RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780979|ref|YP_003065392.1| aspartyl/glutamyl-tRNA
amidotransferase subunit B [Candidatus Liberibacter asiaticus str.
psy62]
(500 letters)
>gnl|CDD|30413 COG0064, GatB, Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit
(PET112 homolog) [Translation, ribosomal structure and
biogenesis].
Length = 483
Score = 673 bits (1738), Expect = 0.0
Identities = 267/488 (54%), Positives = 344/488 (70%), Gaps = 10/488 (2%)
Query: 17 GTTGDWEVVIGIEVHAQLSVVSKLFSGASVNFG-AEPNTQVSFFDAAMPGMLPILNGRCV 75
++EVVIG+EVH QL+ +KLFSG S +FG AEPNT V +PG LP+LN V
Sbjct: 1 ANMMNFEVVIGLEVHVQLNTKTKLFSGCSTDFGGAEPNTNVCPVCLGLPGALPVLNKEAV 60
Query: 76 QQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQ 135
++A+ GL LN IN+ SVF RKNYFYPDLP+GYQISQ DKPI G + + + +
Sbjct: 61 EKAIKAGLALNCEINEKSVFDRKNYFYPDLPKGYQISQFDKPIAENGYLEIELEDGE--- 117
Query: 136 FRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLT 195
+GIERIHLE+DAGK H+ + S +D NR+GV L+EIVT+PD+RS EA+A+L
Sbjct: 118 --EKRIGIERIHLEEDAGKLTHEGSAGYSLVDYNRAGVPLIEIVTEPDIRSPEEARAYLK 175
Query: 196 KLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEA 254
KLRSILRYLG DGNMEEGSMR D NVSV G E +GTR E+KN+NS R + AIEYE
Sbjct: 176 KLRSILRYLGISDGNMEEGSMRCDANVSVRPKGQEEFGTRVEIKNLNSFRNVEKAIEYEI 235
Query: 255 RRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAI 314
+RQI +LE GG I QETR FD + +T S+R+KE+A DYRYF EPDL PLEI +++I +
Sbjct: 236 QRQIELLESGGEIEQETRRFDEATGKTVSMRSKEEAEDYRYFPEPDLPPLEISDEWIEEV 295
Query: 315 KKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRDK-KIVANWVINDL 373
+ +PELPD KRER+I E+G+S YDA VL SDK +ADYFE+ K+ ANW+ N+L
Sbjct: 296 RATLPELPDEKRERYIKEYGLSEYDARVLTSDKELADYFEEAVKAGADAKLAANWLTNEL 355
Query: 374 LGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKD-IFNILWEKGGTPKEIVEEL 432
LG+LN++G ++E++P++P QL ELI LI +GTISGKIAK+ +F IL G P+EI+EE
Sbjct: 356 LGLLNKAGITLEESPLTPEQLAELIKLIDEGTISGKIAKELVFEILANGGKDPEEIIEEK 415
Query: 433 GLRQVTDLSAIEKVVDEVINSNPNNVARI-ATKPNLVSWFVGQVMKNTGGKANPSIVQKM 491
GL Q++D +EK+VDEV+ NP V + K + + VGQVMK T GKANP V ++
Sbjct: 416 GLVQISDEGELEKIVDEVLAENPKAVEDYKSGKEKALGFLVGQVMKATKGKANPQQVNEL 475
Query: 492 LKEKLGIK 499
LKEKLG
Sbjct: 476 LKEKLGKV 483
>gnl|CDD|37649 KOG2438, KOG2438, KOG2438, Glutamyl-tRNA amidotransferase subunit B
[Translation, ribosomal structure and biogenesis].
