RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8743
(154 letters)
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 212 bits (541), Expect = 3e-71
Identities = 80/153 (52%), Positives = 116/153 (75%), Gaps = 1/153 (0%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
EF PPNKR++E+F F+E+GL ++V+ + QASQE KKELQ++L+E I+E +K+I+A
Sbjct: 1 EFFPPNKRTEEHFAEHFKEEGLDELVEFYRKQASQEIKKELQQELKEMIAEEEPVKEIIA 60
Query: 62 DIREIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAP 121
++E K +P+ E++ L+W+ +M VEW+KKE+ +AEQAL+HLK++ PL AF T
Sbjct: 61 AVKEQMKKSSLPEHEVVGLLWTALMDAVEWSKKEDQIAEQALRHLKKYAPLLAAFC-TTA 119
Query: 122 RAELALMLKVQEFCYENMNLMRVFQKIILLFYK 154
RAELAL+ K+QE+CYENM M+VFQKI+ L YK
Sbjct: 120 RAELALLNKIQEYCYENMKFMKVFQKIVKLLYK 152
>gnl|CDD|211395 cd11473, W2, C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon.
This domain is found at the C-terminus of several
translation initiation factors, including the epsilon
chain of eIF2b, where it has been found to catalyze the
conversion of eIF2.GDP to its active eIF2.GTP form. The
structure of the domain resembles that of a set of
concatenated HEAT repeats.
Length = 135
Score = 42.1 bits (99), Expect = 1e-05
Identities = 26/120 (21%), Positives = 57/120 (47%), Gaps = 4/120 (3%)
Query: 39 KKELQEQLEEQISEGAS-IKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWNK-KEE 96
K+L++ L +++ E S + V + + I +E++ ++ + V+ VE
Sbjct: 3 NKKLRDSLLKELEEDKSSDVESVKAAKSKLDLDPISLEEVVKVLLTAVVNAVESADSISL 62
Query: 97 LVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMN--LMRVFQKIILLFYK 154
EQ + LK++ P+ + +L L+LK+++ C + L+ + +KI+ L Y
Sbjct: 63 TQKEQLVLVLKKYGPVLRELLKLIKKDQLYLLLKIEKLCLQLKLSELISLLEKILDLLYD 122
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B epsilon,
eIF-4 gamma and eIF-5.
Length = 83
Score = 35.7 bits (83), Expect = 0.001
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 111 PLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFY 153
PL F +L L+ ++EFC E L ++ KI+ Y
Sbjct: 2 PLL-KFLAKDEEEQLELLYAIEEFCVELEKLGKLLPKILKSLY 43
>gnl|CDD|216850 pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of
unknown function is found at the C-terminus of several
translation initiation factors.
Length = 75
Score = 34.9 bits (81), Expect = 0.002
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 122 RAELALMLKVQEFCY-ENMNLMRVFQKIILLFYK 154
A+ L+ ++ FC EN L+++ KI+ L Y
Sbjct: 1 DAQKDLLGALERFCGKENPELIKLLPKILKLLYD 34
>gnl|CDD|211397 cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic
translation initiation factor 4 gamma 1 and similar
proteins. eIF4G1 is a component of the multi-subunit
eukaryotic translation initiation factor 4F, which
facilitates recruitment of the mRNA to the ribosome, a
rate-limiting step during translation initiation. This
C-terminal domain, whose structure resembles that of a
set of concatenated HEAT repeats, has been associated
with binding to/recruiting the kinase Mnk1, which
phosphorylates eIF4E.
