RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12736
(567 letters)
>gnl|CDD|193256 pfam12780, AAA_8, P-loop containing dynein motor region D4. The
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D4 ATP-binding region of
the motor.
Length = 268
Score = 102 bits (256), Expect = 2e-24
Identities = 50/111 (45%), Positives = 67/111 (60%), Gaps = 3/111 (2%)
Query: 414 YNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFAAGY 473
YNE A ++LVLFEDA H+ RI+R L RG+ ++VGV G GK+SL RLA++ +
Sbjct: 1 YNE---VNAVMNLVLFEDAMAHVCRINRILESPRGNALLVGVGGSGKQSLSRLAAYISSL 57
Query: 474 QVFTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGYQVF 524
VF I L +GY K DL + GVKN TVFL T A++ +E + V
Sbjct: 58 DVFQITLRKGYGIPDLKIDLAAQCIKAGVKNVPTVFLMTDAQVADEQFLVL 108
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 68.5 bits (167), Expect = 7e-12
Identities = 38/226 (16%), Positives = 71/226 (31%), Gaps = 15/226 (6%)
Query: 299 HYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDEDLSLMSGHI 357
+Y + R+L+R ++ + E I + W E R DRL ++ S +
Sbjct: 1697 NYGYKPRELTRSLRAIFGYAETRIDTPDVSLIIDWYCEAIREKIDRLVQQKESSTSRQDL 1756
Query: 358 ADSVKRNFP-QDVNVVMRDPLLFGD-FRNALKETEPRYYEDLLDYSAVGHLFTEILEEYN 415
D R + + F + +DL + + E
Sbjct: 1757 YDFGLRAIREMIAGHIGEAEITFSMILFFGMACLL---KKDLAVF---------VEEVRK 1804
Query: 416 ESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFAAGYQV 475
+ ++ V ++DA H+ R R L + GH ++ GV G + +
Sbjct: 1805 IFGSSHLDVEAVAYKDALLHILRSRRGLLVVGGHGVLKGVLIRGACDAREFVCWLNPRNM 1864
Query: 476 FTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGY 521
I R F++ LK + + VE +
Sbjct: 1865 REIFGHRDELTGDFRDSLKVQDLRRNIHGGRECLFIFESIPVESSF 1910
Score = 29.2 bits (65), Expect = 9.0
Identities = 12/47 (25%), Positives = 21/47 (44%)
Query: 170 GDILVPTTDSTKLTWILSLMNEIKRPCIVVGDTGTSKTATMMNFLRS 216
++++PT+D+ + + R I G G+ K M LRS
Sbjct: 1471 KEVVIPTSDTGFVDSFSNEALNTLRSYIYCGPPGSGKEMLMCPSLRS 1517
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 47.6 bits (113), Expect = 7e-06
Identities = 20/49 (40%), Positives = 26/49 (53%)
Query: 224 VIAELPPTPAKFHYIFNLRDLSRIIQGLTATEKIIFNTKEMFVRAWRNE 272
+ PT KFHY+FNLRDLS I QGL + + +R W +E
Sbjct: 224 IATTFLPTAIKFHYVFNLRDLSNIFQGLLFSSVECLKSPWDLIRLWLHE 272
Score = 47.6 bits (113), Expect = 7e-06
Identities = 20/49 (40%), Positives = 26/49 (53%)
Query: 287 VIAELPPTPAKFHYIFNLRDLSRIIQGLTATEKIIFNTKEMFVRAWRNE 335
+ PT KFHY+FNLRDLS I QGL + + +R W +E
Sbjct: 224 IATTFLPTAIKFHYVFNLRDLSNIFQGLLFSSVECLKSPWDLIRLWLHE 272
Score = 44.2 bits (104), Expect = 8e-05
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 10/88 (11%)
Query: 164 DGDKSFGDILVPTTDSTKLTWILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLSPDKYL 223
D + LV T+++ ++ + + L+ E +RP ++VG+ GT K+ + + L SL PD YL
Sbjct: 4 DPEMPLQACLVHTSETIRVRYFMDLLMERQRPVMLVGNAGTGKSVLVGDKLASLDPDAYL 63
Query: 224 VIAELPPTPAKFHYIFNLRDLSRIIQGL 251
V +P FN S ++Q +
Sbjct: 64 V-KNVP---------FNYYTTSAMLQAV 81
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 35.9 bits (83), Expect = 0.045
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 404 GHLFTEILEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSL 463
E + E ++ L+ V+ D + AL L+ GH ++ G G GK L
Sbjct: 4 IMAPLERVAEI--LGKIRSELEKVVVGDEEV-IELALLAL-LAGGHVLLEGPPGVGKTLL 59
Query: 464 VRLASFAAGYQVFTIQLSRGYNEA 487
R + A G IQ + +
Sbjct: 60 ARALARALGLPFVRIQCTPDLLPS 83
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 32.7 bits (75), Expect = 0.19
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 449 HCMVVGVEGGGKRSLVRLASFA-AGYQVFTIQLSRGYNEASFKEDLKSLYNL 499
