RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780140|ref|YP_003064553.1| putative ABC transporter,
substrate-binding protein [Candidatus Liberibacter asiaticus str.
psy62]
(452 letters)
>gnl|CDD|31652 COG1463, Ttg2C, ABC-type transport system involved in resistance to
organic solvents, periplasmic component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 359
Score = 87.5 bits (216), Expect = 8e-18
Identities = 57/301 (18%), Positives = 101/301 (33%), Gaps = 21/301 (6%)
Query: 1 MESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPG-SVDGLSTDSSVR 59
ME++ VGLF++ L + WL+ G + GL S VR
Sbjct: 1 METRANRVLVGLFLLLGLLAVLLFVLWLATLPGLPGGTGTYTVTAYFDDAGGLYVGSPVR 60
Query: 60 FNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTATIRTQGLAGITYIELSTLRK 119
+ G+ VG++ + LD + PN + I D P+ +TA+IRT GL G YIEL+
Sbjct: 61 YRGVKVGKVASISLDPK-PNGARVTLEIDSDYPIPADSTASIRTTGLLGEKYIELTPGDA 119
Query: 120 EKKTI---FQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPL 176
+ I ER Q + G + + +++ + L
Sbjct: 120 GGPKLRLGATIPLERTQVPIDLEDLLGDLLLLLGGLDP-DRLNAILNEAAAALAGTGPQL 178
Query: 177 TTTIANIETISTVLANNISHIDKMMH-----TTQVTPHSSDSKNTFNTITDLITSLDKMI 231
+ N+ + L I ++ + S + + L +L
Sbjct: 179 NALLDNLAQFTDALNARDGDIGALIANLNQLLDSLAAASDQLDRLLDNLATLTAALAARR 238
Query: 232 KAID---------LQKVNQILENIQVSSNNFVKSSDQVINTVHDVR-ETTQTFQEVGQKI 281
A+D VN +L + + N + + + + D Q +
Sbjct: 239 DALDDALAALSALAATVNDLLAENRPNLNQALANLRPLATLLVDYLPGLEQLLHGLPTYA 298
Query: 282 D 282
Sbjct: 299 A 299
>gnl|CDD|111376 pfam02470, MCE, mce related protein. This family of proteins
contains the mce (mammalian cell entry) proteins from
Mycobacterium tuberculosis. The archetype (Rv0169), was
isolated as being necessary for colonisation of, and
survival within, the macrophage. This family contains
proteins of unknown function from other bacteria.
Length = 80
Score = 57.2 bits (139), Expect = 8e-09
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 48 SVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPD-TPLYPSTTATIRTQGL 106
GL + VR+ G+PVGR+ + LD + I PD + + A IR+ GL
Sbjct: 11 DAGGLEVGAPVRYRGVPVGRVTSIDLDPD-GGGVRVTLRIDPDVVVIPKDSRAGIRSLGL 69
Query: 107 AGITYIELS 115
G YI L
Sbjct: 70 LGEKYIALD 78
>gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome
protein 2 (chromosome condensation complex Condensin,
subunit E) [Chromatin structure and dynamics, Cell cycle
control, cell division, chromosome partitioning].
Length = 1174
Score = 34.5 bits (79), Expect = 0.056
Identities = 37/252 (14%), Positives = 91/252 (36%), Gaps = 23/252 (9%)
Query: 151 AENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHS 210
EN +++ ++K I ++++ L I ++ + L N + +DK+
Sbjct: 813 RENEYERLQLEHEELEKEISSLKQQLEQLEKQISSLKSELGNLEAKVDKVEKDV------ 866
Query: 211 SDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRET 270
+ + ID + ++ +L + + + + H+V +
Sbjct: 867 -------KKAQAELKDQKAKQRDIDTE-ISGLLTSQEKCLSEKSDGELERKKLEHEVTKL 918
Query: 271 TQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIAD-STSNMRSSISAIREITDQRQKII 329
++++ LL K D + + + ++++ ++++K+
Sbjct: 919 ESEKANARKEVEKLLKKHEWIGDEKRLFGKKGTDYDFESYDPHEAREELKKLQEKKEKLE 978
Query: 330 STINTIENITSNLNDSSQKFAELMSKINNI----SALKENNSLFKDAQRAMHTFRDTSEK 385
T+N L + +K A L +K I S +K+ + +R EK
Sbjct: 979 KTVNP--KNMDMLERAEEKEAALKTKKEIIEKDKSKIKKTIEKLDEKKR--EELNKAWEK 1034
Query: 386 INRYIPSIGNNL 397
+N+ SI + L
Sbjct: 1035 VNKDFGSIFSTL 1046
>gnl|CDD|37815 KOG2604, KOG2604, KOG2604, Subunit of cis-Golgi transport vesicle
tethering complex - Sec34p [Intracellular trafficking,
secretion, and vesicular transport].
