits (93), Expect = 0.003
Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 4/111 (3%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLE 75
G + GD A+ + K L + + A L A Y K I ++LE
Sbjct: 608 GRAQLAAGDLNKAVSSFKKLLALQPDS----ALALLLLADAYAVMKNYAKAITSLKRALE 663
Query: 76 IVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLFA 126
+ PD+ +A Q A + E A AK + + P + L+
Sbjct: 664 LKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYL 714
Score = 39.3 bits (92), Expect = 0.004
Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 4/96 (4%)
Query: 5 NMNDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQND 64
L +G S ++ G+ E A + + LK A SH+ L A++ L+ + D
Sbjct: 291 APEYLPALLLAGASEYQLGNLEQAYQYLNQILKY-APNSHQARRLL---ASIQLRLGRVD 346
Query: 65 KVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEA 100
+ I S +L + PDDP AL +AY A+G FE+A
Sbjct: 347 EAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKA 382
Score = 33.1 bits (76), Expect = 0.33
Identities = 16/99 (16%), Positives = 35/99 (35%), Gaps = 4/99 (4%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLE 75
G+ G+ E AL Y KA+ + A + ++ + ++ + L+
Sbjct: 200 GDLLLSLGNIELALAAYRKAIALRPNNIAVLL----ALATILIEAGEFEEAEKHADALLK 255
Query: 76 IVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTN 114
P+ P A + + +E+A + + P
Sbjct: 256 KAPNSPLAHYLKALVDFQKKNYEDARETLQDALKSAPEY 294
Score = 32.4 bits (74), Expect = 0.50
Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 11/105 (10%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYL---KQNQNDKVIEDCSK 72
G+ +Q DY A+ Y KALK + L + K +E
Sbjct: 710 GDLYLRQKDYPAAIQAYRKALKRAPS-----SQNAIKLHRALLASGNTAEAVKTLEA--- 761
Query: 73 SLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAI 117
L+ P+D + Y A +++A + + + P N +
Sbjct: 762 WLKTHPNDAVLRTALAELYLAQKDYDKAIKHYQTVVKKAPDNAVV 806
Score = 30.8 bits (70), Expect = 1.3
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 4/83 (4%)
Query: 22 QGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDDP 81
+ ++ A + L TA+ + A LK + L + + K++ + P++
Sbjct: 172 ENRFDEARALIDEVL--TADPGNVDALLLK--GDLLLSLGNIELALAAYRKAIALRPNNI 227
Query: 82 KALFRRCQAYEAIGKFEEAYTDA 104
L G+FEEA A
Sbjct: 228 AVLLALATILIEAGEFEEAEKHA 250
Score = 29.7 bits (67), Expect = 3.5
Identities = 24/109 (22%), Positives = 43/109 (39%), Gaps = 4/109 (3%)
Query: 18 SAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIV 77
S + G ++ AL A K ++ + A+ A+YL + K E K+L I
Sbjct: 440 SYLRSGQFDKAL----AAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE 495
Query: 78 PDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLFA 126
PD A + G ++A + + ++P N L+ L+
Sbjct: 496 PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYL 544
Score = 28.9 bits (65), Expect = 6.0
Identities = 25/121 (20%), Positives = 43/121 (35%), Gaps = 10/121 (8%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLE 75
G + G E A Y +AL + A + L +N+ D+ + L
Sbjct: 132 GLAYLGLGQLELAQKSYEQALAIDPR----SLYAKLGLAQLALAENRFDEARALIDEVLT 187
Query: 76 IVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLFAIVTKRMQEN 135
P + AL + ++G E A + + P N A+ L A+ T ++
Sbjct: 188 ADPGNVDALLLKGDLLLSLGNIELALAAYRKAIALRPNNIAV------LLALATILIEAG 241
Query: 136 E 136
E
Sbjct: 242 E 242
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 38.7 bits (88), Expect = 0.004
Identities = 34/121 (28%), Positives = 57/121 (47%), Gaps = 2/121 (1%)
Query: 7 NDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKV 66
D + + + ++ GDYE AL+ Y KAL+ E +E A L A+ + ++
Sbjct: 128 PDLAEALLALGALYELGDYEEALELYEKALE-LDPELNELAEALLALGALLEALGRYEEA 186
Query: 67 IEDCSKSLEIVPD-DPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLF 125
+E K+L++ PD D +AL Y +GK+EEA + ++P N L+ L
Sbjct: 187 LELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLL 246
Query: 126 A 126
Sbjct: 247 L 247
Score = 37.1 bits (84), Expect = 0.010
Identities = 30/112 (26%), Positives = 51/112 (45%), Gaps = 3/112 (2%)
Query: 1 MIDNNMNDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQ 60
+ L G G YE AL+ KALK+ ++ E L N +YLK
Sbjct: 159 LDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAE---ALLNLGLLYLKL 215
Query: 61 NQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEP 112
+ ++ +E K+LE+ PD+ +AL+ +G++EEA + ++P
Sbjct: 216 GKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALELDP 267
>gnl|CDD|215568 PLN03088, PLN03088, SGT1, suppressor of G2 allele of SKP1;
Provisional.
