RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780170|ref|YP_003064583.1| cationic amino acid ABC
transporter, periplasmic binding protein [Candidatus Liberibacter
asiaticus str. psy62]
(342 letters)
>gnl|CDD|162200 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein.
Length = 250
Score = 157 bits (400), Expect = 3e-39
Identities = 58/284 (20%), Positives = 100/284 (35%), Gaps = 56/284 (19%)
Query: 32 KRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLA 91
K G ++ G TG F ANG GFDVD +AL + +K +++ N +
Sbjct: 22 KEGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMK---AKCKFVEQNFDGLIPS 78
Query: 92 LQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGI-SSVSQLSGASICV 150
L++K++D + ++ + + F Y GQGF++ K + ++ L G ++ V
Sbjct: 79 LKAKKVDAIMAT--MSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGV 136
Query: 151 QAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDR 210
Q+GTT E L DYFK + ++ + + +A R DA D S L L
Sbjct: 137 QSGTTHEQYLKDYFKP---GVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPN 193
Query: 211 PSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELGITQKNINQVSKDTTN 270
+ + ++ GD GI + +
Sbjct: 194 GKDFKFVGPSVTDEKY-----FGD------------------GYGIGLRKGDT------- 223
Query: 271 PDVQRFLGIDKSSNIGEALGLTKDWTYRIIRHMGNYGEMFDRNL 314
L + IR G Y ++ +
Sbjct: 224 -----------------ELKAAFNKALAAIRADGTYQKISKKWF 250
>gnl|CDD|128376 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 140 bits (356), Expect = 4e-34
Identities = 56/227 (24%), Positives = 97/227 (42%), Gaps = 10/227 (4%)
Query: 36 LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
L+ G N F+ +G+ GFDVD +A++ + K++++ ++ AL+S
Sbjct: 2 LRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELG---LKVEFVEVSFDNLLTALKSG 58
Query: 96 QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
+ID+++ T R + F Y GQ ++ K I S+ L G + V AGTT
Sbjct: 59 KIDVVAAGMTITPERAKQV--DFSDPYYKSGQVILVRKDSPIKSLEDLKGKKVAVVAGTT 116
Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215
E L + + ++ E AA +A R DA D AL AL + P +
Sbjct: 117 GEELLKKL----YPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKI 172
Query: 216 ILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEEL-GITQKNI 261
+ + + A A+ +GD E + ++ + L I +K
Sbjct: 173 VGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADGTLKKIYEKWF 219
>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
aspartate/glutamate-binding protein; Reviewed.
Length = 259
Score = 73.8 bits (181), Expect = 6e-14
Identities = 61/216 (28%), Positives = 98/216 (45%), Gaps = 12/216 (5%)
Query: 9 ILCLIILFFTSFSTNA----SILGDIKKRGFLKCGINTGLVGFAEV-KANGDWKGFDVDF 63
L + L +NA L IK +G L G+ + +A + +A G+ KGF++D
Sbjct: 9 KLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEIDV 68
Query: 64 CRALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITY 123
+ L+ +I D KI+ + +NAK R L + +D + +T+ E F Y
Sbjct: 69 AKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVI--ATFTITPERKRIYNFSEPYY 126
Query: 124 FDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEID 183
D G ++ K+K S++ + GA+I V TT+ + + K + F I
Sbjct: 127 QDAIGLLVLKEKNYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIK 186
Query: 184 AAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPD 219
AA A R DA++ D S L L +D+ ILPD
Sbjct: 187 AALDAKRVDAFSVDKSIL--LGYVDDKS---EILPD 217
>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
protein; Provisional.