Length = 733
Score = 33.8 bits (77), Expect = 0.091
Identities = 25/118 (21%), Positives = 46/118 (38%), Gaps = 10/118 (8%)
Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAIREITDQRQK 327
E + +D LLS S++TSA E + + S + E+ + +K
Sbjct: 106 ECDAILDQTNNALDTLLSLQKKFEFVSQKTSALHE----ACEQLLEEQSKLSELAEGIRK 161
Query: 328 IISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSLFKDAQRAMHTFR 380
+ +E + LN F E+++K++ E N FKDA + ++
Sbjct: 162 KLHYFAELEELNRRLNHPTLSVGKVSFKEMLAKLDECIMFLEENPDFKDAPAYLGKYK 219
>gnl|CDD|177098 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 33.5 bits (77), Expect = 0.12
Identities = 52/326 (15%), Positives = 110/326 (33%), Gaps = 57/326 (17%)
Query: 111 YIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS---NAENTSKKISDSSRHIQK 167
+EL K K + +++A NY I + + K + + I
Sbjct: 42 NLELLLFGKNYKLKYPKYN------LLSAKSYDSNYSIQIYLPLKFINLKTNKI-KFINY 94
Query: 168 IIENIEKPLTTTIANI-------ETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTI 220
+I N+ P T +S ++ + + K + KN+
Sbjct: 95 LIGNL--PKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIK-----------KNSNKIY 141
Query: 221 TDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQK 280
+ + +L K +I I++ N + ++ T Q++ +
Sbjct: 142 SATLIPNRGSWIKFELDKNKEIW--IRIDKNR-------KKPLIIFLKALGLTDQDIYSR 192
Query: 281 IDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREIT--DQRQKIISTINTIEN- 337
+ S+F K+K ++ + + ++S I T D Q + S +N
Sbjct: 193 LTK--SEFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNY 250
Query: 338 ---------ITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINR 388
I + LN + + ++ + +S + + + F D NR
Sbjct: 251 DLGKVGRYKINNKLNLNIPERVRNLTYEDILSII----DKLINLKINKGNFDDIDHLKNR 306
Query: 389 YIPSIGNNLQNFSQSGLNDIQNLVRK 414
+ S+G LQN + GL ++ ++R
Sbjct: 307 RVRSVGELLQNQFRIGLKRLERILRN 332
>gnl|CDD|112929 pfam04136, Sec34, Sec34-like family. Sec34 and Sec35 form a
sub-complex, in a seven protein complex that includes
Dor1 (pfam04124). This complex is thought to be
important for tether vesicles to the Golgi.
Length = 157
Score = 32.9 bits (75), Expect = 0.19
Identities = 25/124 (20%), Positives = 44/124 (35%), Gaps = 24/124 (19%)
Query: 266 DVRETTQTFQEVGQKIDHLLSDFSSKMK------------SKETSAFLENIADSTSNMRS 313
QTF D +L ++ SK+TS E + + +
Sbjct: 4 KKINYLQTFT---NICDQILGQTNNAESTLLSLKEKYEFVSKKTSELSE----ACEQLST 56
Query: 314 SISAIREITDQRQKIISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSL 368
+ E+ D QK ++ +E + L +S F E ++K++ E N
Sbjct: 57 EQMRLSELADGIQKGLTYFAPLEELNRVLRSPTLSVASVSFKEHLTKLDTCIMYIEENPD 116
Query: 369 FKDA 372
FKD+
Sbjct: 117 FKDS 120
>gnl|CDD|39589 KOG4388, KOG4388, KOG4388, Hormone-sensitive lipase HSL [Lipid
transport and metabolism].