Length = 356
Score = 38.6 bits (90), Expect = 0.005
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 10 NKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIED 69
L++ AF D+ A+D YT+A+ + A +RA +K + + D
Sbjct: 3 KDLEDKAKEAFVDDDFALAVDLYTQAI----DLDPNNAELYADRAQANIKLGNFTEAVAD 58
Query: 70 CSKSLEIVPDDPKALFRRCQAYEAIGKFEEA 100
+K++E+ P KA R+ A + +++ A
Sbjct: 59 ANKAIELDPSLAKAYLRKGTACMKLEEYQTA 89
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 34.2 bits (79), Expect = 0.011
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 4/66 (6%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLE 75
+A + GDY+ AL AL A L L+Q + + +L
Sbjct: 4 ARAALRAGDYDEALAALEAALA----RYPLAAEALLLLGEALLRQGRLAEAAALLRAALA 59
Query: 76 IVPDDP 81
PDDP
Sbjct: 60 ADPDDP 65
>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 = 34.6 bits (80), Expect = 0.063
Identities = 25/108 (23%), Positives = 49/108 (45%), Gaps = 3/108 (2%)
Query: 7 NDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKV 66
N+ + L G +QG YE A+ + +A++ R+ L+N LK DK
Sbjct: 97 NNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARS--LENAGLCALKAGDFDKA 154
Query: 67 IEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEA-YTDAKHIHRVEPT 113
+ +++L+I P P++L + Y G++++A ++ T
Sbjct: 155 EKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQT 202
Score = 33.5 bits (77), Expect = 0.15
Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 11/97 (11%)
Query: 20 FKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPD 79
+QGD E A + KAL+ ++ A Y + + +K + ++L + P+
Sbjct: 42 LEQGDLEVAKENLDKALEHDPDDYLAYLA----LALYYQQLGELEKAEDSFRRALTLNPN 97
Query: 80 DPKA-------LFRRCQAYEAIGKFEEAYTDAKHIHR 109
+ L ++ + +A+ +FE+A D +
Sbjct: 98 NGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQP 134
Score = 30.0 bits (68), Expect = 2.1
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 54 AAVYLKQNQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEA 100
A YL+Q + E+ K+LE PDD A Y+ +G+ E+A
Sbjct: 38 ALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKA 84
>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 = 30.2 bits (69), Expect = 0.13
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 16 GNSAFKQGDYETALDFYTKALK 37
G + +K GDYE AL+ Y KAL+
Sbjct: 8 GLAYYKLGDYEEALEAYEKALE 29
Score = 27.5 bits (62), Expect = 1.2
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 47 ATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDD 80
A L N Y K ++ +E K+LE+ P++
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
Score = 27.5 bits (62), Expect = 1.3
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 81 PKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTN 114
+AL+ AY +G +EEA + ++P N
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
>gnl|CDD|222285 pfam13646, HEAT_2, HEAT repeats. This family includes multiple
HEAT repeats.
