RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific
exonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
(600 letters)
>gnl|CDD|30953 COG0608, RecJ, Single-stranded DNA-specific exonuclease [DNA
replication, recombination, and repair].
Length = 491
Score = 365 bits (939), Expect = e-101
Identities = 182/492 (36%), Positives = 262/492 (53%), Gaps = 23/492 (4%)
Query: 68 LMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI 127
L+ DP +L D +KAA RI +AI EKI+I+GDYD DG S A++ + L + + YI
Sbjct: 12 LLLDPFLLKDMEKAAARIAEAIEKGEKILIYGDYDADGITSAAILAKALRRLGADVDYYI 71
Query: 128 PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE 187
P+R +GYG + K EGA LIITVD GS S + + A GIDVIV DHH E
Sbjct: 72 PNRFEEGYG----AIRKLKEEGADLIITVDNGSGSLEEIARAKELGIDVIVTDHHPPGEE 127
Query: 188 EIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVAL 247
A A+VNPN L GV F + + LR+D LLDLVAL
Sbjct: 128 LPDAVAIVNPNLPGCDYPFKELAGVGVAFKLARALLEELRKD-----------LLDLVAL 176
Query: 248 ATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISS-PITAENLGYMIGPSIN 306
TV DV PL G NR V +GL R+ G PG+KAL++ + TA ++G++IGP IN
Sbjct: 177 GTVADVQPLTGENRILVNQGLKRLRKSGRPGIKALLKLAGRDTRQPTASDIGFIIGPRIN 236
Query: 307 AGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQ 366
A GR+G++ G LL+++D ++ E LA +L++LN+ R+ +E+ +L++A V +
Sbjct: 237 AAGRLGDAKAGVELLLTEDDEKAESLAEELELLNEERKKIENELLKEAIKIVEAL--EES 294
Query: 367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIE-GFDIGKMV 425
VIVV + WHPG++G++A+RL FGRP ++ + +G GS RSI G D+ K++
Sbjct: 295 GEYVIVVSEEEWHPGVLGIVASRLLNAFGRPVIVLAGDAEGGAKGSARSIAKGIDLRKLL 354
Query: 426 SFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNA 485
+ +L K GGHAMAAGL+++ N + A I+ +ID L
Sbjct: 355 RKGRSKLLLEKFGGHAMAAGLSLKEENLEEFRGILGEIASMILDKEELREKLEIDFALKD 414
Query: 486 SAVNIALIDMLESAGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETLQAIA 545
+ + L+ LE+ P+G GNP P+F ++ R HL+ + L AI
Sbjct: 415 EDITLELVSALETLEPFGQGNPLPLFLRKAAEVVGGRGG--GHLKAAGANIPK--LDAIE 470
Query: 546 FRVYGTPLGEFL 557
F L
Sbjct: 471 FLKDLDKLLGEQ 482
>gnl|CDD|144819 pfam01368, DHH, DHH family. It is predicted that this family of
proteins all perform a phosphoesterase function. It
included the single stranded DNA exonuclease RecJ.