Length = 880
Score = 31.6 bits (71), Expect = 0.50
Identities = 29/140 (20%), Positives = 53/140 (37%), Gaps = 13/140 (9%)
Query: 90 DTPL--YPSTTATIRTQGLAGITYIELSTLRKE-----KKTIFQIATERNQRA--MITAT 140
D P+ PS A + QG G I+ TLR +T + E + A + +T
Sbjct: 635 DIPMRRSPSEAALAQPQGPLGTDSIKNLTLRDLSLTGNSETSSETHPEMSLSAETLSPST 694
Query: 141 PSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT--TTIANIETISTVLANNISHID 198
PS +N+ + A +T + D+ + + P+ + + ++
Sbjct: 695 PSDVNFLLPTAPSTPLQQEDAGEE-AEAKNELSPPMDRGLGVRAAFPEGFHARRSSQNLQ 753
Query: 199 KMMHTTQVTPHSSD-SKNTF 217
T + +SSD K+ F
Sbjct: 754 DWFGRTPMELYSSDVPKDPF 773
>gnl|CDD|146867 pfam04437, RINT1_TIP1, RINT-1 / TIP-1 family. This family includes
RINT-1, a Rad50 interacting protein which participates
in radiation induced checkpoint control, as well as the
TIP-1 protein from yeast that seems to be involved in a
complex with Sec20p that is required for golgi
transport.
Length = 485
Score = 31.2 bits (71), Expect = 0.65
Identities = 6/46 (13%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 203 TTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKV-NQILENIQ 247
+ SS+ + I+ L++++ +++ Q+L ++
Sbjct: 338 ALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRIWRQLLLSLD 383
Score = 30.0 bits (68), Expect = 1.5
Identities = 23/173 (13%), Positives = 53/173 (30%), Gaps = 45/173 (26%)
Query: 284 LLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTIENITSNLN 343
L D +++ S + F E +I+++ + + I +
Sbjct: 275 SLGDIANRTSSNYGALFDE-----------TINSLERLRLDSEGSIVH-----RLVKGFK 318
Query: 344 DSSQKFAELMSKIN-----NISALKENNSLFKDAQRAMHTFRDTSEKINRYIP------- 391
+ + + KI+ + ++ E+ S + A+ R + R +
Sbjct: 319 AALRNY----FKISTWSSLSSTSALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRI 374
Query: 392 --SIGNNLQN-----------FSQSGLNDIQNLVRKLQETVNHFDDCLNNFER 431
+ +L FS+ G +R L E + + NF +
Sbjct: 375 WRQLLLSLDTYIISSILMLNKFSEGGAAQFHFDMRNLFEVFSLYCMRPENFFK 427
>gnl|CDD|143806 pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP)
signaling domain. This domain is thought to transduce
the signal to CheA since it is highly conserved in very
diverse MCPs.
Length = 213
Score = 30.9 bits (70), Expect = 0.73
Identities = 22/165 (13%), Positives = 50/165 (30%), Gaps = 48/165 (29%)
Query: 160 DSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNT 219
+++ I+ +IE I K + A+I+ T + + ++ +
Sbjct: 93 QAAKEIEALIEEIVKQTNDSTASIQQTRTEVEVGSTIVE-------------STGEALKE 139
Query: 220 ITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQ 279
I D + + ++ + I +S+ DQV V + + TQ
Sbjct: 140 IVDAVAEIADIV------------QEIAAASDEQSAGIDQVNQAVARIDQVTQ------- 180
Query: 280 KIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ 324
+ +A +E A + + + Q
Sbjct: 181 ----------------QNAALVEESAAAAETLEEQAEELTASVAQ 209
>gnl|CDD|34155 COG4477, EzrA, Negative regulator of septation ring formation [Cell
division and chromosome partitioning].
Length = 570
Score = 30.6 bits (69), Expect = 0.88
Identities = 30/216 (13%), Positives = 80/216 (37%), Gaps = 16/216 (7%)
Query: 214 KNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQT 273
+ + + + +++ ++L + + L IQ + ++ + + V E
Sbjct: 254 DSRLERLKEQLVENSELLTQLELDEAEEELGLIQEKIESLYDLLEREVEAKNVVEENLPI 313
Query: 274 FQEVGQKI----DHLLSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQR 325
+ +K +HL + +S + + + S + I E + +
Sbjct: 314 LPDYLEKAKENNEHLKEEIERVKESYRLAETELGSVRKFEKELKELESVLDEILENIEAQ 373
Query: 326 QKIIS----TINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD 381
+ S + IE +++ D +K E ++ + N + + +H +
Sbjct: 374 EVAYSELQDNLEEIEKALTDIEDEQEKVQEHLTSLRKDELEAREN--LERLKSKLHEIKR 431
Query: 382 TSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQE 417
EK N +P + + + ++IQ+L+++L E
Sbjct: 432 YMEKSN--LPGLPETFLSLFFTAGHEIQDLMKELSE 465
>gnl|CDD|58155 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis..