Length = 243
Score = 39.6 bits (92), Expect = 0.001
Identities = 33/121 (27%), Positives = 54/121 (44%), Gaps = 16/121 (13%)
Query: 47 FAEVKANGDWKGFDVDFCRALSSAI-----FDDPSKIQYLPLNAKERFLALQSKQIDILS 101
F + AN GFDVD +AL I F + + +P +L+ ++++ +
Sbjct: 34 FESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIP--------SLKFRRVEAVM 85
Query: 102 RNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLA 161
D T RE + L P Y+D + ++ +SV QL G + VQ GTT + +
Sbjct: 86 AGMDITPEREKQV-LFTTP--YYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIM 142
Query: 162 D 162
D
Sbjct: 143 D 143
>gnl|CDD|181908 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 35.9 bits (83), Expect = 0.016
Identities = 47/174 (27%), Positives = 65/174 (37%), Gaps = 47/174 (27%)
Query: 39 GINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYL--PLNAKERFLALQSKQ 96
+T V F E K + GFD+D L +AI + K+ Y P++ ALQ+K
Sbjct: 30 ATDTAFVPF-EFKQGDKYVGFDID----LWAAIAKEL-KLDYTLKPMDFSGIIPALQTKN 83
Query: 97 IDILSRNTDWTLLREISLGLAFRPIT------------YFDGQGFIMHKKKG--ISSVSQ 142
+D L LA IT Y+ +M K I SV
Sbjct: 84 VD---------------LALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKD 128
Query: 143 LSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAY---RAHRCDA 193
L G + V++GT + DY KA+ + ID AY R DA
Sbjct: 129 LDGKVVAVKSGTGS----VDYAKAN---IKTKDLRQFPNIDNAYLELGTGRADA 175
>gnl|CDD|182740 PRK10797, PRK10797, glutamate and aspartate transporter subunit;
Provisional.
Length = 302
Score = 34.8 bits (80), Expect = 0.031
Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 6/140 (4%)
Query: 25 SILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAI---FDDPS-KIQY 80
S L I K G + G V F+ G+ D+ A+ A+ + P +++
Sbjct: 31 STLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKL 90
Query: 81 LPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSV 140
+P+ ++ R LQ+ D +T L R+ AF + G + K I
Sbjct: 91 IPITSQNRIPLLQNGTFDFECGSTTNNLERQKQA--AFSDTIFVVGTRLLTKKGGDIKDF 148
Query: 141 SQLSGASICVQAGTTTELTL 160
+ L G ++ V +GTT+E+ L
Sbjct: 149 ADLKGKAVVVTSGTTSEVLL 168
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 34.3 bits (79), Expect = 0.045
Identities = 33/135 (24%), Positives = 55/135 (40%), Gaps = 5/135 (3%)
Query: 24 ASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPL 83
+L +K+RG L G+ F+ +G GF+V+F AL+ + K P
Sbjct: 31 EGLLNKVKERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL---GVKASLKPT 87
Query: 84 NAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKG-ISSVSQ 142
+L SK+ID++ + R+ + P T Q + +G I + +
Sbjct: 88 KWDGMLASLDSKRIDVVINQVTISDERKKKYDFS-TPYTVSGIQALVKKGNEGTIKTAAD 146
Query: 143 LSGASICVQAGTTTE 157
L G + V GT E
Sbjct: 147 LKGKKVGVGLGTNYE 161
>gnl|CDD|150404 pfam09724, DUF2036, Uncharacterized conserved protein (DUF2036).
This family of proteins includes members ranging in size
from approximately 300 to 460 residues. There are a
number of well-conserved domains along the length.
Length = 325
Score = 28.8 bits (65), Expect = 2.0
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 58 GFDVDFCRALSSAIFDDP--SKIQY-----LPLNAKERFLAL 92
G D+D + A+ D P IQY LP + KERF L
Sbjct: 267 GMDLDLDQLRGYALLDRPAEETIQYLSEEDLPTDPKERFKEL 308
>gnl|CDD|184972 PRK15010, PRK15010, ABC transporter lysine/arginine/ornithine
binding periplasmic protein; Provisional.
