RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12760
(199 letters)
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 94.4 bits (235), Expect = 1e-22
Identities = 36/110 (32%), Positives = 56/110 (50%)
Query: 82 RDYAKRSKEMQAVLATLNTYCTGYEQCLSKRQKEFDTNFVKIGKRVQECYQMLTFGGKAD 141
Y + + + + E+ ++++ F F KI + E ++ L GG A+
Sbjct: 977 ERYEELKSQREDLEEAKEKLLEVIEELDKEKRERFKETFDKINENFSEIFKELFGGGTAE 1036
Query: 142 LEYKEYSDPYAQGIKYVVRPPRKSWKSIDCLSGGEKTLASLALVFALHYY 191
LE E DP GI+ RPP K +S+ LSGGEK+L +LAL+FA+ Y
Sbjct: 1037 LELTEPDDPLTAGIEISARPPGKKLQSLSLLSGGEKSLTALALLFAIQKY 1086
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains separated
by a hinge in the middle. The eukaryotic SMC proteins
form two kind of heterodimers: the SMC1/SMC3 and the
SMC2/SMC4 types. These heterodimers constitute an
essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 93.1 bits (231), Expect = 4e-22
Identities = 36/81 (44%), Positives = 52/81 (64%)
Query: 111 KRQKEFDTNFVKIGKRVQECYQMLTFGGKADLEYKEYSDPYAQGIKYVVRPPRKSWKSID 170
+R KEF FV I + + + + L GG A+L ++ DP++ GI+ RPP K K++D
Sbjct: 1018 QRFKEFLELFVSINRGLNKVFFYLELGGSAELRLEDSDDPFSGGIEISARPPGKGVKNLD 1077
Query: 171 CLSGGEKTLASLALVFALHYY 191
LSGGEKTL +LAL+FA+ Y
Sbjct: 1078 NLSGGEKTLVALALIFAIQKY 1098
>gnl|CDD|213241 cd03274, ABC_SMC4_euk, ATP-binding cassette domain of eukaryotic
SMC4 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 212
Score = 68.9 bits (169), Expect = 1e-14
Identities = 24/30 (80%), Positives = 28/30 (93%)
Query: 162 PRKSWKSIDCLSGGEKTLASLALVFALHYY 191
P+KSWK+I LSGGEKTL+SLALVFALH+Y
Sbjct: 118 PKKSWKNISNLSGGEKTLSSLALVFALHHY 147
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily
archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and C-terminal
domains of this protein are well conserved, but the
central hinge region is skewed in composition and highly
divergent [Cellular processes, Cell division, DNA
metabolism, Chromosome-associated proteins].
Length = 1164
Score = 64.3 bits (157), Expect = 3e-12
Identities = 31/111 (27%), Positives = 55/111 (49%), Gaps = 5/111 (4%)
Query: 85 AKRSKEMQAVLATLNTYCTGY----EQCLSKRQKEFDTNFVKIGKRVQECYQMLTFGGKA 140
KR E++ A L E+ K+++ F F I + E + L+ GG
Sbjct: 985 LKRLDELKEKRAKLEEERKAILERIEEYEKKKREVFMEAFEAINENFNEIFAELS-GGTG 1043
Query: 141 DLEYKEYSDPYAQGIKYVVRPPRKSWKSIDCLSGGEKTLASLALVFALHYY 191
+L + DP+A G++ +P K + ++ +SGGEK+L +L+ +FA+ Y
Sbjct: 1044 ELILENPDDPFAGGLELSAKPKGKPVQRLEAMSGGEKSLTALSFIFAIQRY 1094
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc gene
is often associated with scpB (TIGR00281) and scpA genes,
where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 63.5 bits (155), Expect = 5e-12
Identities = 26/75 (34%), Positives = 42/75 (56%)
Query: 114 KEFDTNFVKIGKRVQECYQMLTFGGKADLEYKEYSDPYAQGIKYVVRPPRKSWKSIDCLS 173
+ F F ++ + Q + L GG+A+L + D GI+ +PP K +++ LS
Sbjct: 1032 ERFKDTFDQVNENFQRVFPKLFGGGEAELRLTDPEDLLEAGIEIFAQPPGKKNQNLSLLS 1091
Query: 174 GGEKTLASLALVFAL 188
GGEK L +LAL+FA+
Sbjct: 1092 GGEKALTALALLFAI 1106
>gnl|CDD|213242 cd03275, ABC_SMC1_euk, ATP-binding cassette domain of eukaryotic
SMC1 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 247
Score = 50.3 bits (121), Expect = 1e-07
Identities = 19/31 (61%), Positives = 26/31 (83%)
Query: 161 PPRKSWKSIDCLSGGEKTLASLALVFALHYY 191
PP K ++ +D LSGGEKT+A+LAL+FA+H Y
Sbjct: 145 PPGKRFRDMDNLSGGEKTMAALALLFAIHSY 175
>gnl|CDD|213245 cd03278, ABC_SMC_barmotin, ATP-binding cassette domain of barmotin,
a member of the SMC protein family. Barmotin is a tight
junction-associated protein expressed in rat epithelial
cells which is thought to have an important regulatory