Length = 505
Score = 493 bits (1270), Expect = e-140
Identities = 207/488 (42%), Positives = 304/488 (62%), Gaps = 12/488 (2%)
Query: 20 GDWEVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAV 79
W VIG+E+HAQL+ VSKLFSG+ VNFGA PNT VS+FDA++PG LP+LN V+ AV
Sbjct: 21 RKWAAVIGLEIHAQLATVSKLFSGSKVNFGAPPNTSVSYFDASLPGTLPVLNREAVEFAV 80
Query: 80 MTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTI 139
L LN +N S F RK+YFYPDLP GYQI+Q PI G + +S G D
Sbjct: 81 KLSLALNCEVNNVSKFDRKHYFYPDLPAGYQITQQRIPIARNGFIPLSAGLDNVPD---K 137
Query: 140 EVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRS 199
+GI +I LEQD GKS HD + S +DLNR+GV L+EIVTKPD +EA AF+ +L+
Sbjct: 138 TIGILQIQLEQDTGKSTHDDAPSRSLVDLNRAGVPLLEIVTKPDFSDGIEAAAFVKELQL 197
Query: 200 ILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIA 259
ILR+LG GNMEEG++R DVN+S+ G GTR E+KN+NSIR + AI+YE +RQ+
Sbjct: 198 ILRHLGISSGNMEEGALRVDVNISIAPDGSELGTRVELKNLNSIRSISNAIDYEIQRQVE 257
Query: 260 ILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIP 319
+L +GG I+ ETR +D T S+R KE DYR+ EP+L PL + ++ ++++++P
Sbjct: 258 LLNNGGAIQNETRGWDSEGGRTVSMRDKETLQDYRFMPEPNLPPLILHGKYVDSVREELP 317
Query: 320 ELPDAKRERFIGEFGISLYDASVLVSDKSIADYFE------KLAVNRDKKIVANWVINDL 373
ELPDA RE+ + ++G+S DA L ++ + ++++ K K++ W+ +
Sbjct: 318 ELPDATREKLVEQYGLSAKDAVTLANEVELLEFYKDSVRIIKYKAETTPKLITYWIKEEF 377
Query: 374 LGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGG--TPKEIVEE 431
LG L + S + ++P QL +L+ L+ + TIS AK + L + G T ++EE
Sbjct: 378 LGYLRQIALSPNQSIVTPRQLADLLKLLSEETISALSAKQLLRHLLKNPGVMTVSILIEE 437
Query: 432 LGLRQVTDLSAIEKVVDEVINSNPNNVARIAT-KPNLVSWFVGQVMKNTGGKANPSIVQK 490
L Q+ D + IE++V V+ +P V ++ + K + +G VMK++ G+ANP ++K
Sbjct: 438 KRLWQIRDPAEIEELVRSVMEKHPKQVEQLRSGKTKSIKRLIGLVMKSSQGRANPKDLEK 497
Query: 491 MLKEKLGI 498
+L+E L
Sbjct: 498 ILEELLNR 505
>gnl|CDD|145865 pfam02934, GatB_N, GatB/GatE catalytic domain. This domain is
found in the GatB and GatE proteins.
Length = 287
Score = 482 bits (1243), Expect = e-136
Identities = 164/293 (55%), Positives = 204/293 (69%), Gaps = 7/293 (2%)
Query: 23 EVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTG 82
E+VIG+E+H QL+ +KLF G FGAEPNT V +PG LP+LN V+ A+ G
Sbjct: 1 ELVIGLEIHVQLNTKTKLFCGCPTEFGAEPNTNVCPVCLGLPGALPVLNKEAVELAIKAG 60
Query: 83 LGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVG 142
L LN IN S F RKNYFYPDLP+GYQI+Q+D PI G + + + R +G
Sbjct: 61 LALNCEINDESRFDRKNYFYPDLPKGYQITQYDLPIATNGYLEI---EVDGEEKR---IG 114
Query: 143 IERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILR 202
IERIHLE+DAGK IH+ S +DLNR+GV L+EIVT+PD+RS EA+A+L KLR ILR
Sbjct: 115 IERIHLEEDAGKLIHEGGGDYSLVDLNRAGVPLIEIVTEPDIRSPEEARAYLKKLRQILR 174
Query: 203 YLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARRQIAIL 261
YLG DGNMEEGS+R D NVSV G E +GTR E+KN+NS RF+ AIEYE RQI +L
Sbjct: 175 YLGVSDGNMEEGSLRCDANVSVRPKGSEEFGTRVEIKNLNSFRFVEKAIEYEIERQIELL 234
Query: 262 EDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAI 314
E+GG + QETRL+D K ET S+R+KE A DYRYF EPDL P+ I +++I I
Sbjct: 235 EEGGKVPQETRLWDEDKGETVSMRSKEGAADYRYFPEPDLPPIVISDEWIEEI 287
>gnl|CDD|145673 pfam02637, GatB_Yqey, GatB domain. This domain is found in GatB.
It is about 140 amino acid residues long. This domain is
found at the C terminus of GatB, which transamidates
Glu-tRNA to Gln-tRNA.
Length = 148
Score = 185 bits (471), Expect = 3e-47
Identities = 73/148 (49%), Positives = 101/148 (68%), Gaps = 2/148 (1%)
Query: 351 DYFEKLAVN-RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGK 409
D+FE+ D K+ ANW++ +LLG LN+ G I+++P++P L ELI LI +GTISGK
Sbjct: 1 DFFEEAVKAGADPKLAANWLLGELLGYLNKEGLDIDESPLTPEHLAELIKLIDEGTISGK 60
Query: 410 IAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIAT-KPNLV 468
IAK++ L E G +P+EIVEE GL Q++D +EK+VDEVI NP V + K +
Sbjct: 61 IAKEVLEELLENGKSPEEIVEEKGLVQISDEEELEKIVDEVIAENPKAVEDYKSGKEKAL 120
Query: 469 SWFVGQVMKNTGGKANPSIVQKMLKEKL 496
+ VGQVMK T GKA+P +V ++LKEKL
Sbjct: 121 GFLVGQVMKKTRGKADPKLVNELLKEKL 148
>gnl|CDD|32581 COG2511, GatE, Archaeal Glu-tRNAGln amidotransferase subunit E
(contains GAD domain) [Translation, ribosomal structure
and biogenesis].
