RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780690|ref|YP_003065103.1| flagellar biosynthesis protein
FlhB [Candidatus Liberibacter asiaticus str. psy62]
(354 letters)
>2jlj_A YSCU, YOP proteins translocation protein U; cell membrane,
transmembrane, yersinia pesits, protein transport, type
III secretion system, plasmid; 1.3A {Yersinia pestis}
PDB: 2jlh_A* 2v5g_A 2w0r_A
Length = 144
Score = 164 bits (417), Expect = 2e-41
Identities = 39/130 (30%), Positives = 71/130 (54%)
Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALR 280
+LKMSK EIK E K+ G+P IK++++ + M E R+++++ TH A+ +
Sbjct: 3 ELKMSKDEIKREYKEMEGSPEIKSKRRQFHQEIQSRNMRENVKRSSVVVAAATHIAIGIL 62
Query: 281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYK 340
Y + E P++ K + + +RKIA E +PI + LAR+L+ ++ IP +
Sbjct: 63 YKRGETPLPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIE 122
Query: 341 AVAQLIYKIY 350
A A+++ +
Sbjct: 123 ATAEVLRWLE 132
>2jli_A YSCU, YOP proteins translocation protein; cell membrane,
transmembrane, protein transport, type III secretion
system, plasmid, membrane; 1.13A {Yersinia pestis}
Length = 123
Score = 155 bits (394), Expect = 1e-38
Identities = 36/119 (30%), Positives = 66/119 (55%)
Query: 228 EIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTEND 287
EIK E K+ G+P IK++++ + M E R+++++ NPTH A+ + Y + E
Sbjct: 1 EIKREYKEMEGSPEIKSKRRQFHQEIQSRNMRENVKRSSVVVANPTHIAIGILYKRGETP 60
Query: 288 APVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLI 346
P++ K + + +RKIA E +PI + LAR+L+ ++ IP +A A+++
Sbjct: 61 LPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVL 119
>3bzs_A ESCU; auto cleavage protein, intein, T3SS, TTSS, asparagine
cyclization, membrane, membrane protein, protein
transport; 1.48A {Escherichia coli} PDB: 3bzr_A 3bzp_A
3bzt_A 3c03_A
Length = 137
Score = 153 bits (388), Expect = 6e-38
Identities = 42/130 (32%), Positives = 70/130 (53%)
Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALR 280
MSK E+K E K + GNP IK ++ + + ++T+I+ +PTH A+ L
Sbjct: 4 MASMSKDEVKREAKDTDGNPEIKGERRRLHSEIQSGSLANNIKKSTVIVKDPTHIAICLY 63
Query: 281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYK 340
Y E P+++ G++ A ++ K+A ++IP+ E+ LARSL+K + I F++
Sbjct: 64 YKLGETPLPLVIETGKDAKALQIIKLAELYDIPVIEDIPLARSLYKNIHKGQYITEDFFE 123
Query: 341 AVAQLIYKIY 350
VAQLI
Sbjct: 124 PVAQLIRIAI 133
>3bzy_B ESCU; auto cleavage protein, flagella, intein, T3SS, membrane,
membrane protein, protein transport; 1.20A {Escherichia
coli} SCOP: d.367.1.1 PDB: 3c00_B 3bzl_C 3bzo_B 3bzv_B
3c03_C 3bzz_B 3bzx_B
Length = 83
Score = 100 bits (250), Expect = 6e-22
Identities = 28/79 (35%), Positives = 44/79 (55%)
Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331
PTH A+ L Y E P+++ G++ A ++ K+A ++IP+ E+ LARSL K +
Sbjct: 1 PTHIAICLYYKLGETPLPLVIETGKDAKALQIIKLAELYDIPVIEDIPLARSLDKNIHKG 60
Query: 332 SAIPPVFYKAVAQLIYKIY 350
I F++ VAQLI
Sbjct: 61 QYITEDFFEPVAQLIRIAI 79
>2vt1_B Surface presentation of antigens protein SPAS; specificity switch,
virulence, transmembrane, inner membrane, FLHB, YSCU,
T3SS, plasmid; 2.0A {Shigella flexneri} SCOP: d.367.1.1
Length = 93
Score = 98.4 bits (245), Expect = 2e-21
Identities = 23/79 (29%), Positives = 33/79 (41%)
Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331
PTH A+ + + AP + N A +RK A E IP + LAR L+K
Sbjct: 1 PTHIAIGIYFNPEIAPAPFISLIETNQCALAVRKYANEVGIPTVRDVKLARKLYKTHTKY 60
Query: 332 SAIPPVFYKAVAQLIYKIY 350
S + V +LI +
Sbjct: 61 SFVDFEHLDEVLRLIVWLE 79
>3c01_E Surface presentation of antigens protein SPAS; auto cleavage
protein, flagella, ESCU, YSCU, intein, T3SS, membrane,
inner membrane; 2.60A {Salmonella typhimurium} SCOP:
d.367.1.1
Length = 98
Score = 95.3 bits (237), Expect = 2e-20
Identities = 18/79 (22%), Positives = 32/79 (40%)
Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331
PTH + + + P++ N A +R A + +P+ + LARSLFK
Sbjct: 1 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRY 60
Query: 332 SAIPPVFYKAVAQLIYKIY 350
+ V +L+ +
Sbjct: 61 DLVSLEEIDEVLRLLVWLE 79
>3bzy_A ESCU; auto cleavage protein, flagella, intein, T3SS, membrane,
membrane protein, protein transport; 1.20A {Escherichia
coli} SCOP: d.367.1.1 PDB: 3bzl_A 3bzv_A 3bzx_A 3bzo_A
3bzz_A 3c03_B 3c00_A
Length = 54
Score = 74.3 bits (183), Expect = 4e-14
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271
MSK E+K E K + GNP IK ++ + + ++T+I+ N
Sbjct: 4 MASMSKDEVKREAKDTDGNPEIKGERRRLHSEIQSGSLANNIKKSTVIVKN 54
>2vt1_A Surface presentation of antigens protein SPAS; specificity switch,
virulence, transmembrane, inner membrane, FLHB, YSCU,
T3SS, plasmid; 2.0A {Shigella flexneri} SCOP: d.367.1.1
Length = 52
Score = 73.5 bits (181), Expect = 7e-14
Identities = 11/50 (22%), Positives = 24/50 (48%)
Query: 222 LKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271
+ M KQEIK E + G+ K+R++ + + + + +++ N
Sbjct: 3 MMMDKQEIKREYIEQEGHFETKSRRRELHIEILSEQTKSDIRNSKLVVMN 52
>3c01_A Surface presentation of antigens protein SPAS; auto cleavage
protein, flagella, ESCU, YSCU, intein, T3SS, membrane,
inner membrane; 2.60A {Salmonella typhimurium} SCOP:
d.367.1.1
Length = 48
Score = 70.4 bits (173), Expect = 6e-13
Identities = 12/48 (25%), Positives = 28/48 (58%)
Query: 224 MSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271
M K+E+K E+K+ GNP +K++++ + + ++ + +I+ N
Sbjct: 1 MDKEEVKREMKEQEGNPEVKSKRREVHMEILSEQVKSDIENSRLIVAN 48
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 64.6 bits (157), Expect = 3e-11
Identities = 69/484 (14%), Positives = 128/484 (26%), Gaps = 201/484 (41%)
Query: 2 SENDAPDNKTEAPSSKKIE----------DALNEGNAPISREASLFSSILACLIYLLFF- 50
+E A D++ P++ E + + F +L L F
Sbjct: 45 TEGFAADDE---PTTP-AELVGKFLGYVSSLVEPS------KVGQFDQVLNLC--LTEFE 92
Query: 51 --FSPGIYSVTSDLHVLLAS------ATQRKLEDISHIVFLLTHLSLSASRLVIPGLL-- 100
+ G +D+H L A T K +++ ++ L
Sbjct: 93 NCYLEG-----NDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR 147
Query: 101 --------LFMMFG----IGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNF 148
L +FG Y F+ LR+ +Y
Sbjct: 148 AVGEGNAQLVAIFGGQGNTDDY----------------FE--ELRD----LYQT------ 179
Query: 149 MKSFVKIILVGTIITI--SLTEN------YFTM-LDFIS--ANPHSI------------- 184
V L+ L FT L+ + NP +
Sbjct: 180 YHVLVGD-LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC 238
Query: 185 -------LYHAFFTVR-KVL--------------------IMILLFIAT----------- 205
L H + V K+L ++ + IA
Sbjct: 239 PLIGVIQLAH--YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSV 296
Query: 206 ---LTVL-DIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPI----IKNRQKSIARSRIRHK 257
+TVL IG ++ Y + ++D ++ + G P I N + + ++
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN----LTQEQV-QD 351
Query: 258 MMEAT----------------SRATIIITNPT----HYALALRYIQ--TENDAPVLVAKG 295
+ T ++++ P L LR + + D
Sbjct: 352 YVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD-------- 403
Query: 296 QNLIAKKMRKIAYEHN-IPI---FEEPSL--ARSLFKQ--VPINSAIPPVFYKAVAQLIY 347
Q+ I RK+ + + +P+ F L A L + V N + +
Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA------KDIQI 457
Query: 348 KIYH 351
+Y
Sbjct: 458 PVYD 461
Score = 47.6 bits (113), Expect = 4e-06
Identities = 37/175 (21%), Positives = 61/175 (34%), Gaps = 59/175 (33%)
Query: 10 KTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHV-LLAS 68
K +APS L++ P S FS+ F P V S H LL
Sbjct: 395 KAKAPSG------LDQSRIPFSERKLKFSNR----------FLP----VASPFHSHLLVP 434
Query: 69 ATQRKLEDISHIVFLLTHLSLSASRLVIPGLLLFMMF-G-----IGSYLIQRI------- 115
A+ +D + ++S +A + IP ++ F G + + +RI