++VG G GK L + A + VF +QL+R E EDLK N+
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE----EDLKGRRNI 48
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 32.3 bits (74), Expect = 0.26
Identities = 13/90 (14%), Positives = 27/90 (30%), Gaps = 18/90 (20%)
Query: 196 CIVVGDTGTSKTATMMNFL------------------RSLSPDKYLVIAELPPTPAKFHY 237
++ TG+ KT + + R L+ + EL K Y
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGY 62
Query: 238 IFNLRDLSRIIQGLTATEKIIFNTKEMFVR 267
+ + + + L+ I+ T +
Sbjct: 63 LIGGTSIKQQEKLLSGKTDIVVGTPGRLLD 92
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 31.1 bits (71), Expect = 0.88
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 196 CIVVGDTGTSKTATMMNFL-RSLSPDKY 222
C V+G G+ K+A + FL RS S + Y
Sbjct: 7 CFVLGAKGSGKSALLQAFLGRSFSQNAY 34
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 31.9 bits (73), Expect = 0.95
Identities = 29/126 (23%), Positives = 46/126 (36%), Gaps = 45/126 (35%)
Query: 300 YIFNLRDLSRIIQGL------------TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTD 347
+I + + II+ L T E+I K+M VR + I + +
Sbjct: 134 FIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMM-KQMIVRC------KGILEAEGVE 186
Query: 348 EDLSLMSGHIADSVKRNFPQDVNVVMRDPLLFGDFRNALKETEPRYYEDLLDYSAVGHLF 407
D+ + +A VK+NFP DFR + E L Y++ G +
Sbjct: 187 VDMKV----LAALVKKNFP--------------DFRRTINE--------LQRYASTGKID 220
Query: 408 TEILEE 413
IL E
Sbjct: 221 AGILSE 226
>gnl|CDD|132152 TIGR03108, eps_aminotran_1, exosortase A system-associated
amidotransferase 1. The predicted protein-sorting
transpeptidase that we call exosortase (see TIGR02602)
has distinct subclasses that associated with different
types of exopolysaccharide production loci. This model
represents a distinct clade among a set of
amidotransferases largely annotated (not necessarily
accurately) as glutatime-hydrolyzing asparagine
synthases. Members of this clade are essentially
restricted to the characteristic exopolysaccharide (EPS)
regions that contain the exosortase 1 genome (xrtA), in
genomes that also have numbers of PEP-CTERM domain
(TIGR02595) proteins.
Length = 628
Score = 31.6 bits (72), Expect = 1.1
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 19/81 (23%)
Query: 383 RNALKET--EPRYYEDLLDYSAVGHLFTEILEEYNESAGAKARLDLVLFEDAREHL---- 436
NAL+ P + +L Y A+ E+L + A L L + D + +L
Sbjct: 441 DNALRRQLFSPDFRRELQGYRAI-----EVLRRHAARAPTDDALSLAQYLDLKTYLPGDI 495
Query: 437 -TRIHRALRLSRGHCMVVGVE 456
T++ RA M G+E
Sbjct: 496 LTKVDRA-------SMAHGLE 509
>gnl|CDD|188500 TIGR03985, TIGR03985, CRISPR-associated protein, TIGR03985 family.
Members of this protein family belong to
CRISPR-associated (Cas) gene clusters. The majority of
members are Cyanobacterial.
Length = 249
Score = 30.8 bits (70), Expect = 1.5
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 126 LANYTQIPTAESSWYHYTLDR--SKNAWVPWRH 156
L Y Q PT + WY+Y LDR SK A + W
Sbjct: 69 LCAYGQDPTGQVGWYNYRLDRIQSKLAVLSWDD 101
>gnl|CDD|200328 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 31.2 bits (71), Expect = 1.6
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 193 KRPCIVVGDTGTSKTATMMNFLRSLSPDKYLVIAE 227
+ +V G TG+ KT + L + PD+ +V+ E
Sbjct: 178 RLAFLVSGGTGSGKTTLLSALLALVPPDERIVLVE 212
>gnl|CDD|150776 pfam10141, ssDNA-exonuc_C, Single-strand DNA-specific exonuclease,
C terminal domain. Members of this set of prokaryotic
domains are found in a set of single-strand DNA-specific
exonucleases, including RecJ. Their exact function has
not, as yet, been determined.