role in tight junction barrier function. Barmotin
belongs to the SMC protein family. SMC proteins are
large (approximately 110 to 170 kDa), and each is
arranged into five recognizable domains. Amino-acid
sequence homology of SMC proteins between species is
largely confined to the amino- and carboxy-terminal
globular domains. The amino-terminal domain contains a
'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B' motif,
and a motif with homology to the signature sequence of
the ATP-binding cassette (ABC) family of ATPases. The
sequence homology within the carboxy-terminal domain is
relatively high within the SMC1-SMC4 group, whereas SMC5
and SMC6 show some divergence in both of these
sequences. In eukaryotic cells, the proteins are found
as heterodimers of SMC1 paired with SMC3, SMC2 with
SMC4, and SMC5 with SMC6 (formerly known as Rad18).
Length = 197
Score = 41.3 bits (98), Expect = 9e-05
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 153 QG-IKYVVRPPRKSWKSIDCLSGGEKTLASLALVFALHYY 191
QG + ++ P K + + LSGGEK L +LAL+FA+
Sbjct: 94 QGDVSEIIEAPGKKVQRLSLLSGGEKALTALALLFAIFRV 133
>gnl|CDD|213206 cd03239, ABC_SMC_head, The SMC head domain belongs to the
ATP-binding cassette superfamily. The structural
maintenance of chromosomes (SMC) proteins are essential
for successful chromosome transmission during
replication and segregation of the genome in all
organisms. SMCs are generally present as single proteins
in bacteria, and as at least six distinct proteins in
eukaryotes. The proteins range in size from
approximately 110 to 170 kDa, and each has five distinct
domains: amino- and carboxy-terminal globular domains,
which contain sequences characteristic of ATPases, two
coiled-coil regions separating the terminal domains ,
and a central flexible hinge. SMC proteins function
together with other proteins in a range of chromosomal
transactions, including chromosome condensation,
sister-chromatid cohesion, recombination, DNA repair,
and epigenetic silencing of gene expression.
Length = 178
Score = 36.9 bits (86), Expect = 0.002
Identities = 13/20 (65%), Positives = 17/20 (85%)
Query: 172 LSGGEKTLASLALVFALHYY 191
LSGGEK+L++LAL+FAL
Sbjct: 95 LSGGEKSLSALALIFALQEI 114
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 36.2 bits (84), Expect = 0.004
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 168 SIDCLSGGEKTLASLALVFALH 189
+ LSGGEK L++LAL+ AL
Sbjct: 74 TRLQLSGGEKELSALALILALA 95
>gnl|CDD|213239 cd03272, ABC_SMC3_euk, ATP-binding cassette domain of eukaryotic
SMC3 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 243
Score = 35.3 bits (82), Expect = 0.012
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 167 KSIDCLSGGEKTLASLALVFALH 189
+ + LSGG+K+L +LAL+FA+
Sbjct: 154 QEMQQLSGGQKSLVALALIFAIQ 176
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 33.6 bits (77), Expect = 0.059
Identities = 17/35 (48%), Positives = 19/35 (54%)
Query: 154 GIKYVVRPPRKSWKSIDCLSGGEKTLASLALVFAL 188
G VV + I LSGGE+ LASLAL AL
Sbjct: 798 GGLVVVVYDGGEVRPIKTLSGGERFLASLALRLAL 832
>gnl|CDD|213240 cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic
SMC2 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 251
Score = 33.0 bits (76), Expect = 0.059
Identities = 12/24 (50%), Positives = 19/24 (79%), Gaps = 1/24 (4%)
Query: 166 WK-SIDCLSGGEKTLASLALVFAL 188
WK S+ LSGG+++L +L+L+ AL
Sbjct: 160 WKESLTELSGGQRSLVALSLILAL 183
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The conserved
ATP-binding motifs common to Rad50 and the ABC
transporter family include the Walker A and Walker B
motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known as
the ABC signature sequence.