Length = 134
Score = 30.3 bits (69), Expect = 0.23
Identities = 15/99 (15%), Positives = 41/99 (41%), Gaps = 5/99 (5%)
Query: 40 KELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV-EWNKKEELV 98
+Q +L + + E + ++ I+E + + +M V ++ +E+ +
Sbjct: 4 LRVQAELLKLLQEDPNPDELYKWIKENVSPELYASPGFVR----ALMTAVLKYAIEEKSL 59
Query: 99 AEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYE 137
E+ L+++ PL + D + +L + +Q +
Sbjct: 60 PEKEKALLEKYAPLLQKYLDDDEQLQLQALYALQALVHT 98
>gnl|CDD|148491 pfam06898, YqfD, Putative stage IV sporulation protein YqfD. This
family consists of several putative bacterial stage IV
sporulation (SpoIV) proteins. YqfD of Bacillus subtilis
is known to be essential for efficient sporulation
although its exact function is unknown.
Length = 383
Score = 29.6 bits (67), Expect = 0.68
Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 5/80 (6%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
K R + E VKL +A ++ KK +++LE++I + A IKD
Sbjct: 302 PLFLKWKLPISIVRETYYEVQDKV-VKLTKEEAVEKGKKLAKKKLEKEIDKDAKIKDEKV 360
Query: 62 DIREIANKHCIPDQELIVLI 81
+ N L VL
Sbjct: 361 LHERVENGKV----RLRVLY 376
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 29.1 bits (66), Expect = 0.69
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 32 AQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQE 76
A+ ++ K E +L Q A K IVA I+++ ++ I ++
Sbjct: 46 AEEAKAEKAERDRELNRQRQAEAEQKAIVAQIKQLIEQNRIDRKD 90
>gnl|CDD|236356 PRK08944, motB, flagellar motor protein MotB; Reviewed.
Length = 302
Score = 29.2 bits (66), Expect = 0.69
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 24 ADIVKLHMAQASQEA---KKELQEQLEEQISEGA----SIKD-IVADIRE 65
+ VK A A ++ K+L +QLE++I +GA S+ I+ IRE
Sbjct: 130 SAEVKAEKAAAQEQIEDLVKKLAQQLEKEIEDGAIEIESLGQQIIIRIRE 179
>gnl|CDD|236409 PRK09201, PRK09201, amidase; Provisional.
Length = 465
Score = 28.4 bits (64), Expect = 1.5
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 98 VAEQALKHLKQFTPLFGAFTD-TAPRA 123
VA+ L + + P AFT TA RA
Sbjct: 26 VAQATLARIARANPQLNAFTAVTAERA 52
>gnl|CDD|238938 cd01980, Chlide_reductase_Y, Chlide_reductase_Y : Y subunit of
chlorophyllide (chlide) reductase (BchY). Chlide
reductase participates in photosynthetic pigment
synthesis playing a role in the conversion of
chlorophylls(Chl) into bacteriochlorophylls (BChl).
Chlide reductase catalyzes the reduction of the B-ring
of the tetrapyrolle. Chlide reductase is a three subunit
enzyme (subunits are designated BchX, BchY and BchZ).
The similarity between these three subunits and the
subunits for nitrogenase suggests that BchX serves as an
electron donor for the BchY-BchY catalytic subunits.
Length = 416
Score = 28.3 bits (63), Expect = 1.6
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 6/88 (6%)
Query: 48 EQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVAEQALKHLK 107
E +S G +DI IR++A+ P + + S +A+ EEL+ +Q
Sbjct: 68 ETLSTGKLFEDIREAIRKLAD----PPAYTFIPVISLCVAETA-GVAEELLPKQIDGVRV 122
Query: 108 QFTPLFGAFTDTAPRAELA-LMLKVQEF 134
+ P A+ ML + F
Sbjct: 123 ILVRGPAFPIHSHPEAKDVGAMLLLARF 150
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 28.4 bits (64), Expect = 1.6
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 5/64 (7%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
FVPP + E L ++L K + Q E Q E +++ + A
Sbjct: 133 PFVPPEDPENLLHALQQEVLTLKQQLELQ-----AREKAQSQALAEAQQQELVALEGLAA 187
Query: 62 DIRE 65
++ E
Sbjct: 188 ELEE 191
>gnl|CDD|238559 cd01139, TroA_f, Periplasmic binding protein TroA_f. These
proteins are predicted to function as initial receptors
in the ABC metal ion uptake in eubacteria and archaea.
