RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780661|ref|YP_003065074.1| exonuclease I [Candidatus
Liberibacter asiaticus str. psy62]
(471 letters)
>gnl|CDD|32749 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and
repair].
Length = 475
Score = 591 bits (1526), Expect = e-169
Identities = 254/465 (54%), Positives = 329/465 (70%), Gaps = 3/465 (0%)
Query: 1 MTNHFVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFI 60
F+ YDYETFG ALDRPAQFAG+R D ++ I VF+CKPADDYLP P AV I
Sbjct: 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLI 66
Query: 61 TGITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRW 120
TGITPQ+A G+ EA F+ RIH + PNTC++GYNNIRFDD +R IFYRNFYD Y W
Sbjct: 67 TGITPQEAREKGINEAAFAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAW 126
Query: 121 SWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKAD 180
SW NGNSRWDLLDV+RA YA P+GI WP DDG SFKL+ L ANGIEH NAHDA +D
Sbjct: 127 SWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLEHLTKANGIEHSNAHDAMSD 186
Query: 181 VYATLALVWLIREKKPKLFEYLYDYRNKNQLRKLIDIQNMTPLVHVSGMFGASRSNTALI 240
VYAT+A+ L++ +P+LF+YL+ R K++L LIDI NM PLVHVSGMFGA R NT+ +
Sbjct: 187 VYATIAMAKLVKTAQPRLFDYLFQLRKKHKLLALIDIPNMQPLVHVSGMFGAERGNTSWV 246
Query: 241 APVAWHPRYKDSVIGCNLSGDMRVFQDLDSVQLAKRLFTSHDEL-KGLVPVPIKEVHLNK 299
P+AWHP +++VI C+L+GD+ +LD+ L +RL+T +L +G + VP+K VH+NK
Sbjct: 247 LPLAWHPTNRNAVIVCDLAGDISPLLELDADTLRERLYTRKADLGEGELAVPVKLVHINK 306
Query: 300 CPILMPIDYCKKEHFERWGIDHKRCLENLTLLRQQTNLRDRFKAIYNK-PYTSSSQDVDS 358
CPIL P + E +R GID + CL+NL LLR+ ++R++ AI+ + + S DVD+
Sbjct: 307 CPILAPAKTLRPEDADRLGIDRQHCLDNLELLRENPDVREKVVAIFAEEEPFNPSDDVDA 366
Query: 359 QLYDGFFADVDRQIMDRILRTAPEQLSTLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQ 418
QLY+GFF+D DR M + T PE L+ L++ F D+RL EL FRYRARNFP TL++ E+Q
Sbjct: 367 QLYNGFFSDADRAAMKILRETEPENLAALDITFVDKRLEELLFRYRARNFPETLTDAEQQ 426
Query: 419 DWLEHRKKMLTRSRIEEYKNKLQSLSGEYKGDEGKEGLINALYEY 463
WLEHR++ LT + Y+ LQ+L E+ D+ K L+ ALYEY
Sbjct: 427 RWLEHRRQRLTPEL-QGYELTLQALVQEHSDDKEKLALLKALYEY 470
>gnl|CDD|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of
Escherichia coli exonuclease I and similar proteins.
This subfamily is composed of the N-terminal domain of
Escherichia coli exonuclease I (ExoI) and similar
proteins. ExoI is a monomeric enzyme that hydrolyzes
single stranded DNA in the 3' to 5' direction. It plays
a role in DNA recombination and repair. It primarily
functions in repairing frameshift mutations. The
N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5
exonuclease containing three conserved sequence motifs
termed ExoI, ExoII and ExoIII, with a specific Hx(4)D
conserved pattern at ExoIII. These motifs are clustered
around the active site and contain four conserved acidic
residues that serve as ligands for the two metal ions
required for catalysis. The ExoI structure is unique
among DnaQ family enzymes in that there is a large
distance between the two metal ions required for
catalysis and the catalytic histidine is oriented away
from the active site.