Length = 204
Score = 32.6 bits (75), Expect = 0.091
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 169 IDCLSGGEKTLASLALVFAL 188
SGGEK LASL + AL
Sbjct: 113 RGRCSGGEKVLASLIIRLAL 132
>gnl|CDD|213243 cd03276, ABC_SMC6_euk, ATP-binding cassette domain of eukaryotic
SM6 proteins. The structural maintenance of chromosomes
(SMC) proteins are large (approximately 110 to 170 kDa),
and each is arranged into five recognizable domains.
Amino-acid sequence homology of SMC proteins between
species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 198
Score = 30.6 bits (70), Expect = 0.32
Identities = 7/27 (25%), Positives = 18/27 (66%)
Query: 163 RKSWKSIDCLSGGEKTLASLALVFALH 189
+ + + + LSGGE++ +++ L+ +L
Sbjct: 101 KAAVRDVKTLSGGERSFSTVCLLLSLW 127
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 29.9 bits (68), Expect = 0.59
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 167 KSIDCLSGGEKTLASLALVFAL 188
+ + LSGGE LASL+L AL
Sbjct: 119 RPVSTLSGGETFLASLSLALAL 140
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.8 bits (68), Expect = 0.79
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 165 SWKSIDCLSGGEKTLASLALVFA 187
+ + +D LSGGE+ +A A
Sbjct: 132 ADRPVDELSGGERQRVLIARALA 154
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 28.7 bits (64), Expect = 2.1
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 169 IDCLSGGEKTLASLALVFALHYY 191
ID LSGGEKT + AL A+ +
Sbjct: 799 IDSLSGGEKTAVAFALRVAVAQF 821
>gnl|CDD|235230 PRK04158, PRK04158, transcriptional repressor CodY; Validated.
Length = 256
Score = 28.2 bits (64), Expect = 2.5
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 11/39 (28%)
Query: 1 MELEREHHEEIVEKKR-RAIVTRPCSITSWMAV--LSIS 36
ME+ RE EEI E+ R +A+V MA+ LS S
Sbjct: 153 MEILREKAEEIEEEARKKAVVQ--------MAINTLSYS 183
>gnl|CDD|221659 pfam12597, DUF3767, Protein of unknown function (DUF3767). This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 112 and 199 amino
acids in length.
Length = 119
Score = 27.3 bits (61), Expect = 2.8
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 104 GYEQCLSKRQKEFDT 118
G+EQC +R+K F
Sbjct: 84 GWEQCRYRRRKSFQG 98
>gnl|CDD|219833 pfam08418, Pol_alpha_B_N, DNA polymerase alpha subunit B
N-terminal. This is the eukaryotic DNA polymerase alpha
subunit B N-terminal domain which is involved in complex
formation. Also see pfam04058.