They belong to the TroA superfamily of helical backbone
metal receptor proteins that share a distinct fold and
ligand binding mechanism. A typical TroA protein is
comprised of two globular subdomains connected by a
single helix and can bind their ligands in the cleft
between these domains.
Length = 342
Score = 28.4 bits (64), Expect = 1.7
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 20 EKGLA---DIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQE 76
EK L D+V L++ + + + E+LE+ A I + D R+ K+ P
Sbjct: 85 EKVLTLKPDLVILNIWAKTTAEESGILEKLEQ-----AGIPVVFVDFRQKPLKNTTPSMR 139
Query: 77 L 77
L
Sbjct: 140 L 140
>gnl|CDD|168717 PRK06882, PRK06882, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 574
Score = 28.3 bits (63), Expect = 1.9
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIKD--IVADIREIANKHCIPDQ 75
L D KL A + + ++LEE++++ SIKD + D+ +H P Q
Sbjct: 501 LPDFAKLAEAYGHVGIQIDTPDELEEKLTQAFSIKDKLVFVDVNVDETEHVYPMQ 555
>gnl|CDD|232867 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments [DNA metabolism,
DNA replication, recombination, and repair].
Length = 574
Score = 28.1 bits (63), Expect = 2.0
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 36 QEAKKELQEQLEEQIS-----EGASIKDIVADIREIANKHCI 72
QE KEL++++E+ E A I+D +A +RE+ K +
Sbjct: 193 QEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHV 234
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 27.9 bits (63), Expect = 2.8
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 35 SQEAKKELQEQLEEQISEGASIKDIVADIREIANK-----HC 71
++E +E E+LE G+ D++ ++++ A K HC
Sbjct: 110 TEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHC 151
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 27.2 bits (61), Expect = 3.3
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 99 AEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFY 153
E K L ++ PL + + ++ L+L ++EFC E+ +F K++ Y
Sbjct: 69 LEALKKLLSKWGPLLENYVKSQ-DDQVELLLALEEFCLESEEGGPLFAKLLHALY 122
>gnl|CDD|217679 pfam03701, UPF0181, Uncharacterized protein family (UPF0181).
This family contains small proteins of about 50 amino
acids of unknown function. The family includes YoaH.
Length = 52
Score = 25.3 bits (56), Expect = 3.4
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 36 QEAKKELQEQLEEQISEGASIKDIVADIREIANK 69
QEA + +QE + + +S G +I + +IRE K
Sbjct: 14 QEAVERIQELMAQGMSSGEAIAIVAQEIREKHQK 47
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 27.4 bits (62), Expect = 3.8
Identities = 14/37 (37%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 35 SQEAKKELQEQLEEQISEGAS--IKDIVADIREIANK 69
++EAK+ L E++EE+ A+ IK+I + +E A+K
Sbjct: 152 AEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADK 188
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 27.1 bits (60), Expect = 4.2
Identities = 27/114 (23%), Positives = 48/114 (42%), Gaps = 8/114 (7%)
Query: 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIW 82
+ DI + + EA K L +Q+E A + ++ I + + +++
Sbjct: 341 MKDINQHSLDLGLTEAAKLLNKQVERGRITPAKMAGVLNGITPTLSYAGFDNVDIV---- 396
Query: 83 STVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQE-FC 135
V A VE K + V + +H+++ L + T T + LA LK E FC
Sbjct: 397 --VEAVVENPKVKAAVLAEVEQHVREDAIL-ASNTSTISISLLAKALKRPENFC 447
>gnl|CDD|143418 cd07100, ALDH_SSADH1_GabD1, Mycobacterium tuberculosis
succinate-semialdehyde dehydrogenase 1-like.
Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1,
EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
of succinate semialdehyde (SSA) to succinate. SSADH
activity in Mycobacterium tuberculosis (Mtb) is encoded
by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb
GabD1 SSADH1 reportedly is an enzyme of the
gamma-aminobutyrate shunt, which forms a functional link
between two TCA half-cycles by converting
alpha-ketoglutarate to succinate.
