RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11508
(237 letters)
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 57.3 bits (139), Expect = 2e-10
Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 2/71 (2%)
Query: 15 KEFLQSSITDKLMKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEELADM 73
EFL + ++ KL + D EE L EAF LF D D +I L+ + +GE ++DEE+ +
Sbjct: 75 PEFL-TVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKL 133
Query: 74 IKEFDLNQDGK 84
+KE+D + DG+
Sbjct: 134 LKEYDEDGDGE 144
Score = 36.1 bits (84), Expect = 0.005
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 12 NRSKEFLQSSITDKLMKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEEL 70
RSK + +T + ++ + L EAF LF D D ID + L I +G + ++ E+
Sbjct: 1 MRSK--ISDLLTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEI 58
Query: 71 ADMIKEFDLNQDG 83
+ +E D +
Sbjct: 59 NKLFEEIDAGNET 71
Score = 31.9 bits (73), Expect = 0.15
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 31 PEESLNEAFDLFAGDKDFIDFDTLKNIAGV-IGEDVTDEELADMIKEFDLNQDGK 84
E +N+ F+ + +DF + V + +EEL + K FD + DG
Sbjct: 54 SEAEINKLFEEIDAGNETVDFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGY 108
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 56.6 bits (137), Expect = 3e-10
Identities = 33/69 (47%), Positives = 42/69 (60%), Gaps = 2/69 (2%)
Query: 16 EFLQSSITDKLMKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEELADMI 74
EFL +T KL ++DP E + +AF LF DK I LK +A +GE +TDEEL +MI
Sbjct: 74 EFL-DIMTKKLGERDPREEILKAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQEMI 132
Query: 75 KEFDLNQDG 83
E D N DG
Sbjct: 133 DEADRNGDG 141
Score = 30.8 bits (70), Expect = 0.33
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 27 MKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEELADMIKEFDLNQDGK 84
+ +D ++ + EAFDLF D ID LK +G + EE+ MI + D + GK
Sbjct: 11 LTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGK 69
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 49.5 bits (119), Expect = 2e-08
Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 5/53 (9%)
Query: 35 LNEAFDLFAGDKD---FIDFDTLKNIAGVIGEDVTDEELADMIKEFDLNQDGK 84
L EAF LF DKD I D LK +GE +++EE+ +MI+E D + DGK
Sbjct: 2 LREAFRLF--DKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGK 52
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 50.1 bits (120), Expect = 6e-08
Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 2/71 (2%)
Query: 15 KEFLQSSITDKLMKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEELADM 73
EFL + + K+ D EE + EAF +F D + FI L+++ +GE +TDEE+ +M
Sbjct: 67 PEFL-TLMARKMKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEM 125
Query: 74 IKEFDLNQDGK 84
I+E D++ DG+
Sbjct: 126 IREADVDGDGQ 136
Score = 34.0 bits (78), Expect = 0.028
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 24 DKLMKKDPEESLNEAFDLFAGDKD-FIDFDTLKNIAGVIGEDVTDEELADMIKEFDLNQD 82
D+L ++ E EAF LF D D I L + +G++ T+ EL DMI E D + +
Sbjct: 3 DQLTEEQIAE-FKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN 61
Query: 83 G 83
G
Sbjct: 62 G 62
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 41.7 bits (99), Expect = 8e-06
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 45 DKDFIDFDTLKNIAGVIGEDVTDEELADMIKEFDLNQDGK 84
+K I + LK ++G +++EE+ + +EFD + DGK
Sbjct: 1 EKGLITREELKRALALLGISLSEEEVDILFREFDTDGDGK 40
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.0 bits (68), Expect = 0.15
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 7/47 (14%)
Query: 45 DKD---FIDFDTLKNIAGVIGEDVTDEELADMIKE----FDLNQDGK 84
DKD +ID + L+ + +G +TDEE+ ++I+ D + DG+
Sbjct: 4 DKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGR 50
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with the
single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an incoming
dNTP) and thumb (which binds double-stranded DNA)
subdomains.