Length = 239
Score = 28.1 bits (63), Expect = 2.9
Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 8/90 (8%)
Query: 12 VEKKRRAIVTRPCSITSWMAVLSISDILSNSSIHTTPRSANTMAPAS--KWRSPVSGSDV 69
V + +++ + + + ILS + RS + + S + SP S S
Sbjct: 81 VPEAEESLLDSYTTPSD---KGGMLRILSTPELPKRKRSFSASSLESPSLFFSPASFS-- 135
Query: 70 TAAVRPTPELPVRDYAKRSKEMQAVLATLN 99
+A TP ++ RS V+ TLN
Sbjct: 136 PSAAPSTPSPNSAKFSSRS-NPGEVVETLN 164
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 27.6 bits (62), Expect = 2.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 169 IDCLSGGEKTLASLALVFAL 188
+ LSGG++ +LA L
Sbjct: 78 VPQLSGGQRQRVALARALLL 97
>gnl|CDD|215523 PLN02969, PLN02969, 9-cis-epoxycarotenoid dioxygenase.
Length = 610
Score = 28.2 bits (63), Expect = 3.7
Identities = 9/41 (21%), Positives = 18/41 (43%)
Query: 24 CSITSWMAVLSISDILSNSSIHTTPRSANTMAPASKWRSPV 64
++ ++ L++ +S ++ PR A WR PV
Sbjct: 340 AGLSPMISALAVDPSRPSSPVYLLPRFPEKEAGGRDWRVPV 380
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 27.8 bits (62), Expect = 4.8
Identities = 12/17 (70%), Positives = 12/17 (70%)
Query: 172 LSGGEKTLASLALVFAL 188
LSGGE L SLAL AL
Sbjct: 950 LSGGESFLVSLALALAL 966
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 27.0 bits (61), Expect = 5.5
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 167 KSIDCLSGGEKTLASLALVFA 187
+ + LSGGE+ LA A
Sbjct: 93 RPFNELSGGERQRVLLARALA 113
>gnl|CDD|172030 PRK13397, PRK13397, 3-deoxy-7-phosphoheptulonate synthase;
Provisional.
Length = 250
Score = 27.3 bits (60), Expect = 5.7
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 45 HTTPRSANTMAPASKWRSPVSGSDVTAAVRPTPELPVRDYAKR 87
H+T R + + PA+K V + + V P P+ + D A++
Sbjct: 193 HSTGRR-DLLLPAAKIAKAVGANGIMMEVHPDPDHALSDAAQQ 234
>gnl|CDD|222831 PHA01747, PHA01747, putative ATP-dependent protease.
Length = 425
Score = 27.5 bits (61), Expect = 5.9
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 89 KEMQAVLATLNTYCTGYEQCLSKRQKEFDTNFVKIGKRV 127
M+A+ +TL+T G E C+ R +++ I + +
Sbjct: 257 SNMRAINSTLST---GMENCVWTRGAGTESDAATIVRCI 292
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 27.0 bits (61), Expect = 6.4
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 167 KSIDCLSGGEKTLASLALVFAL 188
+S LSGG+K ++A V A+
Sbjct: 130 RSPFTLSGGQKQRVAIAGVLAM 151
>gnl|CDD|185377 PRK15480, PRK15480, glucose-1-phosphate thymidylyltransferase
RfbA; Provisional.
Length = 292
Score = 26.9 bits (59), Expect = 8.1
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 28 SWMAVLSISDILSNSSIHTTPRSANTMAPASKWRSPVSGSDVTAAVRPTPE 78
S + + I DIL S+ TPR + S+W G ++ V+P+P+
Sbjct: 42 STLMLAGIRDILIISTPQDTPRFQQLLGDGSQW-----GLNLQYKVQPSPD 87
>gnl|CDD|216443 pfam01341, Glyco_hydro_6, Glycosyl hydrolases family 6.
Length = 295
Score = 26.8 bits (60), Expect = 8.6
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 137 GGKADLE-YKEYSDPYAQGIKY 157
GG A L YK Y DP A G+K
Sbjct: 83 GGAAGLAAYKTYIDPIAAGLKK 104
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
0.318 0.130 0.397
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,005,990
Number of extensions: 865230
Number of successful extensions: 809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 809
Number of HSP's successfully gapped: 32
Length of query: 199
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 107
Effective length of database: 6,857,034
Effective search space: 733702638
Effective search space used: 733702638
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.4 bits)