Length = 429
Score = 27.0 bits (61), Expect = 4.3
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 34 ASQEAKKELQEQLEEQISEGASI 56
A ++ + EL EQ+EE ++ GA++
Sbjct: 281 ARKDLRDELHEQVEEAVAAGATL 303
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 26.9 bits (60), Expect = 4.5
Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 18 FEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDI-----VADIREIANKHCI 72
++ L D V++ + ++ ++ ++E+L+E+ EG D+ V D++EI +
Sbjct: 2 YKLVELEDTVRIPPSYFGEDLEEAVKEELKEKY-EGKLDGDVGLVVLVLDVKEIGEGIIV 60
Query: 73 P 73
P
Sbjct: 61 P 61
>gnl|CDD|205249 pfam13068, DUF3932, Protein of unknown function (DUF3932). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 80 amino acids in length.
Length = 81
Score = 25.5 bits (55), Expect = 5.6
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 87 AQVEWNKKEELVAEQALKHLKQFTPLF--GAFTDTAPRAELA 126
AQ+EW+ +EL+ E H P + AFT A R A
Sbjct: 28 AQLEWSTLKELIHEYTSSHTNDSLPEYISSAFTYYAQRISTA 69
>gnl|CDD|215275 PLN02498, PLN02498, omega-3 fatty acid desaturase.
Length = 450
Score = 26.7 bits (59), Expect = 5.6
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 6/71 (8%)
Query: 5 PPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKE----LQEQLEEQISEGASIKDIV 60
P + S R L L + +E +E + E E + GA +
Sbjct: 47 PFDLFSRGCSRE--RNWALNVSAPLTVPSGEEEEDEEGVNGVGEDEEGEFDPGAPPPFNL 104
Query: 61 ADIREIANKHC 71
ADIR KHC
Sbjct: 105 ADIRAAIPKHC 115
>gnl|CDD|236312 PRK08617, PRK08617, acetolactate synthase; Reviewed.
Length = 552
Score = 26.7 bits (60), Expect = 6.4
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIK-------DIVADIREIAN 68
+ L ++ S E +EL+ QLEE A ++ I+ +++I
Sbjct: 327 AEKLDGLSLSPQSLEILEELRAQLEELAERPARLEEGAVHPLRIIRALQDIVT 379
>gnl|CDD|239936 cd04490, PolII_SU_OBF, PolII_SU_OBF: A subfamily of OB folds
corresponding to the OB fold found in Pyrococcus abyssi
DNA polymerase II (PolII) small subunit. PolII is a
family D DNA polymerase, having a 3-prime to 5-prime
exonuclease activity. P. abyssi PolII is heterodimeric.
The large subunit appears to be the polymerase, and the
small subunit may be the exonuclease. The small subunit
contains a calcineurin-like phosphatase superfamily
domain C-terminal to this OB-fold domain.
Length = 79
Score = 25.3 bits (56), Expect = 6.4
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 54 ASIKDIVADIREIANKHCI-----PDQELIVLI 81
SI +V D+R N H I + VL+
Sbjct: 2 VSIIGMVNDVRSTKNGHRIVELEDTTGRITVLL 34
>gnl|CDD|191371 pfam05778, Apo-CIII, Apolipoprotein CIII (Apo-CIII). This family
consists of several mammalian apolipoprotein CIII
(Apo-CIII) sequences. Apolipoprotein C-III is a
79-residue glycoprotein. It is synthesised in the
intestine and liver as part of the very low density
lipoprotein (VLDL) and the high density lipoprotein
(HDL) particles. Owing to its positive correlation with
plasma triglyceride (Tg) levels, Apo-CIII is suggested
to play a role in Tg metabolism and is therefore of
interest regarding atherosclerosis. However, unlike
other apolipoproteins such as Apo-AI, Apo E or CII for
which many naturally occurring mutations are known, the
structure-function relationships of apo C-III remains a
subject of debate. One possibility is that apo C-III
inhibits lipoprotein lipase (LPL) activity, as shown by
in vitro experiments. Another suggestion, is that
elevated levels of Apo-CIII displace other
apolipoproteins at the lipoprotein surface, modifying
their clearance from plasma.