Length = 378
Score = 32.2 bits (74), Expect = 0.20
Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 206 SDFSFAIGTSRAIGYYKREGAVQD-FATHGKI 236
SDFS AI +R I + E D FATHGKI
Sbjct: 175 SDFS-AI-EARVIAWLAGEQWRLDVFATHGKI 204
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 31.1 bits (71), Expect = 0.53
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 30 DPEESLNEAFDLFA---GDKDFIDFDTL--KNIAGVIGEDVTDEELADMIKEFDL 79
P+E ++E FDLFA D + +DF + AG D+ D +M FD
Sbjct: 132 RPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPS-DNMAPLFDA 185
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 30.7 bits (70), Expect = 0.64
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 30 DPEESLNEAFDLFA---GDKDFIDFDTL--KNIAGVIGEDVTDEELADMIKEFDL 79
P+E ++E FDLF + +DF + G D DE DM F+
Sbjct: 136 RPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEA-DDMAPLFET 189
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in
yeast. Yra2p belongs to the evolutionarily conserved
REF (RNA and export factor binding proteins) family of
hnRNP-like proteins. It is a major component of
endogenous Yra1p complexes. It interacts with Yra1p and
functions as a negative regulator of Yra1p. Yra2p
consists of two highly conserved N- and C-terminal
boxes and a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 27.7 bits (62), Expect = 1.4
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 61 IGEDVTDEELADMIKEF 77
I DV+D + D+IKEF
Sbjct: 8 IPLDVSDYTIEDLIKEF 24
>gnl|CDD|217211 pfam02743, Cache_1, Cache domain.
Length = 81
Score = 27.6 bits (62), Expect = 1.7
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 51 FDTLKNIAGVIGEDVTDEELADMIKEFDLNQDG 83
+D ++ GVIG DV+ E+L + K L + G
Sbjct: 22 YDRDGDLLGVIGIDVSLEDLLKITKSIKLGKTG 54
>gnl|CDD|234735 PRK00358, pyrH, uridylate kinase; Provisional.
Length = 231
Score = 28.9 bits (66), Expect = 1.8
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 42 FAGDKDF-IDFDTLKNIAGVIGE 63
AG+K F ID + L IA I E
Sbjct: 12 LAGEKGFGIDPEVLDRIAEEIKE 34
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 28.9 bits (64), Expect = 2.7
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 159 TGRVVEYRRLFMQCFENLRMAMTLVQGGEASEKVQENLTCIPGISYYSDFSF 210
T ++++ RL+ CF+N+ + ++ G EK++ L +P + D F
Sbjct: 609 TNKIIDSTRLYGACFKNIIIYNAIISG--IHEKIKHFLKLMPRHGFLLDVHF 658
>gnl|CDD|200354 TIGR04103, rSAM_nif11_3, nif11-class peptide radical SAM maturase
3. Members of this protein family are peptide-modifying
radical SAM enzymes, with a C-terminal additional 4Fe-4S
cluster binding domain like many other peptide-modifying
radical SAM enzymes. This form occurs primarily in the
genera Cyanothece and Nostoc.
Length = 412
Score = 28.4 bits (63), Expect = 3.2
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 62 GEDVTDEELADMIKE-----FDLNQDGKKSTTLHIQGTCKSSKLSRLAINFFTWYPH 113
G ++ D+ L ++++ F+LN G T H+ G CK+ + + L W H
Sbjct: 275 GGNIRDQPLRSIMEQSEELRFNLNA-GTPEGTAHLWGFCKTCEFAELCRGGCNWTAH 330
>gnl|CDD|193592 cd09978, LOTUS_2_Limkain_b1, The second LOTUS domain on Limkain
b1(LKAP). The second LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 71
Score = 26.5 bits (58), Expect = 3.3
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 169 FMQCFENLRMAMTLVQGGEASEKVQENLTCIPGIS 203
F C+ A+ +VQ G+ ++ +TCIPG++
Sbjct: 24 FPDCYAAEFSALEVVQEGQGGVPLEHLITCIPGVN 58
>gnl|CDD|235258 PRK04217, PRK04217, hypothetical protein; Provisional.