Length = 156
Score = 130 bits (330), Expect = 7e-31
Identities = 57/169 (33%), Positives = 82/169 (48%), Gaps = 19/169 (11%)
Query: 88 AIYNSEKIMIFGDY--DVDGAASVALMMRFLSHCSVNANMYIPDRIVDG--YGPNPSLME 143
AI EKI+I G Y D DG S A + L + +P R ++G YG + ++E
Sbjct: 1 AIKEGEKILIVGHYNPDADGIGSAAALALALKRLGAEKDYVVPPREIEGKFYGLSDEIVE 60
Query: 144 KFINEG--AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLD 201
E A L+ITVD GST+ + ++ A GIDVIVIDHH+ ++P +NP
Sbjct: 61 DIAEEKGKADLLITVDTGSTAREEIELAKLLGIDVIVIDHHEPPENDLPPI--INPA--- 115
Query: 202 DLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATV 250
DL L A+ LV + + + N+ +L DL+AL V
Sbjct: 116 DLGPYIDLSASSTAELVAEALLGLELKLNR--------NLADLLALGIV 156
>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 49.9 bits (119), Expect = 2e-06
Identities = 42/160 (26%), Positives = 63/160 (39%), Gaps = 25/160 (15%)
Query: 63 PSIRLLMPDPLILT----DCDKAARRIVQAIYNSEKIMIFGDYDVDG-AASVALMMRFL- 116
P+ + D +L D A+ I +A+ I+I D DG A VAL L
Sbjct: 310 PADVGFLVDSEVLEALKPDMVDVAKEIRRAVLEGRPIIIRHHADADGYCAGVALEKAILP 369
Query: 117 ----SHCSVNANMYIPDR---------IVDGYGPNPSLMEKFINEGAQ--LIITVDCGST 161
H +A ++ R + D +E G + L++ VD GST
Sbjct: 370 LIEDVHPDEDAEYHLFKRRPSKAPFYELEDVTRDLNFALEDAHRHGQKLPLLVLVDNGST 429
Query: 162 SYD--ALQYATNQGIDVIVIDHHQVKSEEIPAY--ALVNP 197
D A++ GID++V+DHH + Y VNP
Sbjct: 430 EEDIPAIKQLKAYGIDIVVVDHHYPDEAVVDEYVDVHVNP 469
>gnl|CDD|145431 pfam02272, DHHA1, DHHA1 domain. This domain is often found
adjacent to the DHH domain pfam01368 and is called DHHA1
for DHH associated domain. This domain is diagnostic of
DHH subfamily 1 members. This domains is also found in
alanyl tRNA synthetase, suggesting that this domain may
have an RNA binding function. The domain is about 60
residues long and contains a conserved GG motif.
Length = 69
Score = 45.7 bits (109), Expect = 3e-05
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 396 RPSFAISFEEDGKGIGSGRSIEGFDI-GKMVSFAVEEGILVKGGGHAMAAGLTVE 449
+P + EEDGK S RS +G D+ G + V E + GGGH AAG +
Sbjct: 2 KPVVLFA-EEDGKVKVSARSSKGLDVKGGELLKEVAEILGGGGGGHPDAAGAGGK 55
>gnl|CDD|30963 COG0618, COG0618, Exopolyphosphatase-related proteins [General
function prediction only].
Length = 332
Score = 45.0 bits (106), Expect = 5e-05
Identities = 24/127 (18%), Positives = 44/127 (34%), Gaps = 10/127 (7%)
Query: 83 RRIVQAIYNSEKIMIFG--DYDVDGAASVALMMRFLSHCSVNANMYI--------PDRIV 132
+++ I +KI+I + D D S + L N + +
Sbjct: 7 AELLELIKAHDKILILTHENPDPDALGSALALAELLKDLGKNKEVLYVGPITHPENRAFL 66
Query: 133 DGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAY 192
+ G +E + L+I VD + Q VIVIDHH ++ +
Sbjct: 67 NLLGDELERIEDDPLDDYDLVIIVDTANLPRIGDQELLLDSKKVIVIDHHPGNNDIYGDF 126
Query: 193 ALVNPNR 199
++P+
Sbjct: 127 VWIDPSA 133
Score = 28.5 bits (63), Expect = 5.0
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 403 FEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQK 462
EEDG S RS ++ + A + G GGGHA+AAG + D +
Sbjct: 267 DEEDGSIRVSDRSKGIGNVNE---IAFKFG----GGGHALAAGARIPLGILESADDLLKL 319
Query: 463 F 463
Sbjct: 320 L 320
>gnl|CDD|145115 pfam01784, NIF3, NIF3 (NGG1p interacting factor 3). This family
contains several NIF3 (NGG1p interacting factor 3)
protein homologues. NIF3 interacts with the yeast
transcriptional coactivator NGG1p which is part of the
ADA complex, the exact function of this interaction is
unknown.
