RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4032
(84 letters)
>gnl|CDD|235797 PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated.
Length = 183
Score = 117 bits (294), Expect = 4e-35
Identities = 45/74 (60%), Positives = 55/74 (74%), Gaps = 1/74 (1%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VISMG A N GG YHYSYSVV+G DRI+PVD+YVPGCPP EAL+YGIL+LQK
Sbjct: 99 MPEPKWVISMGSCA-NSGGMYHYSYSVVQGVDRIVPVDVYVPGCPPRPEALLYGILKLQK 157
Query: 71 KVKRMKILQSWYRR 84
K+++ + + R
Sbjct: 158 KIRQSERERKRGER 171
>gnl|CDD|223454 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and
related Fe-S oxidoreductases [Energy production and
conversion].
Length = 194
Score = 112 bits (282), Expect = 4e-33
Identities = 39/74 (52%), Positives = 49/74 (66%), Gaps = 1/74 (1%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VISMG + N GG Y SYSVV+G DR++PVD+Y+PGCPP EAL+YGIL LQ+
Sbjct: 100 MPEPKWVISMG-SCANSGGMYWNSYSVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQE 158
Query: 71 KVKRMKILQSWYRR 84
K++R
Sbjct: 159 KIRREGRPLRDKPG 172
>gnl|CDD|233656 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit. This
model describes the B chain of complexes that resemble
NADH-quinone oxidoreductases. The electron acceptor is a
quinone, ubiquinone, in mitochondria and most bacteria,
including Escherichia coli, where the recommended gene
symbol is nuoB. The quinone is plastoquinone in
Synechocystis (where the chain is designated K) and in
chloroplast, where NADH may be replaced by NADPH. In the
methanogenic archaeal genus Methanosarcina, NADH is
replaced by F420H2 [Energy metabolism, Electron
transport].
Length = 145
Score = 107 bits (268), Expect = 1e-31
Identities = 41/64 (64%), Positives = 51/64 (79%), Gaps = 1/64 (1%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VISMG A N GG +H SYSVV+G DRI+PVD+Y+PGCPP EAL+YG+++LQK
Sbjct: 82 MPEPKWVISMGACA-NSGGMFHTSYSVVQGVDRIVPVDVYIPGCPPRPEALIYGLIKLQK 140
Query: 71 KVKR 74
K+KR
Sbjct: 141 KIKR 144
>gnl|CDD|214337 CHL00023, ndhK, NADH dehydrogenase subunit K.
Length = 225
Score = 79.0 bits (195), Expect = 7e-20
Identities = 36/75 (48%), Positives = 48/75 (64%), Gaps = 2/75 (2%)
Query: 2 MGVSL--LAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAE 59
M SL L + M P VI+MG GG + SYS VRG D++IPVD+Y+PGCPP E
Sbjct: 85 MAPSLVRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYLPGCPPKPE 144
Query: 60 ALMYGILQLQKKVKR 74
A++ I +L+KK+ R
Sbjct: 145 AVIDAITKLRKKISR 159
>gnl|CDD|173279 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provisional.
Length = 173
Score = 77.3 bits (190), Expect = 1e-19
Identities = 36/70 (51%), Positives = 46/70 (65%), Gaps = 1/70 (1%)
Query: 4 VSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMY 63
LL M P VISMG + N GG + YSV +G D++IPVD+YVPGCPP EAL
Sbjct: 88 ARLLYDQMPEPKYVISMGSCS-NCGGLFQLGYSVCKGVDKVIPVDVYVPGCPPRPEALTE 146
Query: 64 GILQLQKKVK 73
G+L+LQ+ V+
Sbjct: 147 GLLRLQEIVR 156
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit
B/C/D; Provisional.
Length = 788
Score = 80.2 bits (198), Expect = 2e-19
Identities = 35/68 (51%), Positives = 48/68 (70%), Gaps = 2/68 (2%)
Query: 7 LAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGIL 66
L + M P VISMG A N GG Y YSVV+G ++I+PVD+Y+PGCPP EA + G++
Sbjct: 83 LYEQMAEPKWVISMGSCA-NSGGMYDV-YSVVQGVNQILPVDVYIPGCPPRPEAFLQGLM 140
Query: 67 QLQKKVKR 74
LQ+K++R
Sbjct: 141 LLQEKIRR 148
>gnl|CDD|173277 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provisional.
Length = 182
Score = 76.5 bits (188), Expect = 3e-19
Identities = 35/67 (52%), Positives = 47/67 (70%), Gaps = 1/67 (1%)
Query: 7 LAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGIL 66
L M P VI++GG A +GG + SY V+ G D+I+PVD+Y+PGCPP EA YG++
Sbjct: 102 LYDQMADPKYVIAVGGCAVSGGPF-KKSYHVLNGVDKILPVDVYIPGCPPRPEAFYYGMM 160
Query: 67 QLQKKVK 73
QLQ+KVK
Sbjct: 161 QLQRKVK 167
>gnl|CDD|173274 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provisional.