Length = 195
Score = 29.9 bits (68), Expect = 2.5
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 281 LNTDELVIAELPPTPAKFHYIFNLRDLSRIIQGLTATEKIIFN---TKEMFVR 330
L +D +V+ +LP + + + + SRI E + T+E F +
Sbjct: 50 LESDYVVLVDLPDSLEELKQLLEGKQPSRIYFVFYHEESYYLSGMPTREQFAK 102
Score = 28.8 bits (65), Expect = 6.0
Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 11/93 (11%)
Query: 178 DSTKLTWILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLSPDKYLVIAELPPTPAKFHY 237
+I L ++ + V ++ A + + Y+V+ +LP + +
Sbjct: 18 PEEYPFFIHFLEETVQSLLLDVSYYYYAEEADLES--------DYVVLVDLPDSLEELKQ 69
Query: 238 IFNLRDLSRIIQGLTATEKIIFN---TKEMFVR 267
+ + SRI E + T+E F +
Sbjct: 70 LLEGKQPSRIYFVFYHEESYYLSGMPTREQFAK 102
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 30.0 bits (68), Expect = 3.3
Identities = 14/71 (19%), Positives = 23/71 (32%), Gaps = 17/71 (23%)
Query: 194 RPCIVVGDTGTSKTATMMNFLRSLSPDKYLVIAELPPTPAKFHYIFNL---RDLSRIIQ- 249
RP ++G + T ++ P P F F D++R +
Sbjct: 165 RPATILGPGTRNTTRDFLSP-------------RRLPVPGGFDPPFQFLHEDDVARALVL 211
Query: 250 GLTATEKIIFN 260
+ A IFN
Sbjct: 212 AVRAGATGIFN 222
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 29.2 bits (65), Expect = 3.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 189 MNEIKRPCIVVGDTGTSKTATMMNFLRSLSPDKYL 223
M IK C+VVGD KT ++ + + P +Y+
Sbjct: 1 MQSIK--CVVVGDGAVGKTCLLICYTTNAFPKEYI 33
>gnl|CDD|182053 PRK09733, PRK09733, putative fimbrial protein; Provisional.
Length = 181
Score = 29.1 bits (65), Expect = 4.1
Identities = 10/36 (27%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 347 DEDLSLMSGHIADSV----KRNFPQDVNVVMRDPLL 378
DEDL++ G +AD+V +++ + + ++D +L
Sbjct: 45 DEDLTVNLGEVADTVLKSDQKSLAEPFTIHLQDCML 80
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.8 bits (68), Expect = 4.4
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 411 LEEYNESAGAKAR------LDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLV 464
LE+Y+ K R +DL+ E+A E I AL ++ G G + L
Sbjct: 266 LEKYSPKLAEKPRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELC 325
Query: 465 R 465
Sbjct: 326 W 326
>gnl|CDD|234375 TIGR03860, FMN_nitrolo, FMN-dependent oxidoreductase,
nitrilotriacetate monooxygenase family. This model
represents a distinctive clade, in which all
characterized members are FMN-binding, within the larger
family of luciferase-like monooxygenases (LLM), among
which there are both FMN- and F420-binding enzymes. A
well-characterized member is nitrilotriacetate
monooxygenase from Aminobacter aminovorans
(Chelatobacter heintzii), where nitrilotriacetate is a
chelating agent used in detergents [Unknown function,
Enzymes of unknown specificity].
Length = 422
Score = 29.4 bits (67), Expect = 5.0
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 15/78 (19%)
Query: 392 RYYEDLLDYSA--------VGHLFT-----EILEEYNESAGAKARLDLVLFEDAREHLT- 437
+ L+ G + L + AG K+R DL+L RE+LT
Sbjct: 284 AELQSLISPEGGLALLSGWTGIDLSQYDLDAPLPDLPTEAGQKSRFDLILELARRENLTL 343
Query: 438 -RIHRALRLSRGHCMVVG 454
++ L RGH + VG
Sbjct: 344 RQLAERLAGGRGHPVFVG 361
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 28.8 bits (64), Expect = 5.1
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 196 CIVVGDTGTSKTATMMNFLRSLSPDKYL 223
C+VVGD KT +M++ P++Y+
Sbjct: 3 CVVVGDGAVGKTCLLMSYANDAFPEEYV 30
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.5 bits (63), Expect = 6.2
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 193 KRPCIVVGDTGTSKTATMMNFLRSLSPDKYLVIA 226
++VG G+ KT R L P VI
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIY 35
>gnl|CDD|218892 pfam06092, DUF943, Enterobacterial putative membrane protein
(DUF943). This family consists of several hypothetical
putative membrane proteins from Escherichia coli,
Yersinia pestis and Salmonella typhi.