Length = 631
Score = 104 bits (260), Expect = 7e-23
Identities = 76/252 (30%), Positives = 129/252 (51%), Gaps = 13/252 (5%)
Query: 246 LGLAIEYEARRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLE 305
A+E R +E + +ETR P T LR A R + E D+ P+
Sbjct: 386 AKRALEAVIERAKEAIEG---VPEETRGALPDGT-TVYLRPLPGAA--RMYPETDIPPIR 439
Query: 306 IDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRDKKIV 365
IDE+ + IK+ +PELP+ K ER++ E+G+S A L SD + D FE+L +
Sbjct: 440 IDEELLEKIKENLPELPEEKVERYVKEYGLSKELAEQLASDPRV-DLFEELVEKGVDPTL 498
Query: 366 ANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGG-T 424
+ + L L R G I++ + + EL+ L+ +G I+ + ++I L E G
Sbjct: 499 IASTLVNTLPELRREGVEIDN--LDDEHIEELLRLVSEGKIAKEAIEEILKALAENPGKD 556
Query: 425 PKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNTGGKAN 484
EI E+LGL+++++ +EK++DE+I SN + + + +G+VM G+A+
Sbjct: 557 AAEIAEKLGLKELSE-EEVEKIIDEIIESNLDVIK--ERGMGAMGLLMGRVMAKLRGRAD 613
Query: 485 PSIVQKMLKEKL 496
+V ++L+EKL
Sbjct: 614 GKLVSEILREKL 625
Score = 72.2 bits (177), Expect = 3e-13
Identities = 47/133 (35%), Positives = 73/133 (54%), Gaps = 12/133 (9%)
Query: 140 EVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRS 199
VGIE + LE+DA + I ++ V L+R G+ L+EI T+PD+RS +A+ ++
Sbjct: 151 PVGIETLCLEEDAARKIEEKGDTV-VYSLDRLGIPLIEISTEPDIRSPEQAREVAERIGY 209
Query: 200 ILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIA 259
ILR G + G++R DVNVS+ G R E+K V + + +EYE RQ+
Sbjct: 210 ILRSTGKVKRGL--GTIRQDVNVSI-----KGGARVEIKGVQDLDLIPDVVEYEVERQLN 262
Query: 260 ILEDGGHIRQETR 272
+L+ IR E +
Sbjct: 263 LLK----IRDELK 271
>gnl|CDD|39167 KOG3964, KOG3964, KOG3964, Phosphatidylglycerolphosphate synthase
[Lipid transport and metabolism].
Length = 469
Score = 33.0 bits (75), Expect = 0.18
Identities = 40/252 (15%), Positives = 86/252 (34%), Gaps = 21/252 (8%)
Query: 249 AIEYEARRQIAILEDGGHIRQETRLFDPSKNET---RSLRTKEDALDYRYFSEPDLLPLE 305
A+E +++IL D + TR S + + + +D + P L L
Sbjct: 76 ALEKNPSLKVSILLDF---LRGTRELPNSCSALLPVWLGKKFPERVDESLYHTPFLRGLS 132
Query: 306 ---IDEDFIRAIKKQIPELPDAKRERFIGEFGIS-LY-----DASVLVSDKSIADYFEKL 356
+ F + Q ++ E I +S Y D L SD+ +AD++ KL
Sbjct: 133 KSLVPARFNEGLGLQHMKIYGFDDEVIISGANLSNDYFTNRQDRYYLFSDRRLADFYFKL 192
Query: 357 AVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFN 416
+ + ++ G ++ ++ ++ L + G S + ++ +
Sbjct: 193 -HDLVSSFSLQKIPDESDGSIHTKNPRVDPIENLSGANMQMSQL-LTGHSSSLLQQNPID 250
Query: 417 ILWEKGGTPKEIVEELGLRQ-VTDLSAIEKVVDEVINSNPNNVARI---ATKPNLVSWFV 472
P L Q +++V + + A+ NL ++
Sbjct: 251 AAGAFDRRPAPDAWIYPLFQMKPIEIQFKEIVTSTLLTEALRGAKWTLTTGYFNLTQAYM 310
Query: 473 GQVMKNTGGKAN 484
Q++ TG + +
Sbjct: 311 KQLLLGTGAEYS 322
>gnl|CDD|112220 pfam03395, Pox_P4A, Poxvirus P4A protein.