Length = 189
Score = 74.9 bits (184), Expect = 1e-18
Identities = 34/74 (45%), Positives = 51/74 (68%)
Query: 4 VSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMY 63
V L + M P V+SMG + GG Y+ + Y V++G DRIIPVD+YVPGCPP EAL+
Sbjct: 85 VVRLYEQMPEPRYVLSMGSCSNCGGPYWEHGYHVLKGVDRIIPVDVYVPGCPPRPEALIG 144
Query: 64 GILQLQKKVKRMKI 77
G++++Q+ ++ +I
Sbjct: 145 GLMKVQELIRMEQI 158
>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional.
Length = 264
Score = 75.8 bits (186), Expect = 2e-18
Identities = 35/81 (43%), Positives = 50/81 (61%), Gaps = 2/81 (2%)
Query: 4 VSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMY 63
V L M P VISMG A +GG + Y+V+RG D +IPVD+Y+PGCPP EAL++
Sbjct: 89 VVRLYNQMPEPRYVISMGACATSGGPFRD-GYNVLRGIDLLIPVDVYIPGCPPRPEALLH 147
Query: 64 GILQLQKKVKRMKILQS-WYR 83
++ LQK++ + + WY
Sbjct: 148 ALMTLQKQIDAQSLGRVRWYG 168
>gnl|CDD|237821 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provisional.
Length = 183
Score = 70.3 bits (172), Expect = 6e-17
Identities = 32/74 (43%), Positives = 51/74 (68%), Gaps = 2/74 (2%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VI+MG A +GG Y SYSV++G DRI+PVD+Y+ GCPP EA++ +++LQK
Sbjct: 98 MPEPKWVIAMGACASSGGMYR--SYSVLQGVDRILPVDVYISGCPPRPEAILDALIKLQK 155
Query: 71 KVKRMKILQSWYRR 84
K+ + ++ +++
Sbjct: 156 KIDTERAARTLFKK 169
>gnl|CDD|225799 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy
production and conversion].
Length = 148
Score = 68.9 bits (169), Expect = 1e-16
Identities = 27/68 (39%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 9 QAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQL 68
+AM P VI++G A GG + SYSV D++IPVD+ +PGCPP EA++ G++
Sbjct: 72 EAMPEPKIVIAVG-ACALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAA 130
Query: 69 QKKVKRMK 76
K+++
Sbjct: 131 LGKLEKKI 138
>gnl|CDD|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional.
Length = 186
Score = 68.1 bits (166), Expect = 6e-16
Identities = 31/63 (49%), Positives = 46/63 (73%), Gaps = 2/63 (3%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VIS+G A +GG ++ +Y V++G DRI+PVD+YVPGCPP EA++ +++LQ
Sbjct: 98 MAEPKFVISVGACASSGGMFH--TYGVLQGVDRILPVDVYVPGCPPRPEAILDALVKLQT 155
Query: 71 KVK 73
K+K
Sbjct: 156 KLK 158
>gnl|CDD|184833 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provisional.
Length = 180
Score = 65.6 bits (160), Expect = 4e-15
Identities = 30/63 (47%), Positives = 46/63 (73%), Gaps = 2/63 (3%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P V+++G A +GG + +YSV++G DRIIPVD+YVPGCPP E ++ G++++Q+
Sbjct: 98 MAEPRWVVAVGACASSGGIFD--TYSVLQGIDRIIPVDVYVPGCPPRPEQIIDGVMRVQE 155
Query: 71 KVK 73
VK
Sbjct: 156 LVK 158
>gnl|CDD|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional.
Length = 181
Score = 64.2 bits (156), Expect = 2e-14
Identities = 31/65 (47%), Positives = 46/65 (70%), Gaps = 2/65 (3%)
Query: 9 QAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQL 68
+ M P V++ G A +GG ++ +Y+ V+G DRIIPVD+YVPGCPP E ++ GI+ L
Sbjct: 98 EQMADPKWVMAFGVCASSGG--FYDNYATVQGIDRIIPVDVYVPGCPPRPEQVLDGIMLL 155
Query: 69 QKKVK 73
QKK++
Sbjct: 156 QKKIQ 160
>gnl|CDD|216271 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd
subunit.