Length = 70
Score = 25.3 bits (55), Expect = 6.5
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 19 EEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGA 54
E+ L ++ +M QA++ A+ L E Q+++ A
Sbjct: 3 EDSSLLGKMQGYMKQATKTAQDALTSVQESQVAQQA 38
>gnl|CDD|222874 PHA02557, 22, prohead core protein; Provisional.
Length = 271
Score = 26.2 bits (58), Expect = 6.7
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 12 EYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISE 52
E F TVFE VKL + ++ A+K +E +EE + E
Sbjct: 37 EKFSTVFEAAVKQHAVKLAESHIAEIAEK-AEELVEEALEE 76
>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and
multimerization region of GCN4 and related proteins.
Basic leucine zipper (bZIP) transcription factors act
in networks of homo- and hetero-dimers in the
regulation in a diverse set of cellular pathways.
Classical leucine zippers have alpha helices with
leucine residues 7 amino acids apart, which stabilize
dimerization with a parallel leucine zipper domain.
Dimerization creates a pair of basic regions that bind
DNA and undergo conformational change. GCN4 was
identified in Saccharomyces cerevisiae from mutations
in a deficiency in activation with the general amino
acid control pathway. GCN4 encodes a trans-activator of
amino acid biosynthetic genes containing 2 acidic
activation domains and a C-terminal bZIP domain,
comprised of a basic alpha-helical DNA-binding region
and a coiled-coil dimerization region.
Length = 54
Score = 24.2 bits (53), Expect = 9.4
Identities = 9/37 (24%), Positives = 20/37 (54%)
Query: 30 HMAQASQEAKKELQEQLEEQISEGASIKDIVADIREI 66
E K+L++++EE SE + ++D V +++
Sbjct: 16 RSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKKA 52
>gnl|CDD|234547 TIGR04330, cas_Cpf1, CRISPR-associated protein Cpf1, subtype
PREFRAN. This family is the long protein of a novel
CRISPR subtype, PREFRAN, which is most common in
Prevotella and Francisella, although widely distributed.
The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the
helicase Cas3 and endonuclease Cas3-HD.
Length = 1287
Score = 26.3 bits (58), Expect = 9.6
Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 28 KLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMA 87
KL + ++ + Q+ L +QI + S++D + + I ++L+ + +
Sbjct: 82 KLKKFKKDKKDLAKEQDTLRKQIVK--SLQDNLPE----EIFKNIFSKKLLKGVLEDFIK 135
Query: 88 QVEWNKKEELVAEQALKHLKQFTPLFGAF 116
+ ++E +K K FT F F
Sbjct: 136 NTHKDSEDEQNILIDIKEFKGFTTYFSGF 164
>gnl|CDD|218037 pfam04348, LppC, LppC putative lipoprotein. This family includes
several bacterial outer membrane antigens, whose
molecular function is unknown.
Length = 535
Score = 25.9 bits (57), Expect = 9.8
Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 19/102 (18%)
Query: 6 PNKRSDEYFRTVFEEKGL-ADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIR 64
PN S Y + +G + KL A+ E K Q Q A +R
Sbjct: 4 PNASSQFYLNKASQSQGEQQNTYKLLAARVLIEENKIAQAQ---------------ALLR 48
Query: 65 EIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVAEQALKHL 106
E++ + +Q L S + A++ K++ VA Q L H
Sbjct: 49 ELSVQQLTDEQ---KLDKSLLEAELAAAKRQNEVALQQLSHQ 87
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
0.320 0.134 0.378
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,985,678
Number of extensions: 736342
Number of successful extensions: 1451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1439
Number of HSP's successfully gapped: 122
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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 (21.8 bits)
S2: 55 (24.9 bits)