Length = 238
Score = 39.2 bits (92), Expect = 0.003
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 131 IVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI 189
I G G SL+E+ +GA L+IT G + A +GI++I H+ +E
Sbjct: 175 ICGGSGS--SLIEEAKAKGADLLIT---GELKHHDALDAKEKGINLIDAGHYA--TERF 226
>gnl|CDD|33676 COG3887, COG3887, Predicted signaling protein consisting of a
modified GGDEF domain and a DHH domain [Signal
transduction mechanisms].
Length = 655
Score = 36.8 bits (85), Expect = 0.017
Identities = 29/128 (22%), Positives = 49/128 (38%), Gaps = 19/128 (14%)
Query: 85 IVQAIYNSEKIMIFG----DYDVDGAA----SVALMMRFLSHCSVNANMYIPD--RIVDG 134
+ I S+ + I G D D G+A A M + ++ PD R ++
Sbjct: 330 LSDIIKESDNVFIMGHKFPDMDALGSAIGMQKFASMNNKEAFAVLDPEDMSPDVERAINE 389
Query: 135 YGPNPSLMEKFIN-EGAQ-------LIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS 186
N +FI A L++ VD S + ++ V+VIDHH+ +
Sbjct: 390 IEKNSEGKTRFITPSDAMELSTERSLLVIVDTHKPSLVLNEEFLDKFEKVVVIDHHR-RD 448
Query: 187 EEIPAYAL 194
E+ + L
Sbjct: 449 EDFISNPL 456
>gnl|CDD|32540 COG2404, COG2404, Predicted phosphohydrolase (DHH superfamily)
[General function prediction only].
Length = 339
Score = 35.0 bits (80), Expect = 0.055
Identities = 35/132 (26%), Positives = 50/132 (37%), Gaps = 20/132 (15%)
Query: 94 KIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQ 151
I+ D+DG A A++ RF NAN RI + G
Sbjct: 1 VYHIYSHNDLDGYACAAVVKRFFGKNVYNANFGREVSARINSILE-----SAEESGIGDA 55
Query: 152 LIITVDCGST------SYDALQYATNQGIDVIVIDHHQVKSEEIPAYA-LVNPNRLDDLS 204
++I+ D + L+ ATN+G V IDHH+ +E +DD
Sbjct: 56 ILIS-DLDVNLDRFEELVEKLKEATNKGTKVKWIDHHKTANETKEEVREAGVSVYVDD-- 112
Query: 205 GQGHLCAAGVVF 216
CAAGVV+
Sbjct: 113 ---SRCAAGVVY 121
>gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent
4-trimethylaminobutyraldehyde dehydrogenase, ALDH family
9A1. NAD+-dependent, 4-trimethylaminobutyraldehyde
dehydrogenase (TMABADH, EC=1.2.1.47), also known as
aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in
humans, is a cytosolic tetramer which catalyzes the
oxidation of gamma-aminobutyraldehyde involved in
4-aminobutyric acid (GABA) biosynthesis and also
oxidizes betaine aldehyde
(gamma-trimethylaminobutyraldehyde) which is involved in
carnitine biosynthesis.
Length = 457
Score = 33.8 bits (78), Expect = 0.15
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 95 IMIFGDYDVDGAASVALMMRFLSH---CSVNANMYIPDRIVD 133
++IF D D++ A + A+M FLS CS +++ I D
Sbjct: 231 LIIFDDADLENAVNGAMMANFLSQGQVCSNGTRVFVQRSIKD 272
>gnl|CDD|113050 pfam04263, TPK_catalytic, Thiamin pyrophosphokinase, catalytic
domain. Family of thiamin pyrophosphokinase
(EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses
the transfer of a pyrophosphate group from ATP to
vitamin B1 (thiamin) to form the coenzyme thiamin
pyrophosphate (TPP). Thus, TPK is important for the
formation of a coenzyme required for central metabolic
functions. The structure of thiamin pyrophosphokinase
suggest that the enzyme may operate by a mechanism of
pyrophosphoryl transfer similar to those described for
pyrophosphokinases functioning in nucleotide
biosynthesis.