Length = 538
Score = 29.8 bits (67), Expect = 1.4
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 11/101 (10%)
Query: 106 LAGITYIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHI 165
L G Y+E T E++ I MI A G YF ++I+D++
Sbjct: 391 LGGSYYVEALTDEIEEEAWKYIDKIDAMGGMIKAIEDG--YF-------QREIADAAYKY 441
Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQV 206
QK IE+ E+ + N + + +D + Q+
Sbjct: 442 QKEIESGERIVVG--VNKFVVEEEPPIILLKVDDEVEERQI 480
>gnl|CDD|147584 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 809
Score = 28.8 bits (65), Expect = 2.8
Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTT-QVTPHSSDSKNTFNTITDLI 224
+I+EN+E+ + ++I I K+ + T V P D K +++ I
Sbjct: 320 TEILENLEEVVKADFSSIVQEGNSTFEEIP--SKVKNQTSSVVP---DVKAALDSLGTDI 374
Query: 225 TSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQ 259
S+ + + L ++QIL N Q SSN ++ +Q
Sbjct: 375 KSVAEDLPLQVLSVLSQILNNTQSSSNPYLPYVEQ 409
Score = 28.1 bits (63), Expect = 5.7
Identities = 21/133 (15%), Positives = 45/133 (33%), Gaps = 39/133 (29%)
Query: 326 QKIISTINTIENITSNLNDSSQ--KFAELMSKINNISALKENNSLFKDAQRAMHTFRDTS 383
++ ++T N+ + S + ++ ++N L+ Q ++ D +
Sbjct: 502 NELFQVLDTPGNLNPGYLNLSGTLELKINLTISEVYRDCEQNEPLYTVLQ--LNNSYDLN 559
Query: 384 EK--INRYIPSIGN---------------------NLQNFSQSGLNDIQNLVRKLQETVN 420
E I +Y P I NL++ + SGL+DI
Sbjct: 560 ELLDIKQYTPEIDQELESLKVNLSTITLLTPEARRNLEDLASSGLDDI------------ 607
Query: 421 HFDDCLNNFERNP 433
+F + L ++
Sbjct: 608 NFSNFLKQIQKPL 620
>gnl|CDD|34381 COG4768, COG4768, Uncharacterized protein containing a divergent
version of the methyl-accepting chemotaxis-like domain
[General function prediction only].
Length = 139
Score = 28.8 bits (64), Expect = 3.1
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSK 295
L K N + E++Q V + D V + V D+ ++ + + + ++ K + K
Sbjct: 58 LHKTNTLAEDVQGK----VATLDPVFDAVKDLGQSVSDLNQSVRHLATRATNAVEKNEKK 113
Query: 296 ETSAFLENIA 305
A + N+A
Sbjct: 114 IAQAVVSNVA 123
>gnl|CDD|34711 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase
[Transcription].
Length = 1117
Score = 28.9 bits (64), Expect = 3.4
Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 343 NDSSQKFAELMSKINNISALKE---NNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQN 399
+ + F +S + ++L E N F +++ + +F D ++ +P I ++
Sbjct: 15 SKIGKDFIIDLSYKSGTASLFEACVYNGDFLRSKQLLKSFIDHNKGDKILLPMINLYIRE 74
Query: 400 FSQSGLNDIQNLVRKLQE 417
Q G ++ +++ +E
Sbjct: 75 IIQRGSFELTDVLSNAKE 92
>gnl|CDD|113356 pfam04582, Reo_sigmaC, Reovirus sigma C capsid protein.