Length = 88
Score = 31.2 bits (71), Expect = 0.21
Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 19/84 (22%)
Query: 219 LKRLYMSKNENIRVRALVGLCKLGSMGGSDASIRPFADGSTRKLAEACRRFLVNPARDPD 278
L+ L + +R A L +LG + A L +P DP+
Sbjct: 5 LEALLSDPDPEVRAAAARALGELGD----------------PEALPALLELLKDP--DPE 46
Query: 279 IRRWAAEGLAYLTLDAEVKEALIE 302
+RR AAE L L D E AL+E
Sbjct: 47 VRRAAAEALGKLG-DPEALPALLE 69
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 29.6 bits (67), Expect = 1.0
Identities = 25/92 (27%), Positives = 35/92 (38%), Gaps = 12/92 (13%)
Query: 277 PDIRRW-AAEGLAYLTLDAEVKEALIEDKPALAALVDVASSVKYKNVWNGTQSDALKDVD 335
++ W A E+ +AL E ALA LV +W Q +A + +
Sbjct: 39 KVLKEWREELRAALAPAAPELPDALSE---ALAELV--------AALWEAAQEEAEERLA 87
Query: 336 KAFDEFMEEVAKLEKEEAEMLETLYQDEKELA 367
A E A+LE E AE E+EL
Sbjct: 88 AARAAAEAERAELEAELAEAAAEAEALEEELE 119
>gnl|CDD|176974 CHL00033, ycf3, photosystem I assembly protein Ycf3.
Length = 168
Score = 30.0 bits (68), Expect = 1.2
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLE 75
G SA +G+Y AL Y +A+++ + ++R+ L N ++ ++ K +E ++LE
Sbjct: 42 GMSAQSEGEYAEALQNYYEAMRLE-IDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE 100
Query: 76 IVPDDPKAL 84
P P+AL
Sbjct: 101 RNPFLPQAL 109
>gnl|CDD|234447 TIGR04046, MSMEG_0569_nitr, flavin-dependent oxidoreductase,
MSMEG_0569 family. Members of this protein family
belong to a conserved seven-gene biosynthetic cluster
found sparsely in Cyanobacteria, Proteobacteria, and
Actinobacteria. Distant homologies to characterized
proteins suggest that members are enzymes dependent on a
flavinoid cofactor.
Length = 400
Score = 30.8 bits (70), Expect = 1.2
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 275 RDPDIRRWAAEGLA-YLTLDAEVKEALIEDKPALAALVDVASSV 317
RD D+RR+A EG+ Y L+ +++E + P L A +D A +V
Sbjct: 244 RDIDLRRFALEGMQLYGRLE-DIREGQLRFAPDLKANLDGADAV 286
>gnl|CDD|225605 COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 250
Score = 30.5 bits (69), Expect = 1.4
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 21 KQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDD 80
QG E A+ + +AL A E + L+N LK Q D+ E ++LE+ P
Sbjct: 115 AQGRPEEAMQQFERALADPA--YGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQF 172
Query: 81 PKAL 84
P AL
Sbjct: 173 PPAL 176
Score = 28.9 bits (65), Expect = 4.3
Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 20 FKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPD 79
+QGDY A KAL+ + S+ A + RA Y K +ND E K+L + P+
Sbjct: 46 LQQGDYAQAKKNLEKALE--HDPSYYLAHLV--RAHYYQKLGENDLADESYRKALSLAPN 101
Query: 80 DPKALFRRCQAYEAIGKFEEAY 101
+ L A G+ EEA
Sbjct: 102 NGDVLNNYGAFLCAQGRPEEAM 123
>gnl|CDD|217277 pfam02901, PFL, Pyruvate formate lyase.