Length = 183
Score = 293 bits (752), Expect = 7e-80
Identities = 108/182 (59%), Positives = 131/182 (71%), Gaps = 1/182 (0%)
Query: 6 VIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITP 65
+ YDYETFG + + D+ QFA +R D + +IE FC+ D LP PEA+ +TGITP
Sbjct: 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIE-PFNIFCRLPPDVLPSPEALIVTGITP 59
Query: 66 QKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDNG 125
Q+ L++G+ E EF +IH+ F+ P TCI+GYNNIRFDD + R FYRN YD Y W W NG
Sbjct: 60 QQLLKEGLSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNG 119
Query: 126 NSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADVYATL 185
NSRWDLLDV+RA YA PDGI WP DDG SFKL+DLA ANGIEH NAHDA +DV AT+
Sbjct: 120 NSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQANGIEHSNAHDALSDVEATI 179
Query: 186 AL 187
AL
Sbjct: 180 AL 181
>gnl|CDD|144506 pfam00929, Exonuc_X-T, Exonuclease. This family includes a variety
of exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 162
Score = 78.2 bits (193), Expect = 5e-15
Identities = 46/185 (24%), Positives = 62/185 (33%), Gaps = 24/185 (12%)
Query: 5 FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGIT 64
V+ D ET G D DR + A V + E I + KP EA GIT
Sbjct: 1 LVVIDCETTGLDPEKDRIIEIAAVSIVGG-ENIGPVFDTYVKPERL--ITDEATKFHGIT 57
Query: 65 PQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDN 124
P+ LR+ E +F ++G+N FD + R +
Sbjct: 58 PEM-LRNAPSFEEVLEAFLEFLK-KLKILVGHNA-SFDVGFLLYDDLRFLKLPH----PK 110
Query: 125 GNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHV-NAHDAKADVYA 183
N D L + +A Y L LA G+E + AH A D A
Sbjct: 111 LNDVIDTLILDKATYKGFK-------------RRSLDALAEKLGLEKIQRAHRALDDARA 157
Query: 184 TLALV 188
T L
Sbjct: 158 TAELF 162
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh
exonucleases, part of the DnaQ-like (or DEDD)
exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. These proteins contain four
invariant acidic residues in three conserved sequence
motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
are classified as such because of the presence of
specific Hx(4)D conserved pattern at the ExoIII motif.
The four conserved acidic residues are clustered around
the active site and serve as ligands for the two metal
ions required for catalysis. Most DEDDh exonucleases are
the proofreading subunits (epsilon) or domains of
bacterial DNA polymerase III, the main replicating
enzyme in bacteria, which functions as the chromosomal
replicase. Other members include other DNA and RNA
exonucleases such as RNase T, Oligoribonuclease, and RNA
exonuclease (REX), among others.
Length = 159
Score = 74.6 bits (184), Expect = 5e-14
Identities = 49/182 (26%), Positives = 61/182 (33%), Gaps = 25/182 (13%)
Query: 6 VIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITP 65
V++D ET G D DR + V+VD E +E E P PEA I GIT
Sbjct: 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFE-TLVNP--GRPIPPEATAIHGITD 57
Query: 66 QKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDNG 125
+ L D E +F ++ +N FD R N