Length = 326
Score = 28.7 bits (64), Expect = 3.7
Identities = 27/124 (21%), Positives = 57/124 (45%), Gaps = 5/124 (4%)
Query: 301 LENIADSTSNMRSSISAI-REITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNI 359
L N+ +T+++ S+S I ++D + ++++ + LN L + ++++
Sbjct: 37 LTNLESATASLSESVSTISSRLSDLSADLQDMTTSLDDAKATLNGLITTVQALQTSVDSL 96
Query: 360 SALKENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLN--DIQNLVRKLQE 417
S+ + SL A A + T+ N I N + S +GLN D++ V+ L+
Sbjct: 97 SSELADLSLTVSAHDAAISDLQTTVHANS--TDISNLKSSVSANGLNITDLEQRVKSLES 154
Query: 418 TVNH 421
+H
Sbjct: 155 GSSH 158
>gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA
processing and modification].
Length = 519
Score = 28.4 bits (63), Expect = 3.8
Identities = 24/122 (19%), Positives = 44/122 (36%), Gaps = 20/122 (16%)
Query: 165 IQKIIENIEKPLTTTIANIETIST---VLANNISHIDKMMHTTQVTPHSSDSKNTFNTIT 221
I+KI+ I +P T+ T LA + + Q+ + + I
Sbjct: 260 IRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNP-----IQINVGNKKELKANHNIR 314
Query: 222 DLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVI---NTVHDVRETTQTFQEVG 278
++ D+ K L+K+ ++LE+I S +VI T E + + G
Sbjct: 315 QIVEVCDETAK---LRKLGKLLEDISSDSEG------KVIIFCETKRTCDELARNLRRKG 365
Query: 279 QK 280
Sbjct: 366 WP 367
>gnl|CDD|38731 KOG3522, KOG3522, KOG3522, Predicted guanine nucleotide exchange
factor [Signal transduction mechanisms].
Length = 925
Score = 28.4 bits (63), Expect = 3.9
Identities = 41/227 (18%), Positives = 70/227 (30%), Gaps = 44/227 (19%)
Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDH-----------L 284
LQ +LE + N + +D++ E +E+ + + L
Sbjct: 150 LQLALTLLETLAEKINEHKRFADEI-------NELQAALREIEVRSELMEDLGAGRRQLL 202
Query: 285 LSDFSSKMK----SKETSAFLENI-ADSTSNMRSSISAIREIT----------------- 322
L D S+ K+ AFL +T R+S S+ + T
Sbjct: 203 LQDLVSETVYTGRKKDRKAFLFRDLIVNTDLKRASGSSRKPSTAASVVDTAKYKLLWKDP 262
Query: 323 -DQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMH--TF 379
+ S IE I + + A L K + L +D QR +H
Sbjct: 263 LVFADVVKSRAGNIEEIPILIAHLVEDCAHLRQKTKENKVYVGPHQLLQDLQRLLHALDV 322
Query: 380 RDTSEK-INRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDC 425
R SE+ R + N + N +Q L+ + +
Sbjct: 323 RRLSERQARRLSLNYQNLNLELAADWPNGLQRLIFVFEAEIGSTPLE 369
>gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome
protein 4 (chromosome condensation complex Condensin,
subunit C) [Chromatin structure and dynamics, Cell cycle
control, cell division, chromosome partitioning].
Length = 1293
Score = 28.4 bits (63), Expect = 4.5
Identities = 32/260 (12%), Positives = 88/260 (33%), Gaps = 27/260 (10%)
Query: 113 ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENI 172
+ L+ + I + Q+ + ++ ++ + I S R+I K + +
Sbjct: 886 RIKELQNKIDEIGGEKVQA-QKDKVEKINEQLDKLEADIAKLTVAIKTSDRNIAKAQKKL 944
Query: 173 EKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIK 232
+ L I + E L + +++ + K ++ ++ L +
Sbjct: 945 SE-LEREIEDTEKELDDLTEELKGLEEKA-----AELEKEYKEAEESLKEIKKELRDLKS 998
Query: 233 AI-DLQKVNQILENIQVSSNNFVKSSDQVINTV----------------HDVRETTQTFQ 275
+ +++K L+ ++ N +++ + +N + ++ ET +
Sbjct: 999 ELENIKKSENELKAERIDIENKLEAINGELNEIESKIKQPEKELKKLSLCNMTETRPQIE 1058
Query: 276 EVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTI 335
+ L + E A LE + + + I E + + + + +
Sbjct: 1059 L-DVESPEELEAEMLEDNINEKIALLEKRVEELREV--DLGVIAEYAKKVELYLKRVAEL 1115
Query: 336 ENITSNLNDSSQKFAELMSK 355
E T ++ +K EL +
Sbjct: 1116 EKFTQKRDEHREKLEELRKR 1135
>gnl|CDD|38897 KOG3693, KOG3693, KOG3693, Uncharacterized conserved protein
[Function unknown].