Length = 646
Score = 30.7 bits (70), Expect = 1.5
Identities = 24/90 (26%), Positives = 32/90 (35%), Gaps = 16/90 (17%)
Query: 277 PDIRRWAAEGLAYLTLDAEVKEALIEDKPALAALVDVASSVKYKNVWNGTQSDALKDVDK 336
D RR GL L + E E AL + YK A+
Sbjct: 161 GDYRRVLLYGLDGLIAEKE------EKLAALDLTDPEDADKIYK---------AMIISCD 205
Query: 337 AFDEFMEEVAKLEKEEAEMLETLYQDEKEL 366
A + E A+L +E AE ET + + EL
Sbjct: 206 AVINYAERYARLAEELAEQ-ETDPKRKAEL 234
>gnl|CDD|205550 pfam13371, TPR_9, Tetratricopeptide repeat.
Length = 73
Score = 28.3 bits (64), Expect = 1.6
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 50 LKNRAAVYLKQNQNDKVIEDCSKSLEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHR 109
LK YL++ ++ + + L + PDDP R Y +G F+ A D ++
Sbjct: 1 LKAI---YLREEDFERALAVVERLLLLAPDDPYERRDRGLLYAQLGCFQAALADLEYFLE 57
Query: 110 VEPTNKAIQPVLSRL 124
+ P + + +L
Sbjct: 58 LCPDAPDAERIREQL 72
>gnl|CDD|213363 cd12829, Alr1p-like, Saccharomyces cerevisiae Alr1p-like subfamily.
This eukaryotic subfamily belongs to the Thermotoga
maritima CorA (TmCorA)-family of the MIT superfamily of
essential membrane proteins involved in transporting
divalent cations (uptake or efflux) across membranes.
This subfamily includes three Saccharomyces cerevisiae
members: two plasma membrane proteins, the Mg2+
transporter Alr1p/Swc3p and the putative Mg2+
transporter, Alr2p, and the vacuole membrane protein
Mnr2p, a putative Mg2+ transporter. Thermotoga maritima
CorA forms funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by Alr1p. Natural variants in this signature
sequence may be associated with the transport of
different divalent cations. The functional diversity of
the MIT superfamily may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 305
Score = 30.3 bits (69), Expect = 1.7
Identities = 13/78 (16%), Positives = 38/78 (48%), Gaps = 11/78 (14%)
Query: 142 VHNMFKYVFDTSAP----MDKRVTAVNNLVVLAREMSGAEMLLKSGVA-KQINTLLKCET 196
++ + + D+ P ++K V +++ LV+L +++L + G +++ +LL+
Sbjct: 110 LYALLDSIVDSFFPLVDSIEKEVDSIDELVLLISSSDQSDLLRRIGDLRRRVTSLLRL-- 167
Query: 197 NEEIYLGEEDFITSIIKQ 214
+ D + ++K+
Sbjct: 168 ----LFAKSDVLKQLLKR 181
>gnl|CDD|223423 COG0346, GloA, Lactoylglutathione lyase and related lyases [Amino
acid transport and metabolism].
Length = 138
Score = 29.3 bits (65), Expect = 2.1
Identities = 12/102 (11%), Positives = 26/102 (25%), Gaps = 9/102 (8%)
Query: 24 DYETALDFYTKALKVT-AEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDDPK 82
D E ++DFYT L + +++ A ++L + + +
Sbjct: 12 DLEASIDFYTDVLGLRLVKDTVNEADDGGGYHLLFLDGDGGPGELLA--------FFGFE 63
Query: 83 ALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRL 124
+ H+ L+ L
Sbjct: 64 GRAGTGFVGDVALGVPGGDLGLGHLAFEVDDEAFGDAALAFL 105
>gnl|CDD|173083 PRK14620, PRK14620, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 326
Score = 29.4 bits (66), Expect = 3.1
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 208 ITSIIKQGVDILKRLYMSKNENIRVRALVGLCKLGSM 244
++I +G++ +K LY +KN +I + L+G LG +
Sbjct: 210 HAAVITKGMNEIKTLYSAKNGSIDLNTLIGPSCLGDL 246
>gnl|CDD|237099 PRK12428, PRK12428, 3-alpha-hydroxysteroid dehydrogenase;
Provisional.