Sbjct: 58 E-MLADAPPFEEVLPEFLEFLG--GRVLVAHN-ASFD----LRFLNRELRRLGGPPLPN- 108
Query: 126 NSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADVYATL 185
W +D +R P S G LA GI AH A AD AT
Sbjct: 109 --PW--IDTLRLARRLLPG---LRSHRLGL------LLAERYGIPLEGAHRALADALATA 155
Query: 186 AL 187
L
Sbjct: 156 EL 157
>gnl|CDD|32359 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 40.6 bits (95), Expect = 9e-04
Identities = 42/193 (21%), Positives = 71/193 (36%), Gaps = 33/193 (17%)
Query: 5 FVIYDYETFGRDVALDRPAQFAGVRV--DRQWEKIESTEVFFCKPADDYLPDPEAVF-IT 61
+V++D ET G D + A V++ R +K + FF KP P + +T
Sbjct: 423 YVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQ----FFIKPGR---PLSATITELT 475
Query: 62 GITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWS 121
GIT + L + E + +F I+ +N FD + + + Y +
Sbjct: 476 GIT-DEMLENAPEIEEVLEKFREFI---GDSILVAHNASFDMGFLNTNYEK--YGLEPLT 529
Query: 122 WDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADV 181
N D L++ RA+ S +L L G+E H A D
Sbjct: 530 ----NPVIDTLELARALNP-------------EFKSHRLGTLCKKLGVELERHHRADYDA 572
Query: 182 YATLALVWLIREK 194
AT + ++ +
Sbjct: 573 EATAKVFFVFLKD 585
>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 39.8 bits (92), Expect = 0.002
Identities = 48/228 (21%), Positives = 70/228 (30%), Gaps = 31/228 (13%)
Query: 5 FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGIT 64
FV+ D ET G + DR + V ++ +E + P PE I GIT
Sbjct: 15 FVVIDLETTGLNPKKDRIIEIGAVTLEDG-RIVERSFHTLVNPERPI--PPEIFKIHGIT 71
Query: 65 PQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDN 124
+ L D AE F ++ + N FD + R R +
Sbjct: 72 DEM-LADAPKFAEVLPEFLDFIG-GLRLLVAH-NAAFDVGFLRVESERLGIE------IP 122
Query: 125 GNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHV--NAHDAKADVY 182
G+ D L + R + G L LA GI+ + H A D
Sbjct: 123 GDPVLDTLALARRHFP-------------GFDRSSLDALAERLGIDRNPFHPHRALFDAL 169
Query: 183 ATLALVWLIREKKPKLFEYLYDYRNKNQLRKLIDIQNMTPLVHVSGMF 230
A L L++ L KL L + +F
Sbjct: 170 ALAELFLLLQTGLLL----KAPLTAILDLDKLAHKALYDTLKTAARLF 213
>gnl|CDD|31618 COG1429, CobN, Cobalamin biosynthesis protein CobN and related
Mg-chelatases [Coenzyme metabolism].
Length = 1388
Score = 31.1 bits (70), Expect = 0.66
Identities = 19/96 (19%), Positives = 29/96 (30%), Gaps = 11/96 (11%)
Query: 114 FYDSYRWSWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVN 173
+YR W+ +S DV + DG P K + +V
Sbjct: 299 SSGTYREQWEESDSGLGPADVAYQVALPELDGRIEP----IPIGGKEKRDDGTEVEAYV- 353
Query: 174 AHDAKADVYATLALVWL------IREKKPKLFEYLY 203
+ + A A+ W EKK + Y Y
Sbjct: 354 PIPERIEWLADRAIRWARLRRKPNAEKKVAIIYYNY 389
>gnl|CDD|35991 KOG0772, KOG0772, KOG0772, Uncharacterized conserved protein,
contains WD40 repeat [Function unknown].
Length = 641
Score = 28.9 bits (64), Expect = 3.1
Identities = 8/38 (21%), Positives = 20/38 (52%)
Query: 233 SRSNTALIAPVAWHPRYKDSVIGCNLSGDMRVFQDLDS 270
++ + A + WHP K+ + C+ G +R++ ++
Sbjct: 264 TKGHIAELTCGCWHPDNKEEFLTCSYDGTLRIWDVNNT 301
>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
[Cytoskeleton].