Sbjct: 435 ASDLINKD-----LVKNNVSFNAKDIQIP---VYDTFDGSDLRVLSGSISERIVDCIIRL 486
Query: 116 PV-----LNLN--HVKPSFKRVSLREGIKRIYSINNLVNFMK--SFVKIILVGTI 161
PV H+ L G + L + K + V++I+ GT+
Sbjct: 487 PVKWETTTQFKATHI--------LDFGPGGASGLGVLTHRNKDGTGVRVIVAGTL 533
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.0 bits (66), Expect = 0.77
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 6/24 (25%)
Query: 278 ALRYIQT------ENDAPVLVAKG 295
AL+ +Q ++ AP L K
Sbjct: 21 ALKKLQASLKLYADDSAPALAIKA 44
Score = 27.7 bits (60), Expect = 3.7
Identities = 7/29 (24%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 12 EAPSSKKIEDALN---EGNAP-ISREASL 36
E + KK++ +L + +AP ++ +A++
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATM 46
>2ctw_A DNAJ homolog subfamily C member 5; J-domain, chaperone,
helix-turn-helix, structural genomics, NPPSFA; NMR {Mus
musculus}
Length = 109
Score = 28.6 bits (63), Expect = 2.4
Identities = 13/56 (23%), Positives = 22/56 (39%)
Query: 218 WYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPT 273
Y L + K D+IK+SY +K + + + A I+T+ T
Sbjct: 19 LYHVLGLDKNATSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTDAT 74
>2qx2_A Sex pheromone staph-CAM373; structural genomics, PSI-2, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.90A {Staphylococcus aureus subsp}
Length = 344
Score = 28.2 bits (63), Expect = 2.6
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 21/79 (26%)
Query: 276 ALALR---YIQTENDAP---------VLVAKGQ---NLIAKKMRKIAYEHNIPIFEEPSL 320
LA+ Y + E D P + +G+ + I ++R+ +IPI
Sbjct: 135 GLAMNSVYYYKKEKDGPTFSKKLDDSEVKKQGKQMASEILSRLRENDDLKDIPIH----- 189
Query: 321 ARSLFKQVPINSAIPPVFY 339
+++KQ +S P F
Sbjct: 190 -FAIYKQSSEDSITPGEFI 207
>2csu_A 457AA long hypothetical protein; structural genomics, PH0766, riken
structural genomics/proteomics initiative, RSGI, NPPSFA;
2.20A {Pyrococcus horikoshii OT3} SCOP: c.2.1.8 c.23.4.1
c.23.4.1
Length = 457
Score = 28.2 bits (62), Expect = 2.7
Identities = 9/46 (19%), Positives = 21/46 (45%)
Query: 276 ALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLA 321
+ + N+ PVL +++K +++ ++ IP +E P
Sbjct: 392 GIIRAVKEVNNEKPVLAMFMAGYVSEKAKELLEKNGIPTYERPEDV 437
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.9 bits (61), Expect = 3.8
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 203 IAT--LTVLDIG-WSYHQWYSKLKMSKQ-----EIKDEIKQSYGNPIIKNRQK 247
+AT LT+ D+G S+H +K + E+ + +S GNP+I QK
Sbjct: 1327 LATYGLTIDDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQK 1379
>1q3q_A Thermosome alpha subunit; chaperone, chaperonin; HET: ANP; 2.30A
{Thermococcus SP} SCOP: a.129.1.2 c.8.5.2 d.56.1.2 PDB:
1q2v_A* 1q3s_A* 1q3r_A
Length = 548
Score = 26.9 bits (59), Expect = 7.6
Identities = 24/134 (17%), Positives = 48/134 (35%), Gaps = 23/134 (17%)
Query: 233 IKQSYGNPIIKNRQKSIARS-RIRH---KMMEATSRAT-----------IIITNPTHYAL 277
+ S G+ ++ N +I ++H KMM ++ ++I L
Sbjct: 52 LVDSLGDIVVTNDCATILDKIDLQHPAAKMMVEVAKTQDKEAGDGTTTAVVIAG----EL 107
Query: 278 ---ALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAI 334
A + +N P ++ KG L A+K ++I E I + + I
Sbjct: 108 LRKAEELL-DQNIHPSIITKGYALAAEKAQEILDEIAIRVDPDDEETLLKIAATSITGKN 166
Query: 335 PPVFYKAVAQLIYK 348
+ +A+L +
Sbjct: 167 AESHKELLAKLAVE 180
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.324 0.137 0.389
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,884,987
Number of extensions: 130547
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 599
Number of HSP's successfully gapped: 35
Length of query: 354
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 261
Effective length of database: 3,438,538
Effective search space: 897458418
Effective search space used: 897458418
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.9 bits)