Length = 241
Score = 29.2 bits (66), Expect = 3.2
Identities = 22/90 (24%), Positives = 31/90 (34%), Gaps = 11/90 (12%)
Query: 286 GLAYLTLDAEVKEALIEDKPALAALVDVASSVKYKNVWNGTQSDALKDVDKAFDEFMEEV 345
GL +LT EAL+ A+V+VAS + AL +E
Sbjct: 74 GLRHLT------EALLPRMAPGGAIVNVASLAGAEWPQRLELHKALAAT-----ASFDEG 122
Query: 346 AKLEKEEAEMLETLYQDEKELADFYSLLST 375
A L T YQ KE +++
Sbjct: 123 AAWLAAHPVALATGYQLSKEALILWTMRQA 152
>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 = 27.2 bits (61), Expect = 3.4
Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 7/80 (8%)
Query: 21 KQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEIVPDD 80
QG+YE A+ K L +T Y Q Q + E K
Sbjct: 1 DQGNYENAIFLAEKLLALTPSNEDAYLLAQ-----CYFLQGQYKRAYELLRKLKLDNSSG 55
Query: 81 PKALFRRCQAYEAIGKFEEA 100
+ L +C +GK++EA
Sbjct: 56 CRYLLAQC--LLKLGKYDEA 73
>gnl|CDD|187833 cd09702, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as TIGR02710 family.
Length = 378
Score = 29.5 bits (66), Expect = 3.5
Identities = 25/115 (21%), Positives = 42/115 (36%), Gaps = 5/115 (4%)
Query: 19 AFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQNDKVIEDCSKSLEI-V 77
AF GDYETAL L+ E+H + YL ++ + E+ L +
Sbjct: 141 AFNAGDYETALAILENLLRRVLAENHTFYEAMIKLTRAYLHWDRFE--HEEALDYLNSDL 198
Query: 78 PDDP-KALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLFAIVTKR 131
+ +A Q + + D + R + +P+L L A +R
Sbjct: 199 VNSLEEAEDVLKQNKSIVHEIASISLDQQAS-RNGARKQKYRPLLPDLLANAERR 252
>gnl|CDD|214492 smart00055, FCH, Fes/CIP4 homology domain. Alignment extended from
original report. Highly alpha-helical. Also known as the
RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Length = 87
Score = 27.7 bits (62), Expect = 3.6
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 336 KAFDEFMEEVAKLEKEEAEMLETLYQ 361
+ +FM E AK+E+E A+ L+ L +
Sbjct: 26 EDLKKFMRERAKIEEEYAKKLQKLSK 51
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 26.0 bits (58), Expect = 3.7
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 21 KQGDYETALDFYTKALKVTAEESHER 46
K GDYE A+ Y +AL + +
Sbjct: 11 KLGDYEKAISLYERALALAKDPEDRE 36
>gnl|CDD|225647 COG3105, COG3105, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 138
Score = 28.2 bits (63), Expect = 3.7
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 331 LKDVDKAFDEFMEEVAKLEKEEAEMLETLYQDEKELADFYSLLST 375
L+ V DE+ +E+ K AE+L+TL QD ++L + ST
Sbjct: 43 LEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQKLYQHMAKSST 87
>gnl|CDD|205609 pfam13431, TPR_17, Tetratricopeptide repeat.
Length = 34
Score = 26.0 bits (58), Expect = 4.0
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 70 CSKSLEIVPDDPKALFRRCQAYEAIGKFEEA 100
K+LE+ P++ +A + +G+++EA
Sbjct: 2 YEKALELDPNNAEAYYNLALLLLNLGQYDEA 32
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 29.0 bits (66), Expect = 4.6
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 147 KYVFDTSAPMDKRVTAVNN--LVVLAREMSGAEMLLKSGV 184
+ D +AP D VTA++N L +AR +GA +G+
Sbjct: 403 DHTHDVTAPRDGYVTAIDNRRLARIARL-AGAPKDKGAGI 441
>gnl|CDD|217441 pfam03232, COQ7, Ubiquinone biosynthesis protein COQ7. Members of
this family contain two repeats of about 90 amino acids,
that contains two conserved motifs. One of these DXEXXH
may be part of an enzyme active site.