Length = 122
Score = 59.9 bits (146), Expect = 2e-13
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 17 VISMGGAAPNGG--GYYHYSYSV-VRGCDRIIPVDIYVPGCPPTAEALMYGILQL 68
VI++G A GG + SY V V ++PVDI +PGCPP EA++ +L L
Sbjct: 68 VIAVGTCAAYGGIPAAGNNSYGVGVGPVLEVVPVDINIPGCPPHPEAILGTLLAL 122
>gnl|CDD|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit
[Energy production and conversion].
Length = 247
Score = 36.2 bits (84), Expect = 6e-04
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 38 VRGCDRIIPVDIYVPGCPPTAEA 60
V +I VD +PGCPP+ E
Sbjct: 120 VVPLGEVIDVDYAIPGCPPSPEE 142
>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma. This
model represents that clade of F420-dependent
hydrogenases (FRH) beta subunits found exclusively and
universally in methanogenic archaea. This protein
contains two 4Fe-4S cluster binding domains (pfam00037)
and scores above the trusted cutoff to model pfam01058
for the "NADH ubiquinone oxidoreductase, 20 Kd subunit"
family.
Length = 228
Score = 32.1 bits (73), Expect = 0.018
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 44 IIPVDIYVPGCPPTAEAL 61
+I VD+ +PGCPP+ EA+
Sbjct: 116 VIDVDLAIPGCPPSPEAI 133
>gnl|CDD|215209 PLN02369, PLN02369, ribose-phosphate pyrophosphokinase.
Length = 302
Score = 28.9 bits (65), Expect = 0.22
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 38 VRGCDRIIPVDIYVPGCPPTAEALM 62
VRGCD V + P CPP E LM
Sbjct: 36 VRGCD----VFLVQPTCPPANENLM 56
>gnl|CDD|215557 PLN03069, PLN03069, magnesiumprotoporphyrin-IX chelatase subunit H;
Provisional.
Length = 1220
Score = 27.1 bits (60), Expect = 0.96
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 43 RIIPVDIYVPGCPPTAE 59
R++P ++V G PP+AE
Sbjct: 751 RLLPCGLHVIGEPPSAE 767
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 27.3 bits (61), Expect = 1.00
Identities = 16/36 (44%), Positives = 16/36 (44%), Gaps = 11/36 (30%)
Query: 43 RIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 78
RII PTA AL YG L K K KIL
Sbjct: 162 RIIN--------EPTAAALAYG---LDKSKKDEKIL 186
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 27.1 bits (60), Expect = 1.0
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 33 YSYSVVRGCD-------RIIPVDIYVPGCPPTAEALMYGILQ--LQKKVKRMK 76
Y V G RI P D +P A+ ++ ++ LQK + ++
Sbjct: 1103 YVEIVPNGEKILKDPVRRIYPDDDSIPVDDGRADQYLFEVIYEALQKHFQGIQ 1155
>gnl|CDD|237117 PRK12493, PRK12493, magnesium chelatase subunit H; Provisional.
Length = 1310
Score = 26.8 bits (60), Expect = 1.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 42 DRIIPVDIYVPGCPPTAEAL 61
R+IP ++V G PPTAE
Sbjct: 738 SRLIPCGLHVIGKPPTAEEA 757
>gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional.
Length = 618
Score = 26.2 bits (58), Expect = 2.3
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 8 AQAMLGPVGVISMGGAAPNGG 28
A+A PV V+SMGG A +GG
Sbjct: 392 ARAAGKPV-VVSMGGMAASGG 411
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 25.4 bits (57), Expect = 3.7
Identities = 13/23 (56%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 56 PTAEALMYGILQLQKKVKRMKIL 78
PTA AL YG L KK KIL
Sbjct: 170 PTAAALAYG---LDKK-GDEKIL 188
>gnl|CDD|233097 TIGR00705, SppA_67K, signal peptide peptidase SppA, 67K type. This
model represents the signal peptide peptidase A (SppA,
protease IV) as found in E. coli, Treponema pallidum,
Mycobacterium leprae, and several other species, in
which it has a molecular mass around 67 kDa and a
duplication such that the N-terminal half shares
extensive homology with the C-terminal half. This enzyme
was shown in E. coli to form homotetramers. E. coli
SohB, which is most closely homologous to the C-terminal
duplication of SppA, is predicted to perform a similar
function of small peptide degradation, but in the
periplasm. Many prokaryotes have a single SppA/SohB
homolog that may perform the function of either or both
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 584
Score = 25.2 bits (55), Expect = 4.4
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 7 LAQAMLGPVGVISMGGAAPNGG 28
AQA PV ++SMG A +GG
Sbjct: 373 RAQARGKPV-IVSMGAMAASGG 393
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae
Stress-seventy subfamily Q protein 1/Ssq1p (also called
Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae
Stress-Seventy subfamily C/Ssc1p (also called mtHSP70,
Endonuclease SceI 75 kDa subunit). It belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly, and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively.