Length = 122
Score = 32.3 bits (74), Expect = 0.41
Identities = 20/79 (25%), Positives = 26/79 (32%), Gaps = 12/79 (15%)
Query: 103 VDGAASVALMMRFLSHCSVNANMYIPDRIV-DGYGPNPSLMEKFINEGAQLIITVDCGST 161
DG A+ + PD +V D L + G LI + T
Sbjct: 21 ADGGANHLR----------DFLSLKPDFVVGDFDSITEELRAYYKEAGVNLIHFPEKDDT 70
Query: 162 SYD-ALQYATNQGIDVIVI 179
+ AL A G D IVI
Sbjct: 71 DLELALDEALELGADEIVI 89
>gnl|CDD|32480 COG2327, WcaK, Uncharacterized conserved protein [Function
unknown].
Length = 385
Score = 31.5 bits (71), Expect = 0.71
Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 16/109 (14%)
Query: 314 SNLGSRLLISDDSQEL-EMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIV 372
+ L+ S +L A+ VL+ L+ S + +L CD +
Sbjct: 237 ALWRITLIDYGASDDLAVADAIAQLVLDSAEILVSSDEYAEELGGILAACD--------L 288
Query: 373 VEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDI 421
+ G R H I+ L FG P+ AI+++ +G+ + GF I
Sbjct: 289 IVGMRLHSAIMAL-------AFGVPAIAIAYDPKVRGLMQDLGLPGFAI 330
>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 31.4 bits (71), Expect = 0.84
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 157 DCGSTSYDALQYATNQGIDVIVID 180
D + ++DA+Q A +GIDV++ID
Sbjct: 205 DPAAVAFDAIQAAKARGIDVVLID 228
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 31.0 bits (71), Expect = 0.91
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 165 ALQYATNQGIDVIVIDHHQVK---SEEIPAYALVNPNRLDD 202
+QYA G+ VI ID K ++E+ A A V+ + DD
Sbjct: 182 GVQYAKAMGLRVIAIDVGDEKLELAKELGADAFVDFKKSDD 222
>gnl|CDD|107304 cd06309, PBP1_YtfQ_like, Periplasmic binding domain of ABC-type
YtfQ-like transport systems. Periplasmic binding domain
of ABC-type YtfQ-like transport systems. The YtfQ
protein from Escherichia coli is up-regulated under
glucose-limited conditions and shares homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily. Members
of this group are predicted to be involved in the
transport of sugar-containing molecules across cellular
and organellar membranes; however their ligand
specificity is not determined experimentally.
Length = 273
Score = 29.9 bits (68), Expect = 2.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 143 EKFINEGAQLIITVDCGSTSYD-ALQYATNQGIDVIVIDHH 182
FI +G +II T +D L+ A GI VI++D
Sbjct: 49 RSFIAQGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRG 89
>gnl|CDD|31923 COG1737, RpiR, Transcriptional regulators [Transcription].
Length = 281
Score = 29.5 bits (66), Expect = 3.0
Identities = 28/157 (17%), Positives = 55/157 (35%), Gaps = 14/157 (8%)
Query: 79 DKAARRIVQAIYNSEKIMIFGDYDVDGAASVAL-MMRFLSHCSVNANMYIPDRIVDGYGP 137
++A R V+ + + +I FG + + VA + L +N + D +G
Sbjct: 117 EEALERAVELLAKARRIYFFG---LGSSGLVASDLAYKLMRIGLNVVA-----LSDTHGQ 168
Query: 138 NPSLMEKFINEGAQLIITVDCGSTS--YDALQYATNQGIDVIVIDHHQVKS-EEIPAYAL 194
L + G +I G T +A + A +G VI I ++ L
Sbjct: 169 LMQLA--LLTPGDVVIAISFSGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVL 226
Query: 195 VNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNK 231
+ P + + L+ LI + ++ +
Sbjct: 227 LVPVAEESFFRSPISSRIAQLALIDALITAVAQRRGE 263
>gnl|CDD|143460 cd07142, ALDH_F2BC, Arabidosis aldehyde dehydrogenase family 2 B4,
B7, C4-like. Included in this CD is the Arabidosis
aldehyde dehydrogenase family 2 members B4 and B7
(EC=1.2.1.3), which are mitochondrial homotetramers
that oxidize acetaldehyde and glycolaldehyde, but not
L-lactaldehyde. Also in this group, is the Arabidosis
cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme
involved in the oxidation of sinapalehyde and
coniferaldehyde.