Length = 260
Score = 27.7 bits (61), Expect = 4.6
Identities = 37/151 (24%), Positives = 62/151 (41%), Gaps = 10/151 (6%)
Query: 8 SILCLIILFFTSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRAL 67
SIL L +L S AS + + + G +T F+ A GD+ GFD+D +
Sbjct: 4 SILALSLL--VGLSAAASSYAALPETV--RIGTDTTYAPFSSKDAKGDFVGFDIDLGNEM 59
Query: 68 SSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQ 127
+ K ++ + +L++K+ID + + T R+ +AF Y
Sbjct: 60 CKRM---QVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQE--IAFSDKLYAADS 114
Query: 128 GFIMHKKKGIS-SVSQLSGASICVQAGTTTE 157
I K I ++ L G + V G+T E
Sbjct: 115 RLIAAKGSPIQPTLDSLKGKHVGVLQGSTQE 145
>gnl|CDD|180730 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 27.6 bits (62), Expect = 5.3
Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 21/105 (20%)
Query: 15 LFFTSFSTNA------SILGDIKKRGFLKCGINTGLVGFAEVKAN-GDWKGFDVDF--C- 64
LF + + S+ +K R FLK TG + A + +GFDV+ C
Sbjct: 192 LFLGAITPKGAVDFVPSLTEGVKNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCG 251
Query: 65 -----------RALSSAIFDDPSKIQYLPLNAKERFLALQSKQID 98
L+ AIFD + +Y P + + + + ID
Sbjct: 252 FDPDSLDMVIIPELNFAIFDSTAPHEYFPSREGDEIIDMYDELID 296
>gnl|CDD|184492 PRK14081, PRK14081, triple tyrosine motif-containing protein;
Provisional.
Length = 667
Score = 27.3 bits (61), Expect = 6.0
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 75 PSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREI 112
P++I Y+ L KE +L +I+++ +NT L++ I
Sbjct: 480 PAEIDYILLPVKEYYLVGDDIEIEVIIQNTKDVLIKYI 517
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 27.1 bits (60), Expect = 6.7
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 14/69 (20%)
Query: 121 ITYFDGQGFIMHKKKGISSVSQLS---GASICVQAGTTTEL-----------TLADYFKA 166
+ + G GF+ +G+ SQ + GA+ AG ++ TL+DY+
Sbjct: 323 LGWAWGAGFVDGIGQGMERASQPAVGLGATAAYGAGDVLKMGIGGGASKAAQTLSDYYIK 382
Query: 167 HNMKYHPIV 175
+YHP++
Sbjct: 383 RAEQYHPVI 391
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes the aerobic cobalamin pathway Pseudomonas
denitrificans CobT gene product, which is a cobalt
chelatase subunit, with a MW ~70 kDa. The aerobic
pathway cobalt chelatase is a heterotrimeric,
ATP-dependent enzyme that catalyzes cobalt insertion
during cobalamin biosynthesis. The other two subunits
are the P. denitrificans CobS (TIGR01650) and CobN
(pfam02514 CobN/Magnesium Chelatase) proteins. To avoid
potential confusion with the nonhomologous Salmonella
typhimurium/E.coli cobT gene product, the P.
denitrificans gene symbol is not used in the name of
this model.
Length = 600
Score = 27.2 bits (60), Expect = 6.9
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 22 TNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKG 58
T A+ DI R +CG+ ++GF +A WKG
Sbjct: 411 TVAATCADILARTLERCGVKVEILGFT-TRA---WKG 443
>gnl|CDD|179119 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 27.0 bits (61), Expect = 6.9
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 201 LYALKLTNDRPSEHVILPDIISKSPLAPAIIQG 233
L+A N RP + P + SPL P I+ G
Sbjct: 101 LFA----NLRP--AKLYPGLADASPLKPEIVAG 127
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.322 0.138 0.418
Gapped
Lambda K H
0.267 0.0590 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,668,018
Number of extensions: 361042
Number of successful extensions: 696
Number of sequences better than 10.0: 1
Number of HSP's gapped: 688
Number of HSP's successfully gapped: 23
Length of query: 342
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 248
Effective length of database: 3,963,321
Effective search space: 982903608
Effective search space used: 982903608
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: 57 (26.0 bits)