Length = 170
Score = 28.3 bits (64), Expect = 4.7
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 332 KDVDKAFDEFMEEVAKLEKEEAEMLETLYQDEKELADFYSLLSTLV 377
D DK E E +AK EE E +T + E A Y LLS +
Sbjct: 114 LDDDK---ELKETIAKFRDEELEHRDTAIEHGAEQAPAYPLLSGAI 156
>gnl|CDD|233875 TIGR02457, TreS_Cterm, trehalose synthase-fused probable
maltokinase. Three pathways for the biosynthesis of
trehalose, an osmoprotectant that in some species is
also a precursor of certain cell wall glycolipids.
Trehalose synthase, TreS, can interconvert maltose and
trehalose, but while the equilibrium may favor
trehalose, physiological concentrations of trehalose may
be much greater than that of maltose and TreS may act
largely in its degradation. This model describes a
domain found only as a C-terminal fusion to TreS
proteins. The most closely related proteins outside this
family, Pep2 of Streptomyces coelicolor and Mak1 of
Actinoplanes missouriensis, have known maltokinase
activity. We suggest this domain acts as a maltokinase
and helps drive conversion of trehalose to maltose
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 528
Score = 28.9 bits (65), Expect = 5.5
Identities = 23/117 (19%), Positives = 32/117 (27%), Gaps = 11/117 (9%)
Query: 258 STRKLAEACRRFLVNPARDPDIRRWAAEGLAYLTLDAEVKEALIEDKPALAALVDVA--- 314
+ L L A G YL + L E ALAA +
Sbjct: 254 TLGHLKRYIEEQLSPCANGAL--APTLIGAGYLEFAGLLGRRLAELHLALAAGGEDPAFA 311
Query: 315 ---SSVKYKNVWNGTQSDALKDVDKAFDEFMEEVAKLEKEEAEMLETLYQDEKELAD 368
S Y+ W D ++A + L + + L KELA
Sbjct: 312 PEPISTLYQRSW---YQDMRAQAERALQLLAQSRDGLPAAARALADRLLAQRKELAA 365
>gnl|CDD|233137 TIGR00811, sit, silicon transporter. Marine diatoms such as
Cylindrotheca fusiformis encode at least six silicon
transport protein homologues which exhibit similar size
and topology. One characterized member of the family
(Sit1) functions in the energy-dependent uptake of
either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by
a Na+ symport mechanism. The system is found in marine
diatoms which make their "glass houses" out of silicon
[Transport and binding proteins, Other].
Length = 545
Score = 28.8 bits (64), Expect = 5.8
Identities = 12/44 (27%), Positives = 20/44 (45%)
Query: 5 NMNDYNKLKESGNSAFKQGDYETALDFYTKALKVTAEESHERAT 48
N+ + ++ + S ++ +E AL KAL E E AT
Sbjct: 490 NIRELREMINNAISDEEKTTFEAALAIEVKALDKLNAEEEEEAT 533
>gnl|CDD|225819 COG3280, TreY, Maltooligosyl trehalose synthase [Carbohydrate
transport and metabolism].