Length = 476
Score = 29.0 bits (65), Expect = 3.9
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 95 IMIFGDYDVDGAASVALMMRFLSH---CSVNANMYIPDRIVDGY 135
++ D DVD A +A F + C + ++ + I D +
Sbjct: 258 FIVCEDADVDKAVELAHFALFFNQGQCCCAGSRTFVHESIYDEF 301
>gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 29.1 bits (66), Expect = 4.0
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 157 DCGSTSYDALQYATNQGIDVIVID---HHQVKS---EEIPAYA-LVNPNR----LDDLSG 205
D + ++DA++ A + DV+++D Q +E+ ++ P+ LD +G
Sbjct: 67 DPAAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKKIKRVIAPDEVLLVLDATTG 126
Query: 206 Q 206
Q
Sbjct: 127 Q 127
>gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor,
alpha subunit [Intracellular trafficking, secretion, and
vesicular transport].
Length = 587
Score = 28.8 bits (64), Expect = 4.3
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 157 DCGSTSYDALQYATNQGIDVIVID 180
D + +A+Q A NQG DV++ID
Sbjct: 450 DAAGVAKEAIQEARNQGFDVVLID 473
>gnl|CDD|133113 cd06256, M14_ASTE_ASPA_like_6, A functionally uncharacterized
subgroup of the Succinylglutamate desuccinylase
(ASTE)/aspartoacylase (ASPA) subfamily which is part of
the M14 family of metallocarboxypeptidases. ASTE
catalyzes the fifth and last step in arginine catabolism
by the arginine succinyltransferase pathway, and
aspartoacylase (ASPA, also known as aminoacylase 2, and
ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid
(NAA) into aspartate and acetate. NAA is abundant in the
brain, and hydrolysis of NAA by ASPA may help maintain
white matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 327
Score = 28.4 bits (64), Expect = 5.6
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 10/69 (14%)
Query: 9 VECSISGFRWVSLLGQEGINRAL-----AITQKHAIPDI-----VARVLVNRNVSIDYAK 58
+EC +G +EG+ L + Q DI ARV + V+ + +
Sbjct: 181 LECGGAGDEAGVAHAREGLQAYLSLPEVFLAQPGHHYDIDLFHTPARVEIPEGVTFGFGE 240
Query: 59 DFLNPSIRL 67
+ I
Sbjct: 241 SADDADITF 249
>gnl|CDD|107295 cd06300, PBP1_ABC_sugar_binding_like_1, Periplasmic sugar-binding
component of uncharacterized ABC-type transport systems
that are members of the pentose/hexose sugar-binding
protein family of the type I periplasmic binding protein
superfamily. Periplasmic sugar-binding component of
uncharacterized ABC-type transport systems that are
members of the pentose/hexose sugar-binding protein
family of the type I periplasmic binding protein
superfamily, which consists of two alpha/beta globular
domains connected by a three-stranded hinge. This Venus
flytrap-like domain undergoes transition from an open to
a closed conformational state upon ligand binding.
Members of this group are predicted to be involved in
the transport of sugar-containing molecules across
cellular and organellar membranes; however their
substrate specificity is not known in detail.