Length = 110
Score = 27.2 bits (60), Expect = 3.7
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 92 QGTCKSSKLSRLAINFFTWYPHFRASLMEVSPPSTP 127
+G + K+ I F HF ++ V PP P
Sbjct: 7 RGRGRRRKMR--MIGFIPQVRHFYPAIPPVGPPKPP 40
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 25.1 bits (56), Expect = 4.5
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 69 ELADMIKEFDLNQDGK 84
EL + KEFD + DGK
Sbjct: 1 ELKEAFKEFDKDGDGK 16
>gnl|CDD|220716 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
Fmp27_WPPW is a conserved domain of a family of
proteins involved in RNA polymerase II transcription
initiation. It contains characteristic HQR and WPPW
sequence motifs. and is towards the C-terminal in
members which contain Fmp27_SW pfam10305.
Length = 470
Score = 28.0 bits (63), Expect = 4.6
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 14 SKEFLQSSITDKLMKKDPEESLNE--AFDLFAGDKDFIDFD 52
S F +++ + L D S ++ +FD+F D +ID D
Sbjct: 54 SASFDETAYDEILANSDDLSSSDDQPSFDIFDNDFSWIDMD 94
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 28.3 bits (64), Expect = 4.7
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 2/78 (2%)
Query: 19 QSSITDKLMKKDPEESLNEAFDLFAGDKDFIDFDTLKNIAGVIGEDVTD--EELADMIKE 76
+ + L+ DP SLNE G+ + L+ +A G D+ ++L + ++
Sbjct: 281 KLEVDPDLVIPDPNLSLNEGAIAPWGNTNSYYLQMLQALAEHYGFDLDTPWKDLPEEQQD 340
Query: 77 FDLNQDGKKSTTLHIQGT 94
L G + +
Sbjct: 341 IILYGSGDEVIPFYFNDR 358
>gnl|CDD|130853 TIGR01793, cit_synth_euk, citrate (Si)-synthase, eukaryotic. This
model includes both mitochondrial and peroxisomal forms
of citrate synthase. Citrate synthase is the entry point
to the TCA cycle from acetyl-CoA. Peroxisomal forms,
such as SP:P08679 from yeast (recognized by the
C-terminal targeting motif SKL) act in the glyoxylate
cycle. Eukaryotic homologs excluded by the high trusted
cutoff of this model include a Tetrahymena thermophila
citrate synthase that doubles as a filament protein, a
putative citrate synthase from Plasmodium falciparum (no
TCA cycle), and a methylcitrate synthase from
Aspergillus nidulans.
Length = 427
Score = 27.9 bits (62), Expect = 5.4
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 30 DPEESLNEAFDLFAG------DKDFIDFDTLKNIAGVIGEDVTDEELADMI 74
DP S A + AG +++ + + LK++ GE+VT E+L D I
Sbjct: 254 DPYLSFAAALNGLAGPLHGLANQEVLLW--LKSVVSECGENVTKEQLKDYI 302
>gnl|CDD|188709 cd08755, RGS_p115RhoGEF, Regulator of G protein signaling (RGS)
domain found in the Rho guanine nucleotide exchange
factor (GEF), p115 RhoGEF. The RGS (Regulator of
G-protein Signaling) domain is an essential part of the
p115RhoGEF protein, a member of the RhoGEF (Rho guanine
nucleotide exchange factor) subfamily of the RGS protein
family. The RhoGEFs are peripheral membrane proteins
that regulate essential cellular processes, including
cell shape, cell migration, cell cycle progression of
cells, and gene transcription by linking signals from
heterotrimeric G-alpha12/13 protein-coupled receptors to
Rho GTPase activation, leading to various cellular
responses, such as actin reorganization and gene
expression. The RhoGEF subfamily includes p115RhoGEF,
LARG, PDZ-RhoGEF and its rat specific splice variant
GTRAP48. The RGS domain of RhoGEFs has very little
sequence similarity with the canonical RGS domain of the
RGS proteins and is often refered to as RH (RGS
Homology) domain. In addition to being a G-alpha13/12
effector, the p115RhoGEF protein also functions as a
GTPase-activating protein (GAP) for G-alpha13. RGS
proteins play critical regulatory role as GTPase
activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins play critical
regulatory role as GTPase activating proteins (GAPs) of
the heterotrimeric G-protein G-alpha-subunits. RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 193
Score = 27.2 bits (60), Expect = 6.4
Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 107 FFTWYPHF--RASLMEVSPPSTPSGEITRLDESLVSKQVGNVFSQLVQQIMVDSTGRVVE 164
F +Y F + ++++VS PS + E+ R L++++ + +Q + R +E
Sbjct: 45 FGDFYNTFLEKGAVLKVSVPSNVAFELDRTRPELINEEQQRRYVNEIQFAQSPAILRQLE 104
>gnl|CDD|218939 pfam06207, DUF1002, Protein of unknown function (DUF1002). This
protein family has no known function. Its members are
about 300 amino acids in length. It has so far been
detected in Firmicute bacteria and some archaebacteria.