Length = 889
Score = 29.0 bits (65), Expect = 6.1
Identities = 26/115 (22%), Positives = 42/115 (36%), Gaps = 2/115 (1%)
Query: 239 CKLGSMGGSDASIRPFADGSTRKLAEACRRFLVNPARDPDIRRWAAEGLAYLTLDAEVKE 298
LG++ I R+ R L P+I E LA D E +
Sbjct: 180 FLLGNLNAILERIAAVPSTRERETQAQFRAALAEILATPNIAACLDECLARFNADPEQLD 239
Query: 299 ALIEDKP-ALAALVDVASSVKYKNVWNGTQSDALKDVDKA-FDEFMEEVAKLEKE 351
AL E + LA+ A + Y+ ++ L+ D A F+ + +L +E
Sbjct: 240 ALHERQHYRLASWRVAADEINYRRFFDVNSLAGLRVEDPAVFEATHRLIFELLRE 294
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 28.0 bits (63), Expect = 7.5
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 139 QNKVHNMFKYVFDTSAPMDKRVTAVNNLVVLAREMSGAEMLLKSGVAKQ-INTLL 192
++ + K F +A DK V A N+V L + E L + +N+ L
Sbjct: 39 ESNAGDPKKIGFSRAARTDKGVHAARNVVSLKVIIDDPEGLGILEDLVEKLNSHL 93
>gnl|CDD|197854 smart00745, MIT, Microtubule Interacting and Trafficking molecule
domain.
Length = 77
Score = 26.5 bits (59), Expect = 7.8
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 21 KQGDYETALDFYTKALK-----VTAEESHERATCLKNRAAVYLK 59
+ G+YE AL+ Y KA++ + E +R LK +AA YL
Sbjct: 20 EAGNYEEALELYKKAIEYLLEGIKVESDSKRREALKAKAAEYLD 63
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.4 bits (64), Expect = 7.9
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 327 QSDALKDVDKAFDEFMEEVAKLEKEEAEMLETLYQDEKELAD 368
++ D D+ E E+A LE E A LE +Q EKEL +
Sbjct: 441 EAALGADHDERLAELRAELAALEAELAA-LEARWQQEKELVE 481
>gnl|CDD|226687 COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 287
Score = 28.1 bits (63), Expect = 8.3
Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 7/128 (5%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCLKNRAAVYLKQNQND--KVIEDCSKS 73
G + G AL Y AL++ A ++ E L A+Y + Q K ++
Sbjct: 163 GRAYMALGRASDALLAYRNALRL-AGDNPEILLGLAE--ALYYQAGQQMTAKARALLRQA 219
Query: 74 LEIVPDDPKALFRRCQAYEAIGKFEEAYTDAKHIHRVEPTNKAIQPVLSRLFAIVTKRMQ 133
L + P + +AL A G + EA + + + P + + ++ R +I Q
Sbjct: 220 LALDPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIER--SIARALAQ 277
Query: 134 ENEQLQNK 141
+ Q
Sbjct: 278 RSAQGPAA 285
>gnl|CDD|211352 cd07255, Glo_EDI_BRP_like_12, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 125
Score = 27.1 bits (61), Expect = 8.4
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 16 GNSAFKQGDYETALDFYTKALKVTAEESHERATCL---KNRAAVYLKQN 61
G + D E +L FY L + E + L R + L+++
Sbjct: 4 GAVTLRVADLERSLAFYQDVLGLEVLERTDSTAVLGTGGKRPLLVLEED 52
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 330
Score = 27.9 bits (63), Expect = 9.1
Identities = 19/76 (25%), Positives = 26/76 (34%), Gaps = 17/76 (22%)
Query: 254 FADGSTRKLAEACRRFLVNPARDPDIRRWAAEGLA----YL-------TLDAEVKEALIE 302
F + +LA ++ P D D L L LDAE+
Sbjct: 15 FGPAALARLAALAE--VLPPTPDADFAAEELRALLAGVEVLVTGWGTPPLDAELLARA-- 70
Query: 303 DKPALAALVDVASSVK 318
P L A+V A SV+
Sbjct: 71 --PRLRAVVHAAGSVR 84
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
0.315 0.131 0.364
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,308,785
Number of extensions: 2003482
Number of successful extensions: 2855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2816
Number of HSP's successfully gapped: 129
Length of query: 401
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 302
Effective length of database: 6,546,556
Effective search space: 1977059912
Effective search space used: 1977059912
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: 60 (27.0 bits)