Length = 272
Score = 28.4 bits (64), Expect = 5.9
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 142 MEKFINEGAQLIITVDCGSTSY--DALQYATNQGIDVIVID 180
+ I +G II ++ S + ++ A GI V+ D
Sbjct: 53 IRNLIAQGVDAII-INPASPTALNPVIEEACEAGIPVVSFD 92
>gnl|CDD|146279 pfam03557, Bunya_G1, Bunyavirus glycoprotein G1. Bunyavirus has
three genomic segments: small (S), middle-sized (M), and
large (L). The S segment encodes the nucleocapsid and a
non-structural protein. The M segment codes for two
glycoproteins, G1 and G2, and another non-structural
protein (NSm). The L segment codes for an RNA
polymerase. This family contains the G1 glycoprotein
which is the viral attachment protein.
Length = 871
Score = 28.1 bits (63), Expect = 7.8
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 440 HAMAAGLTVERVNFGRLCDFFQKFAHN 466
H M LT+E + CD++ +F N
Sbjct: 43 HEM---LTLEYAFLTKYCDYYTQFEDN 66
>gnl|CDD|119332 cd06562, GH20_HexA_HexB-like, Beta-N-acetylhexosaminidases catalyze
the removal of beta-1,4-linked N-acetyl-D-hexosamine
residues from the non-reducing ends of
N-acetyl-beta-D-hexosaminides including
N-acetylglucosides and N-acetylgalactosides. The hexA
and hexB genes encode the alpha- and beta-subunits of
the two major beta-N-acetylhexosaminidase isoenzymes,
N-acetyl-beta-D-hexosaminidase A (HexA) and
beta-N-acetylhexosaminidase B (HexB). Both the alpha
and the beta catalytic subunits have a TIM-barrel fold
and belong to the glycosyl hydrolase family 20 (GH20).
The HexA enzyme is a heterodimer containing one alpha
and one beta subunit while the HexB enzyme is a
homodimer containing two beta-subunits. Hexosaminidase
mutations cause an inability to properly hydrolyze
certain sphingolipids which accumulate in lysosomes
within the brain, resulting in the lipid storage
disorders Tay-Sachs and Sandhoff. Mutations in the
alpha subunit cause in a deficiency in the HexA enzyme
and result in Tay-Sachs, mutations in the beta-subunit
cause in a deficiency in both HexA and HexB enzymes and
result in Sandhoff disease. In both disorders GM(2)
gangliosides accumulate in lysosomes. The GH20
hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself..
Length = 348
Score = 27.9 bits (63), Expect = 8.9
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 452 NFGRLCDFFQKFAHNIVPALITTPVF 477
++ L +F + A +IV +L TP+
Sbjct: 182 DYSDLESYFIQRALDIVRSLGKTPIV 207
>gnl|CDD|107249 cd01536, PBP1_ABC_sugar_binding_like, Periplasmic sugar-binding
domain of active transport systems that are members of
the type I periplasmic binding protein (PBP1)
superfamily. Periplasmic sugar-binding domain of active
transport systems that are members of the type I
periplasmic binding protein (PBP1) superfamily. The
members of this family function as the primary receptors
for chemotaxis and transport of many sugar based solutes
in bacteria and archaea. The sugar binding domain is
also homologous to the ligand-binding domain of
eukaryotic receptors such as glutamate receptor (GluR)
and DNA-binding transcriptional repressors such as LacI
and GalR. Moreover, this periplasmic binding domain,
also known as Venus flytrap domain, undergoes transition
from an open to a closed conformational state upon the
binding of ligands such as lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars.
This family also includes the periplasmic binding domain
of autoinducer-2 (AI-2) receptors such as LsrB and LuxP
which are highly homologous to periplasmic
pentose/hexose sugar-binding proteins.
Length = 267
Score = 27.6 bits (62), Expect = 9.7
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 140 SLMEKFINEGAQLIITVDCGSTSY-DALQYATNQGIDVIVID 180
+E I +G II S + AL+ A GI V+ +D
Sbjct: 46 QQIEDLIAQGVDGIIISPVDSAALTPALKKANAAGIPVVTVD 87
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 0.406
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,215,971
Number of extensions: 397297
Number of successful extensions: 993
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 33
Length of query: 600
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 501
Effective length of database: 4,124,446
Effective search space: 2066347446
Effective search space used: 2066347446
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: 60 (26.9 bits)