Length = 1117
Score = 28.2 bits (62), Expect = 5.0
Identities = 18/54 (33%), Positives = 23/54 (42%)
Query: 47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTAT 100
GS+DGLS +S + VGR + L + P SLA I P P
Sbjct: 114 GSMDGLSMNSFSMPFSVSVGRQMSLTPPLDVPATSLAIHKIPSSAPTLPFKFMK 167
>gnl|CDD|39873 KOG4674, KOG4674, KOG4674, Uncharacterized conserved coiled-coil
protein [Function unknown].
Length = 1822
Score = 28.0 bits (62), Expect = 5.7
Identities = 41/277 (14%), Positives = 101/277 (36%), Gaps = 19/277 (6%)
Query: 153 NTSKKISD----SSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTP 208
+T KK+++ + + +++ + +E S N + ++ +
Sbjct: 280 STQKKLNELWKSKLEELSHEVAELQRAIEELEKLLEDASERNKENTDQLKELEQS----- 334
Query: 209 HSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVR 268
S ++ ++ L L+ ++ + ++ +++ ++ +
Sbjct: 335 LSKLNEKLEKKVSRLEGELEDANDSLSATGESSMVSEKAALASSLIRPGSSLTKLYSKYS 394
Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAI-REITDQRQ 326
+ Q + + +++ L + SS + K+ + L+ M+ + + + E+ Q
Sbjct: 395 KLQQQLESLKLELERLQNILSSFKEEVKQKAPILKEQRSELERMQETKAELSEELDFSNQ 454
Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKI 386
KI +E++ LND ++ L +I+++S L D R +S+
Sbjct: 455 KIQKLEKELESLKKQLNDLERENKLLEQQISDLSRQVNVLLLELDELRKGSKITVSSDST 514
Query: 387 NRYIPS---IGNNLQNFSQSGLNDIQNLVRKLQETVN 420
S I L FS +I L K E +N
Sbjct: 515 ENESDSEEIISERLVEFS-----NINELQEKNVELLN 546
>gnl|CDD|37906 KOG2695, KOG2695, KOG2695, WD40 repeat protein [General function
prediction only].
Length = 425
Score = 27.7 bits (61), Expect = 5.9
Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 7/92 (7%)
Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD-------T 382
S I T E + + K N + + + ++ RD
Sbjct: 31 SNIYTKERLKPGKRFENISQKRTKGKGLNPVFNRSTYLFDRQFSQYPYSCRDDRDYCAKN 90
Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLVRK 414
+ IN +G LQ L K
Sbjct: 91 LKVINLRQLPVGTELQKIGWLREVTTIILTSK 122
>gnl|CDD|111435 pfam02534, TraG, TraG/TraD family. These proteins contain a P-loop
and walker-B site for nucleotide binding. TraG is
essential for DNA transfer in bacterial conjugation.
These proteins are thought to mediate interactions
between the DNA-processing (Dtr) and the mating pair
formation (Mpf) systems.
Length = 468
Score = 27.8 bits (62), Expect = 6.6
Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 24/130 (18%)
Query: 32 NQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT 91
P+ V V L +G P V LD E+P+ L K
Sbjct: 272 LTVVSPLLRVFF---QMVVELLYLKLPNGDGRPKE--VLFLLD-EFPS--LGK------L 317
Query: 92 PLYPSTTATIRTQGLAGITYI--ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS 149
+ ATIR G+ +T I +S L+ + +++++ I + S
Sbjct: 318 EILEEALATIRGYGI-RLTTICQSISQLK-------ETYGGEGAKSILSNHAVVICFAAS 369
Query: 150 NAENTSKKIS 159
N E T+K IS
Sbjct: 370 NDEETAKYIS 379
>gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA. These proteins have
been shown to function in the ABC uptake of Zn2+ and
Mn2+ and in competence for genetic transformation and
adhesion. The AcdA proteins belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and they bind their ligand in the
cleft between these domains. In addition, many of these
proteins have a low complexity region containing metal
binding histidine-rich motif (repetitive HDH sequence)..