Length = 1930
Score = 28.7 bits (64), Expect = 4.0
Identities = 32/147 (21%), Positives = 58/147 (39%), Gaps = 13/147 (8%)
Query: 322 KRCLENLTLLRQQTNLRDRFKAIYNKPYTSSSQDVDSQLYDGFFADVDRQIMDRILRTAP 381
K+ ++L L++Q + KA K + +++ + +++ +++ +
Sbjct: 1185 KKHADSLAELQEQLEQLQKDKAKLEKEKSDLQREIADLAAELEQLSSEKKDLEKKDKKLE 1244
Query: 382 EQLSTLNLPFSD-RRLPELFFRYRAR------NFPHTLSEKEKQDWLEHRKKMLTRSRIE 434
QLS L L + RL R+R L E E + R K S++E
Sbjct: 1245 AQLSELQLKLDEQERLRNDLTAKRSRLQNENEELSRQLEEAEAKLSALSRDKQALESQLE 1304
Query: 435 EYKNKLQSLSGEYKGDEGKEGLINALY 461
E K +L+ + E K L NAL
Sbjct: 1305 ELKRQLEEETRE------KSALENALR 1325
>gnl|CDD|37245 KOG2034, KOG2034, KOG2034, Vacuolar sorting protein PEP3/VPS18
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 911
Score = 28.4 bits (63), Expect = 4.3
Identities = 15/70 (21%), Positives = 22/70 (31%), Gaps = 2/70 (2%)
Query: 386 TLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQDWLEHRKKMLTRSRIEEYKNKLQSLSG 445
L P + E F R P ++E + W + + Y N+ Q L
Sbjct: 215 ELEHPIRSFKSDEGFSNLRFSTMPKNIAEPKTWAWKSP--DGINFGNVNIYANRDQDLLE 272
Query: 446 EYKGDEGKEG 455
E E G
Sbjct: 273 EEFNIELPLG 282
>gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 428
Score = 28.3 bits (64), Expect = 4.4
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 407 NFPHTLSEKE-KQDWLEHRKKMLTRS---RIEEYKNKLQSLSGEYK 448
P L+ KE +++LEHR ++ R +E+ + +L L G K
Sbjct: 300 GGPKYLNLKEILKEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLK 345
>gnl|CDD|185714 cd07905, Adenylation_DNA_ligase_LigC, Adenylation domain of
Mycobacterium tuberculosis LigC-like ATP-dependent DNA
ligases. Bacterial DNA ligases are divided into two
broad classes: NAD-dependent and ATP-dependent. All
bacterial species have a NAD-dependent DNA ligase
(LigA). Some bacterial genomes contain multiple genes
for DNA ligases that are predicted to use ATP as their
cofactor, including Mycobacterium tuberculosis LigB,
LigC, and LigD. This group is composed of ATP-dependent
DNA ligases similar to Mycobacterium tuberculosis LigC.
ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA ligases
play a vital role in the diverse processes of DNA
replication, recombination and repair. Members of this
group contain adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains, comprising a catalytic core unit that is common
to all members of the ATP-dependent DNA ligase family.
The adenylation domain binds ATP and contains many of
the active-site residues. The common catalytic core unit
comprises six conserved sequence motifs (I, III, IIIa,
IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 194
Score = 28.0 bits (63), Expect = 5.7
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 4/42 (9%)
Query: 385 STLNLPFSDRR--LPELFFRYRA--RNFPHTLSEKEKQDWLE 422
P +RR L L + P T E ++WLE
Sbjct: 120 DLRGRPLRERRAALEALLAGWGPPLHLSPATTDRAEAREWLE 161
>gnl|CDD|185735 cd08994, GH43_like_2, Glycosyl hydrolase 43-like family consists of
hypothetical proteins. This subfamily mostly contains
uncharacterized proteins similar to glycosyl hydrolase
family 43 (GH43) which includes enzymes with
beta-xylosidase (EC 3.2.1.37) and
alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly
bifunctional xylosidase/arabinofuranosidase activities.
GH43 are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 291
Score = 28.1 bits (63), Expect = 6.3
Identities = 12/59 (20%), Positives = 18/59 (30%), Gaps = 12/59 (20%)
Query: 93 IIGYNNIRFDD---YYSRNIFYRNFYDSYRWSWDNGNSRWDLLDVMRAIYAFSPDGIQW 148
I +N +D +Y + F+ D + Y S DGI W
Sbjct: 198 IEPGDNGNTEDPFVWYDKGQFHMIVKDMLGYVTGE---------KGGGAYFRSKDGIHW 247
>gnl|CDD|176462 cd01357, Aspartase, Aspartase. This subgroup contains Escherichia
coli aspartase (L-aspartate ammonia-lyase), Bacillus
aspartase and related proteins. It is a member of the
Lyase class I family, which includes both aspartase
(L-aspartate ammonia-lyase) and fumarase class II
enzymes. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. Aspartase catalyzes the reversible deamination
of aspartic acid.
