RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1009
(129 letters)
>gnl|CDD|222604 pfam14222, MOR2-PAG1_N, Cell morphogenesis N-terminal. This family
is the conserved N-terminal region of proteins that are
involved in cell morphogenesis.
Length = 538
Score = 29.9 bits (68), Expect = 0.33
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 15/47 (31%)
Query: 53 TKLLLPTNR---------------QIFQLISSVHCALCFRHPLFPLL 84
+ L P + QI + I H CFR +FPLL
Sbjct: 268 LRSLFPKGKRTILTTDPEPLDPLVQIIRFIGFKHPDFCFREIIFPLL 314
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 28.6 bits (64), Expect = 1.0
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 69 SVHCALCFRHPLFPLLALIFEKC 91
S+ C L +R L ALIFEKC
Sbjct: 309 SIRCGLQYRSAL---NALIFEKC 328
>gnl|CDD|184042 PRK13415, PRK13415, flagella biosynthesis protein FliZ;
Provisional.
Length = 219
Score = 27.8 bits (62), Expect = 1.7
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 38 ELKRLAQNRNEWRRRTK 54
ELK L + R+E +R K
Sbjct: 195 ELKELKEKRSEGLKRLK 211
>gnl|CDD|215242 PLN02441, PLN02441, cytokinin dehydrogenase.
Length = 525
Score = 28.0 bits (63), Expect = 1.7
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 45 NRNEWRRRTKLLLPTNRQIFQLISSVHCALCFRHPLFPLLAL---IFEKCELA 94
NR++W RT ++P + IF L++ + AL L LLA I CE A
Sbjct: 419 NRSKWDNRTSAVIP-DEDIFYLVALLRSALPSGDDLEHLLAQNKEILRFCEKA 470
>gnl|CDD|213580 TIGR01060, eno, phosphopyruvate hydratase. Alternate name: enolase
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 425
Score = 27.7 bits (62), Expect = 1.9
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 84 LALIFEKCELATCTPREPGVAGGDVCSSESFNEDIAVF 121
L +I E E A P E D +SE ++E+ +
Sbjct: 216 LEIIVEAIEKAGYKPGEDVALALDCAASEFYDEEDGKY 253
>gnl|CDD|177918 PLN02279, PLN02279, ent-kaur-16-ene synthase.
Length = 784
Score = 27.5 bits (61), Expect = 2.1
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 5 LIEGMVEGTNQRGRPRKEYIRDVETAMGYQNYMELKRLAQNR 46
L +G+ + R RK ++VE A+ + Y L+RLA R
Sbjct: 387 LEQGLSNWSKTADRLRKYIKKEVEDALNFPYYANLERLANRR 428
>gnl|CDD|117912 pfam09370, TIM-br_sig_trns, TIM-barrel signal transduction protein.
This domain is likely to have a TIM barrel fold related
to IGPS. Although this family of proteins are
functionally uncharacterized this domain is found as an
N-terminal domain of sigma 54 -dependent transcriptional
activators (enhancer-binding proteins) suggesting a
potential role in signal recognition/receiving and
signal transduction.
Length = 268
Score = 26.8 bits (60), Expect = 3.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 28 ETAMGYQNYMELKRLAQNR 46
ET MGY +E+ RLA +
Sbjct: 131 ETGMGYDLEVEMIRLAHEK 149
>gnl|CDD|185746 cd08915, V_Alix_like, Protein-interacting V-domain of mammalian
Alix and related domains. This superfamily contains the
V-shaped (V) domain of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), Bro1 and Rim20 (also known as PalA) from
Saccharomyces cerevisiae, and related domains. Alix,
HD-PTP, Bro1, and Rim20 all interact with the ESCRT
(Endosomal Sorting Complexes Required for Transport)
system. Alix, also known as apoptosis-linked gene-2
interacting protein 1 (AIP1), participates in membrane
remodeling processes during the budding of enveloped
viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. The Alix V-domain contains a binding
site, partially conserved in this superfamily, for the
retroviral late assembly (L) domain YPXnL motif. The
Alix V-domain is also a dimerization domain. Members of
this superfamily have an N-terminal Bro1-like domain,
which binds components of the ESCRT-III complex. The
Bro1-like domains of Alix and HD-PTP can also bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many
members, including Alix, HD-PTP, and Bro1, also have a
proline-rich region (PRR), which binds multiple partners
in Alix, including Tsg101 (tumor susceptibility gene
101, a component of ESCRT-1) and the apoptotic protein
ALG-2. The C-terminal portion (V-domain and PRR) of Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes; it interacts with a
YPxL motif in Doa4s catalytic domain to stimulate its
deubiquitination activity. Rim20 may bind the ESCRT-III
subunit Snf7, bringing the protease Rim13 (a
YPxL-containing transcription factor) into proximity
with Rim101, and promoting the proteolytic activation of
Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor
suppressor gene candidate often absent in human kidney,
breast, lung, and cervical tumors. HD-PTP has a
C-terminal catalytically inactive tyrosine phosphatase
domain.
Length = 342
Score = 26.2 bits (58), Expect = 6.5
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 12 GTNQRGRPRKEYIRDVETAMGYQNYMELK 40
+N PR+E ++D+E + Y+ Y+ELK
Sbjct: 285 NSNDSLDPREEALQDLEAS--YKKYLELK 311
>gnl|CDD|213552 TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/SpoT family. The
functions of E. coli RelA and SpoT differ somewhat. RelA
(EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP
(or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also
act as a secondary ppGpp synthetase. The two proteins
are strongly similar. In many species, a single homolog
to SpoT and RelA appears reponsible for both ppGpp
synthesis and ppGpp degradation. (p)ppGpp is a
regulatory metabolite of the stringent response, but
appears also to be involved in antibiotic biosynthesis
in some species [Cellular processes, Adaptations to
atypical conditions].
Length = 683
Score = 25.8 bits (57), Expect = 9.2
Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 24/109 (22%)
Query: 5 LIEGMVEGTNQRGRPRKEYIRDVETAMGYQNYMEL---------------KRLAQNRNEW 49
++E + + + +YI+ + ++ EL K LAQN ++W
Sbjct: 463 ILEKELGRSGLKLEDLTQYIQKRLNRLRFKKLSELLAEIGKGNFSSKEVAKLLAQNNSKW 522
Query: 50 RRRTKLLLPTNRQIFQLISSVHCALCFRHPLFPLLALIFEKCELATCTP 98
+ TK + F + + + +I KC C+P
Sbjct: 523 QALTK----PLKFAFSPKVFENSSFESIEGIEITKIVI-AKC----CSP 562
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
0.324 0.138 0.418
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,491,077
Number of extensions: 551899
Number of successful extensions: 609
Number of sequences better than 10.0: 1
Number of HSP's gapped: 607
Number of HSP's successfully gapped: 18
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)