Length = 889
Score = 30.6 bits (69), Expect = 1.1
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 342 VLVSDKSIADYFEKLAVNRD------KKIVANWVINDLLGVLNRSGKSIEDTPISPNQLG 395
+SD A+ EK D ++A I LL ++ RSG+SI+ T I P++L
Sbjct: 789 ARISDDVKAEGLEKYKAFSDISSSLYNDLIAIETIKALLYIIKRSGRSIDGTEIGPDELR 848
Query: 396 ELIDLI 401
+ +LI
Sbjct: 849 KSYELI 854
>gnl|CDD|145457 pfam02312, CBF_beta, Core binding factor beta subunit. Core
binding factor (CBF) is a heterodimeric transcription
factor essential for genetic regulation of hematopoiesis
and osteogenesis. The beta subunit enhances DNA-binding
ability of the alpha subunit in vitro, and has been show
to have a structure related to the OB fold.
Length = 170
Score = 29.3 bits (66), Expect = 2.3
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 182 PDMRSSLEAKAFLTKLR--SILRYLGTCDGNMEEGSMRADVNVSVCRPGEA 230
PD RS E+ KL S ++Y G D EE R + CR G A
Sbjct: 6 PDQRSKFESDELFRKLSRESEIKYTGYRDRPAEERRDRF---QNHCREGHA 53
>gnl|CDD|58085 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution..
Length = 87
Score = 28.2 bits (63), Expect = 5.1
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 12/41 (29%)
Query: 125 SVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSC 165
++ +GPD+ G FR + V KSIH S V
Sbjct: 32 TLLLGPDQDGSFRPVTV------------KSIHRNRSPVRV 60
>gnl|CDD|147176 pfam04876, Tenui_NCP, Tenuivirus major non-capsid protein. This
protein of unknown function accumulates in large amounts
in tenuivirus infected cells. It is found in all forms
of the inclusion bodies that are formed after infection.
Length = 175
Score = 28.3 bits (63), Expect = 5.4
Identities = 24/119 (20%), Positives = 47/119 (39%), Gaps = 21/119 (17%)
Query: 303 PLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRDK 362
PLE D F + + K +PE + E +G + S+ D + + K
Sbjct: 63 PLETDPLFTK-VHKHMPEFCHSFLEHLLG---------GEDSTTNSLIDIGVFFVILQPK 112
Query: 363 KIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEK 421
+ +W+ + L NR +S +Q+ L+ II+ + + + +W+K
Sbjct: 113 --LGDWITKNYLKHPNR---------MSKDQIKTLLTQIIEMAKAESSDTETYEKVWKK 160
>gnl|CDD|31267 COG1069, AraB, Ribulose kinase [Energy production and conversion].
Length = 544
Score = 27.9 bits (62), Expect = 6.1
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 366 ANWVINDLLGVLNRSGKSI--------EDTPISPNQLGELIDLIIDGTISGKIAKDIFNI 417
A+W+ L G + RS + + + + I L + K+ +DI
Sbjct: 167 ADWLTWKLTGSIARSRCTAGCKWNWLEHEGGLWSADFFDKIGLDDLRELDSKLPEDIVPA 226
Query: 418 LWEKGGTPKEIVEELGLRQVTDLSA 442
GG E +ELGL + T +SA
Sbjct: 227 GEPVGGLTPEAAQELGLPEGTVVSA 251
>gnl|CDD|147253 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyse the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 27.6 bits (62), Expect = 7.6
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 395 GELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVE 430
GELI +ID + GK + +I++++ G P+E V+
Sbjct: 99 GELISGVIDKKLGGKSLGSLIHIIYKEYG-PEETVK 133
>gnl|CDD|34765 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 27.4 bits (60), Expect = 9.0
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 9/78 (11%)
Query: 420 EKGGTPKEIVEELGLRQVTDLSAIEKVVDE--VINSNPNNVARIATKPNLVSWFVGQVMK 477
E G E + LG+ + D + + V NV +ATK S +K
Sbjct: 269 ESRGGKFE-GQSLGIVKHFDFGETVSIKENNGVFVKIEGNVCIVATKDFTES------LK 321
Query: 478 NTGGKANPSIVQKMLKEK 495
K NP + + K
Sbjct: 322 VDLDKMNPPVTVNLQNPK 339
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
0.317 0.136 0.387
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,949,650
Number of extensions: 320484
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 805
Number of HSP's successfully gapped: 25
Length of query: 500
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 402
Effective length of database: 4,146,055
Effective search space: 1666714110
Effective search space used: 1666714110
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)