Length = 155
Score = 28.1 bits (63), Expect = 6.9
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 161 YVHDGDKSFGDILV---PTTDSTKLTWILSLMNEIKR 194
VH D DILV P TD K+ W L + +K
Sbjct: 32 AVHQ-DNGSSDILVRNFPITDKGKINWWLENKDMLKA 67
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 28.9 bits (65), Expect = 7.1
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 185 ILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLSPDKYLVI 225
L L E ++ I+ G T + KT T++N L P + ++
Sbjct: 135 YLWLAIEARKSIIICGGTASGKT-TLLNALLDFIPPEERIV 174
>gnl|CDD|239588 cd03511, Rhizopine-oxygenase-like, This CD includes the putative
hydrocarbon oxygenase, MocD, a bacterial rhizopine
(3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and
other related proteins. It has been proposed that MocD,
MocE (Rieske-like ferredoxin), and MocF (ferredoxin
reductase) under the regulation of MocR, act in concert
to form a ferredoxin oxygenase system that demethylates
3-O-MSI to form scyllo-inosamine. This domain family
appears to be structurally related to the membrane fatty
acid desaturases and the alkane hydroxylases. They all
share in common extensive hydrophobic regions that would
be capable of spanning the membrane bilayer at least
twice. Comparison of sequences also reveals the
existence of three regions of conserved histidine
cluster motifs that contain eight histidine residues:
HXXXH, HXXHH, and HXXHH. These histidine residues are
reported to be catalytically essential and proposed to
be the ligands for the iron atoms contained within
homologs, stearoyl CoA desaturase and alkane
hydroxylase.
Length = 285
Score = 28.9 bits (65), Expect = 7.2
Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 14/97 (14%)
Query: 16 DVNVVMRDP-LLFGDFRNALKETEPRYYEDLLDYSAVGHLFTEIVQLCQMLQASLDEANL 74
+ RDP L T Y LL S + + + ++ + + ++ EA
Sbjct: 105 YTQIPGRDPELAVPR-----PPTLREY---LLALSGLPYWWGKLRTVFRHAFGAVSEAEK 156
Query: 75 GSMSPEELEAVFIQS-----VYASLGASLVAEAQTVF 106
+ EE V ++ VYA L A + +
Sbjct: 157 PFIPAEERPKVVREARAMLAVYAGLIALSLYLGSPLL 193
>gnl|CDD|176225 cd08264, Zn_ADH_like2, Alcohol dehydrogenases of the MDR family.
This group resembles the zinc-dependent alcohol
dehydrogenases of the medium chain dehydrogenase family.
However, this subgroup does not contain the
characteristic catalytic zinc site. Also, it contains an
atypical structural zinc-binding pattern:
DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 28.9 bits (65), Expect = 8.4
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 444 RLSRGHCMVVGVEGGGKRSLVRLASFAAGYQVFTIQLSRGYNEASFKEDLKSLYN 498
L ++G GG ++ L+ L A +V + + KE LK L++
Sbjct: 266 DLYSKQISIIGSTGGTRKELLELVKIAKDLKVKV---WKTFKLEEAKEALKELFS 317
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 27.6 bits (62), Expect = 8.9
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 193 KRPCIVVGDTGTSKTATMMNFLRSLSPDKYLVIAELPPT 231
++ G++G+ KT + R L + + + E P
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLARQLPNRRVVYV-EAPSL 41
>gnl|CDD|233073 TIGR00653, GlnA, glutamine synthetase, type I. Alternate name:
glutamate--ammonia ligase. This model represents the
dodecameric form, which can be subdivided into 1-alpha
and 1-beta forms. The phylogeny of the 1-alpha and
1-beta forms appears polyphyletic. E. coli,
Synechocystis PCC6803, Aquifex aeolicus, and the
crenarcheon Sulfolobus acidocaldarius have form 1-beta,
while Bacillus subtilis, Thermotoga maritima, and
various euryarchaea has form 1-alpha. The 1-beta
dodecamer from the crenarcheon Sulfolobus acidocaldarius
differs from that in E. coli in that it is not regulated
by adenylylation [Amino acid biosynthesis, Glutamate
family].
Length = 459
Score = 28.9 bits (65), Expect = 9.3
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 12/47 (25%)
Query: 64 MLQASLD------------EANLGSMSPEELEAVFIQSVYASLGASL 98
ML A LD + NL +SPEEL I + SL +L
Sbjct: 366 MLMAGLDGIKNKIDPGEPVDKNLYELSPEELREKGIPQLPGSLEEAL 412
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
0.321 0.136 0.397
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,463,829
Number of extensions: 2956781
Number of successful extensions: 2850
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2845
Number of HSP's successfully gapped: 46
Length of query: 567
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 465
Effective length of database: 6,413,494
Effective search space: 2982274710
Effective search space used: 2982274710
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 (21.9 bits)
S2: 62 (28.1 bits)