Length = 282
Score = 27.5 bits (61), Expect = 7.2
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 329 ISTINTIENITSNLNDSSQKFAELMSKINNISALKE 364
+ +N +E +T D + + LM + N+ LK
Sbjct: 246 LLVLNPLETLTKEEIDDGKDYFSLMKE--NLETLKR 279
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 27.7 bits (62), Expect = 7.3
Identities = 37/210 (17%), Positives = 74/210 (35%), Gaps = 45/210 (21%)
Query: 219 TITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQ--E 276
+ L + L ++ K+++L ++ + + ET + E
Sbjct: 12 YLDSLESQLKQLYKSLEL----------------VSSQRKELASATEEFAETLEALSSLE 55
Query: 277 VGQKIDHLLSDFSS-KMKSKETSAFLENIADSTSNMRS--------SISAIREITDQRQK 327
+ + + LL+ + + + KE+ LE A SI ++R QRQK
Sbjct: 56 LSKSLSDLLAALAEVQKRIKES---LERQALQDVLTLGVTLDEYIRSIGSVRAAFAQRQK 112
Query: 328 IISTINTIENITSNLNDSSQKFAELMSKINNISA-LKENNSLFKDAQRAMHT----FRDT 382
+ + E+ L+ + +L + L S ++A+R F +
Sbjct: 113 LWQYWQSAES---ELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEV 169
Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLV 412
SE I L+ F + + D +N V
Sbjct: 170 SELIKS-------ELERFERERVEDFRNSV 192
>gnl|CDD|37518 KOG2307, KOG2307, KOG2307, Low density lipoprotein receptor
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 705
Score = 27.6 bits (61), Expect = 7.8
Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 10/146 (6%)
Query: 272 QTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331
++ Q ++ L + S S + S + + RE + +I
Sbjct: 89 DALNKIEQPLNQLREEIKSTRGSVGEAERALR------QQCSELCSNREKKIELLDLIYV 142
Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIP 391
+ IE ++ L K + + AL+ N F + F + E+I
Sbjct: 143 LVAIEKLSKMLLSPPSKEQQDGATSLERIALELNQLKFHASHLKGSLFPHSEERIAAEKI 202
Query: 392 SIGNNLQNFSQSGLN----DIQNLVR 413
+ +L GL D+QN +R
Sbjct: 203 ILSQSLAVLFAEGLQSAAGDLQNCLR 228
>gnl|CDD|29484 cd00386, Heme_Cu_Oxidase_III_like, Heme-copper oxidase subunit
III. Heme-copper oxidases are transmembrane protein
complexes in the respiratory chains of prokaryotes and
mitochondria which couple the reduction of molecular
oxygen to water to, proton pumping across the membrane.
The heme-copper oxidase superfamily is diverse in terms
of electron donors, subunit composition, and heme
types. This superfamily includes cytochrome c and
ubiquinol oxidases. Bacterial oxidases typically
contain 3 or 4 subunits in contrast to the 13 subunit
bovine cytochrome c oxidase (CcO). Subunits I, II, and
III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Subunits I, II and
III of ubiquinol oxidase are homologous to the
corresponding subunits in CcO. This group additionally
contains proteins which are fusions between subunits I
and III, such as Sulfolobus acidocaldarius SoxM, a
subunit of the SoxM terminal oxidase complex. It also
includes NorE which has been speculated to be a subunit
of nitric oxide reductase. Some archaebacterial
cytochrome oxidases lack subunit III. Although not
required for catalytic activity, subunit III is
believed to play a role in assembly of the multimer
complex. Rhodobacter CcO subunit III stabilizes the
integrity of the binuclear center in subunit I. It has
been proposed that archaea acquired heme-copper
oxidases through gene transfer from gram-positive
bacteria..