Length = 450
Score = 27.9 bits (63), Expect = 7.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 169 IEHVNAHDAKADVYAT---LALVWLIREKKPKL 198
+HVN + DVY T LAL+ L+R+ L
Sbjct: 127 NDHVNMSQSTNDVYPTALRLALILLLRKLLDAL 159
>gnl|CDD|80331 cd04448, DEP_PIKfyve, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in fungal RhoGEF (GDP/GTP exchange factor)
PIKfyve-like proteins. PIKfyve contains N-terminal Fyve
finger and DEP domains, a central chaperonin-like domain
and a C-terminal PIPK (phosphatidylinositol phosphate
kinase) domain. PIKfyve-like proteins are important
phosphatidylinositol (3)-monophosphate
(PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which
plays a major role in multivesicular body (MVB) sorting
and control of retrograde traffic from the vacuole back
to the endosome and/or Golgi. PIKfyve itself has been
shown to be play a role in regulating
early-endosome-to-trans-Golgi network (TGN) retrograde
trafficking..
Length = 81
Score = 27.5 bits (61), Expect = 8.9
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 402 RYRARNFPHTLSEKEKQDWLEHRKKMLTR 430
RYR R + + + KE +WL + K TR
Sbjct: 19 RYRLRTYTNCILGKELVNWLIRQGKAATR 47
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
subgroup of the DEDDh 3'-5' exonuclease domain family
with similarity to the epsilon subunit of DNA polymerase
III. This subfamily is composed of uncharacterized
bacterial proteins with similarity to the epsilon
subunit of DNA polymerase III (Pol III), a multisubunit
polymerase which is the main DNA replicating enzyme in
bacteria, functioning as the chromosomal replicase. The
Pol III holoenzyme is a complex of ten different
subunits, three of which (alpha, epsilon, and theta)
compose the catalytic core. The Pol III epsilon subunit,
encoded by the dnaQ gene, is a DEDDh-type 3'-5'
exonuclease which is responsible for the proofreading
activity of the polymerase, increasing the fidelity of
DNA synthesis. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The epsilon
subunit of Pol III also functions as a stabilizer of the
holoenzyme complex.
Length = 156
Score = 27.5 bits (62), Expect = 9.1
Identities = 44/191 (23%), Positives = 63/191 (32%), Gaps = 54/191 (28%)
Query: 5 FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGIT 64
FV D+ET D A V+V +I T +P + DP + I GIT
Sbjct: 1 FVAIDFETANADRA--SACSIGLVKVRDG--QIVDTFYTLIRPPTRF--DPFNIAIHGIT 54
Query: 65 PQKALRDGVVEA----EFSRRIHQFFSVPNTCIIGYNNIRFD--------DYYSRNIFYR 112
P+ V +A E I F + ++ + N FD + Y
Sbjct: 55 PED-----VADAPTFPEVWPEIKPFLG--GSLVVAH-NASFDRSVLRAALEAYGLPPPPY 106
Query: 113 NFYDSYRWSWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHV 172
+ + R + R WP + KL +A GIE +
Sbjct: 107 QYLCTVR--------------LARR---------VWP----LLPNHKLNTVAEHLGIE-L 138
Query: 173 NAHDAKADVYA 183
N HDA D A
Sbjct: 139 NHHDALEDARA 149
>gnl|CDD|33001 COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 835
Score = 27.2 bits (60), Expect = 9.9
Identities = 29/121 (23%), Positives = 40/121 (33%), Gaps = 27/121 (22%)
Query: 45 CKPADDYLPDPEAVFITG------ITPQKAL----RDGVVEAEFSRRIHQFFSVPNTCII 94
C D LP F PQ AL R V + + I+ N +
Sbjct: 119 CLDLADALPGASVTFDVAQQRLDISIPQAALEPSARGYVPPSLWDEGINAALL--NYNLN 176
Query: 95 GYNNIRFDDYYSRNIFYRNF-------------YDSYRWSWDNGNSRWDLLD--VMRAIY 139
+ + SRN +Y N SY +S NG S+W + + RAI
Sbjct: 177 ASRSEYRNGGSSRNSYYANLNSGLNLGAWRLRNDSSYSYSDGNGQSKWQSIRTYLQRAIP 236
Query: 140 A 140
A
Sbjct: 237 A 237
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.139 0.431
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,239,152
Number of extensions: 347837
Number of successful extensions: 876
Number of sequences better than 10.0: 1
Number of HSP's gapped: 870
Number of HSP's successfully gapped: 25
Length of query: 471
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 374
Effective length of database: 4,167,664
Effective search space: 1558706336
Effective search space used: 1558706336
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: 59 (26.4 bits)