Length = 376
Score = 25.3 bits (56), Expect = 4.8
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 56 PTAEALMYGILQLQKKVKRMKIL 78
PTA AL YG+ K KIL
Sbjct: 171 PTAAALAYGL----DKKGNEKIL 189
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 205
Score = 24.9 bits (55), Expect = 5.2
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 22 GAAPNGGGYYHYSYSVVRGCDRIIPVDI 49
GAAP GG+ + + +I+ VDI
Sbjct: 53 GAAP--GGWSQVAAKKLGAGGKIVAVDI 78
>gnl|CDD|240531 cd13126, MATE_like_11, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. This
family might function as a translocase for
lipopolysaccharides, such as O-antigen. The integral
membrane proteins from the MATE family are involved in
exporting metabolites across the cell membrane and are
responsible for multidrug resistance (MDR) in many
bacteria and animals. A number of family members are
involved in the synthesis of peptidoglycan components in
bacteria.
Length = 396
Score = 25.0 bits (55), Expect = 6.0
Identities = 15/59 (25%), Positives = 23/59 (38%)
Query: 8 AQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGIL 66
AQA+L P+ + G A G Y + +G R+ V AL+ G +
Sbjct: 311 AQALLLPLILAQAGAALAVGPAAYLLALGRAKGTLRVNLVGAPQLLGLGLTGALLGGAV 369
>gnl|CDD|200578 cd10954, CE4_CtAXE_like, Catalytic NodB homology domain of
Clostridium thermocellum acetylxylan esterase and its
bacterial homologs. This family is represented by
Clostridium thermocellum acetylxylan esterase (CtAXE, EC
3.1.1.72), a member of the carbohydrate esterase 4 (CE4)
superfamily. CtAXE deacetylates O-acetylated xylan, a
key component of plant cell walls. It shows no
detectable activity on generic esterase substrates
including para-nitrophenyl acetate. It is specific for
sugar-based substrates and will precipitate acetylxylan,
as a consequence of deacetylation. CtAXE is a monomeric
protein containing a catalytic NodB homology domain with
the same overall topology and a deformed (beta/alpha)8
barrel fold as other CE4 esterases. However, due to
differences in the topography of the substrate-binding
groove, the chemistry of the active center, and metal
ion coordination, CtAXE has different metal ion
preference and lacks activity on N-acetyl substrates. It
is significantly activated by Co2+. Moreover, CtAXE
displays distinctly different ligand coordination to the
metal ion, utilizing an aspartate, a histidine, and four
water molecules, as opposed to the conserved His-His-Asp
zinc-binding triad of other CE4 esterases.
Length = 180
Score = 24.5 bits (54), Expect = 6.5
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 48 DIYVPGCPPTAEALMYGILQLQKK 71
DIY P T EA I +L+K+
Sbjct: 151 DIY----PSTVEAAETIIPELKKR 170
>gnl|CDD|199990 TIGR00072, hydrog_prot, hydrogenase maturation protease. HycI
and HoxM are well-characterized as responsible for
C-terminal protease activity on their respective
hydrogenase large chains. A large number of homologous
proteins appear responsible for the maturation of
various forms of hydrogenase.
Length = 145
Score = 24.4 bits (54), Expect = 7.2
Identities = 13/55 (23%), Positives = 18/55 (32%), Gaps = 9/55 (16%)
Query: 4 VSLLAQAMLGP--VGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPP 56
L + P V V+ G ++ G DR+I VD G P
Sbjct: 20 AERLEERYEFPPGVEVLDGGTLGL------ELLDAI-EGADRVIVVDAVDSGAEP 67
>gnl|CDD|234136 TIGR03173, pbuX, xanthine permease. All the seed members of this
model are observed adjacent to genes for either xanthine
phosphoribosyltransferase (for the conversion of
xanthine to guanine, GenProp0696, ) or genes for the
conversion of xanthine to urate and its concomitant
catabolism (GenProp0640, GenProp0688, GenProp0686 and
GenProp0687). A number of sequences scoring higher than
trusted to this model are found in different genomic
contexts, and the possibility exist that these transport
related compounds in addition to or instead of xanthine
itself. The outgroup to this family are sequences which
are characterized as uracil permeases or are adjacent to
established uracil phosphoribosyltransferases.
Length = 406
Score = 24.4 bits (54), Expect = 8.6
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 1 MMGVSLLAQAMLGPVGVISMGGAAPNGG 28
++G+SL+ PV + G A
Sbjct: 121 LIGLSLM------PVAINWAAGGAGAPD 142
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 0.142 0.447
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,471,278
Number of extensions: 365977
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 548
Number of HSP's successfully gapped: 44
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
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 (21.5 bits)
S2: 53 (24.1 bits)