Length = 183
Score = 27.5 bits (61), Expect = 8.0
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 1 MESKNYYTSVGLFVVS--ILFFSFFSIYWLSRSNQYDGPMAEV 41
+ LF++S +LF SFF Y+ SR + A +
Sbjct: 4 SVRSGGRLGMWLFILSEVMLFGSFFWAYFHSRLSPPVEFGAGL 46
>gnl|CDD|32784 COG2964, COG2964, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 220
Score = 27.5 bits (61), Expect = 8.1
Identities = 23/149 (15%), Positives = 45/149 (30%), Gaps = 24/149 (16%)
Query: 278 GQKIDHLLSDFSSKM------KSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331
G+++ ++D + + K A ++SS IR ++ +II
Sbjct: 53 GRQVGSPITDLALDLLHNKEGSEKSVIGNYFTRAKDGRLIKSSSIFIR---NKEGRIIGM 109
Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYI- 390
+ I S L S M + N F + E + +
Sbjct: 110 L-CINMDLSLLVPVSAFLQTFMPTDETPKRVSSVN------------FASSVEDLVAQLL 156
Query: 391 -PSIGNNLQNFSQSGLNDIQNLVRKLQET 418
+I + S + +V+ L E
Sbjct: 157 EWTIQEVNADRLLSNNAKNREIVKALYEK 185
>gnl|CDD|153293 cd07609, BAR_SIP3_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of
fungal Snf1p-interacting protein 3. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. This group is composed of mostly
uncharacterized fungal proteins with similarity to
Saccharomyces cerevisiae Snf1p-interacting protein 3
(SIP3). These proteins contain an N-terminal BAR domain
followed by a Pleckstrin Homology (PH) domain. SIP3
interacts with SNF1 protein kinase and activates
transcription when anchored to DNA. It may function in
the SNF1 pathway. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 214
Score = 27.2 bits (61), Expect = 8.4
Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 240 NQILENIQVSSNNFVKSSDQVINTVHDV-RETTQTFQEVGQKIDHLLSDFSSKMKSKETS 298
+L ++ + + + + + +E + F+ +K D +L+ + ++ K+KE S
Sbjct: 77 GGVLSALKGNDSLILDPLRSFVKSDIRPYKELRKNFEYYQRKYDSMLARYVAQSKTKEPS 136
Query: 299 A 299
+
Sbjct: 137 S 137
>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
[Cytoskeleton].
Length = 1930
Score = 27.1 bits (60), Expect = 9.2
Identities = 35/212 (16%), Positives = 82/212 (38%), Gaps = 26/212 (12%)
Query: 228 DKMIKAID--LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLL 285
++ ++A + +QK+ + L+ + + +++ +D++E Q +E + + LL
Sbjct: 837 EEEMRAKEEEIQKLKEELQKSESKRKELEEKLVKLLEEKNDLQEQLQAEKENLAEAEELL 896
Query: 286 SDFSSKMKS-----KETSAFLENI----ADSTSNMRSSISAIREITDQ-------RQKII 329
++ + KE LE A+ R ++E+ +Q QK+
Sbjct: 897 ERLRAEKQELEKELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELELTLQKLE 956
Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRY 389
N EN NL + E +SK++ E ++ Q + + ++ +N+
Sbjct: 957 LEKNAAENKLKNLEEEINSLDENISKLSKEKKELEERI--RELQDDLQAEEEKAKSLNKA 1014
Query: 390 IPSIGNNLQNF------SQSGLNDIQNLVRKL 415
+ L + + +++ RKL
Sbjct: 1015 KAKLEQQLDDLEVTLEREKRIRMELEKAKRKL 1046
>gnl|CDD|31758 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 27.2 bits (60), Expect = 9.7
Identities = 20/155 (12%), Positives = 62/155 (40%), Gaps = 5/155 (3%)
Query: 277 VGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ--RQKIISTINT 334
VG + D L+DF + +++ +A E + ++ + + ++ + R+ +
Sbjct: 232 VGHETDFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQRRLHRALRRLLDQKKQR 291
Query: 335 IENITSNL--NDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPS 392
+E++ L + +E +++ + A++ +L ++++N I
Sbjct: 292 LEHLARRLQFRSPERLLSEQQQRLDEL-AIRLRRALENQLALKKQRLERLTQRLNPQIQR 350
Query: 393 IGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLN 427
LQ + ++ +++ +E + + L
Sbjct: 351 QQQRLQQLERRLDKALRRQLKRKRERLEALVEQLE 385
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
0.314 0.129 0.350
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,847,080
Number of extensions: 243456
Number of successful extensions: 976
Number of sequences better than 10.0: 1
Number of HSP's gapped: 972
Number of HSP's successfully gapped: 98
Length of query: 452
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 355
Effective length of database: 4,167,664
Effective search space: 1479520720
Effective search space used: 1479520720
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 (21.6 bits)
S2: 59 (26.5 bits)