Length = 222
Score = 27.1 bits (61), Expect = 6.5
Identities = 6/27 (22%), Positives = 16/27 (59%)
Query: 62 GEDVTDEELADMIKEFDLNQDGKKSTT 88
G D+++ + +++K F ++ D + T
Sbjct: 2 GADLSESQKQEVLKYFGVDPDNVTTIT 28
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 24.6 bits (55), Expect = 6.6
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 69 ELADMIKEFDLNQDGK 84
EL + + FD + DGK
Sbjct: 1 ELKEAFRLFDKDGDGK 16
>gnl|CDD|234198 TIGR03400, 18S_RNA_Rcl1p, 18S rRNA biogenesis protein RCL1.
Members of this strictly eukaryotic protein family are
not RNA 3'-phosphate cyclase (6.5.1.4), but rather a
homolog with a distinct function, found in the nucleolus
and required for ribosomal RNA processing. Homo sapiens
has both a member of this RCL (RNA terminal phosphate
cyclase like) family and EC 6.5.1.4, while Saccharomyces
has a member of this family only.
Length = 360
Score = 27.6 bits (62), Expect = 6.7
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 196 LTCIPGISYYSDFSFAIGTSRAIGYY 221
+ PG+ + TSR IGYY
Sbjct: 66 VIYKPGLITGGSVTHECPTSRGIGYY 91
>gnl|CDD|226910 COG4535, CorC, Putative Mg2+ and Co2+ transporter CorC [Inorganic
ion transport and metabolism].
Length = 293
Score = 27.4 bits (61), Expect = 7.5
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 11 SNRSKEFLQSSITDKLMKKDPEESLNEAFDLF--AGDKDFIDFDTLKNIAGVIGEDVTDE 68
+N+ K F + + +L +P+ + E +L + + ID DTL + GV+ D+ D
Sbjct: 12 ANKKKSFFER-LLSQLFHGEPK-NREELLELIRDSEQNELIDADTLDMLEGVM--DIADL 67
Query: 69 ELAD-MI 74
+ D MI
Sbjct: 68 RVRDIMI 74
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 26.8 bits (60), Expect = 7.7
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 29 KDPEESLNEAFDLF---AGDKDFIDFDTL 54
PEE ++E FDLF + +DF +
Sbjct: 132 ARPEEVVDEVFDLFLELNATDEQLDFPIV 160
>gnl|CDD|143441 cd07123, ALDH_F4-17_P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, ALDH families 4 and 17.
Delta(1)-pyrroline-5-carboxylate dehydrogenase
(EC=1.5.1.12 ), families 4 and 17: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), also known as ALDH4A1 in humans,
is a mitochondrial homodimer involved in proline
degradation and catalyzes the NAD + -dependent
conversion of P5C to glutamate. This is a necessary step
in the pathway interconnecting the urea and
tricarboxylic acid cycles. The preferred substrate is
glutamic gamma-semialdehyde, other substrates include
succinic, glutaric and adipic semialdehydes. Also
included in this CD is the Aldh17 Drosophila
melanogaster (Q9VUC0) P5CDH and similar sequences.
Length = 522
Score = 27.2 bits (61), Expect = 9.0
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 105 INFFTWYPHFRASLMEVSPPSTPSGEITRLD 135
I+F + + L P S+P+G RL+
Sbjct: 136 IDFLRFNVKYAEELYAQQPLSSPAGVWNRLE 166
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
0.319 0.134 0.382
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,940,053
Number of extensions: 1103936
Number of successful extensions: 1306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1299
Number of HSP's successfully gapped: 49
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 57 (25.4 bits)