RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781112|ref|YP_003065525.1| putative amino acid-binding
periplasmic ABC transporter protein [Candidatus Liberibacter asiaticus
str. psy62]
(274 letters)
>gnl|CDD|128376 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 169 bits (429), Expect = 9e-43
Identities = 86/223 (38%), Positives = 124/223 (55%), Gaps = 9/223 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
LRVGT+G YPP SF D GELTGFD+DL K +A L LKVEF E + L+T L + +
Sbjct: 2 LRVGTNGDYPPFSFA--DEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDNLLTALKSGK 59
Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
DV+ + ITPER K+ DFS PY +++VR D I+S +DL K VA + GT
Sbjct: 60 IDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKD-SPIKSLEDLKGKKVAVVAGTTGE 118
Query: 162 RFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA-DR 218
K+L ++ +V + ++L L + R DA + +++ H KI D
Sbjct: 119 ELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQ--HGLPELKIVGDP 176
Query: 219 MKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
+ AF +RKG+ +L IN+ L + DGT KKI++++F
Sbjct: 177 LDTPEGYAFAVRKGDPELLDKINKALKELKADGTLKKIYEKWF 219
>gnl|CDD|162200 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein.
Length = 250
Score = 126 bits (319), Expect = 6e-30
Identities = 74/230 (32%), Positives = 115/230 (50%), Gaps = 16/230 (6%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+R+GT+ YPP F ++D G+L GFD+DL K + R+ K +F E GLI L +
Sbjct: 26 VRIGTETGYPP--FESKDANGKLVGFDVDLAKALCKRMKAKCKFVEQNFDGLIPSLKAKK 83
Query: 103 YDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D ++ ++ITP+RQK+ DFS PY A VV+ ++ +DL KTV GT
Sbjct: 84 VDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGVQSGTTHE 143
Query: 162 RFAK-ELKS--HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA-- 216
++ K K +V +++ + L + R DA + D +P +G FK
Sbjct: 144 QYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDA-VFTDASVLAEGFLKPPNGKDFKFVGP 202
Query: 217 -----DRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
D + +RKG+ +L + N+ L AI DGTY+KI ++F
Sbjct: 203 SVTDEKYFGDGYGIG--LRKGDTELKAAFNKALAAIRADGTYQKISKKWF 250
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 126 bits (318), Expect = 6e-30
Identities = 69/234 (29%), Positives = 125/234 (53%), Gaps = 17/234 (7%)
Query: 36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLI 95
+ +++ L VG +G YPP SF Q G+LTGF+++ + +A L +K T G++
Sbjct: 36 KVKERGTLLVGLEGTYPPFSF--QGEDGKLTGFEVEFAEALAKHLGVKASLKPTKWDGML 93
Query: 96 TGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQD-IRSFKDLTDKTVA 153
LD+ R DV++N V I+ ER+KKYDFS PY + +V+ + I++ DL K V
Sbjct: 94 ASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIKTAADLKGKKVG 153
Query: 154 QILGTDLSRFAKE-LKSHLVFSHNFEQS-LQLLLSKRTDATMIPDIPFFNFLERRPHD-- 209
LGT+ ++ ++ ++ V +++ + + Q L R DA ++ + + +++
Sbjct: 154 VGLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLA 213
Query: 210 --GNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
G F + S VA +RKGN L +++N+ + + DGT K + +++F
Sbjct: 214 VAGEAFS-----RQESGVA--LRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWF 260
>gnl|CDD|181908 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 95.2 bits (237), Expect = 2e-20
Identities = 69/228 (30%), Positives = 107/228 (46%), Gaps = 21/228 (9%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
L V TD + P F D + GFDIDL +A L L SG+I L T
Sbjct: 27 LVVATDTAFVPFEFKQGD---KYVGFDIDLWAAIAKELKLDYTLKPMDFSGIIPALQTKN 83
Query: 103 YDV-LVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D+ L + IT ER+K DFS Y +L++V+++ DI+S KDL K VA GT
Sbjct: 84 VDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKDLDGKVVAVKSGTGSV 143
Query: 162 RFAKELKSHLVFSH-----NFEQSLQLLLSKRTDATM--IPDIPFFNFLERRPHDGNLFK 214
+A K+++ N + + L + R DA + P+I +F + +G
Sbjct: 144 DYA---KANIKTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYF---IKTAGNGQFKA 197
Query: 215 IADRMK-DNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
+ D ++ +AF KG+ L +N L + +GTY +I+ ++F
Sbjct: 198 VGDSLEAQQYGIAF--PKGSE-LREKVNGALKTLKENGTYAEIYKKWF 242
>gnl|CDD|185334 PRK15437, PRK15437, histidine ABC transporter substrate-binding
protein HisJ; Provisional.
Length = 259
Score = 87.4 bits (216), Expect = 4e-18
Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 11/232 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+R+GTD Y P F +++ +GEL GFDIDL KE+ R+N + F E + LI L +
Sbjct: 28 IRIGTDPTYAP--FESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKK 85
Query: 103 YDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D ++ +++IT +RQ++ F+ A LVV + + + L K V + GT
Sbjct: 86 IDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQE 145
Query: 162 RFAKEL---KSHLVFSHNFEQSLQL-LLSKRTDATMIPDIPFFN-FLERRPHDGNLF--- 213
F E K + S+ + ++ L + R DA ++ FL++ F
Sbjct: 146 TFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGP 205
Query: 214 KIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ D +RK +N+L ++N+ + DGTY+K+ +YFD ++
Sbjct: 206 SVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDV 257
>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
protein; Provisional.
Length = 243
Score = 82.0 bits (202), Expect = 2e-16
Identities = 62/228 (27%), Positives = 105/228 (46%), Gaps = 14/228 (6%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+R T+ YPP F + D ++ GFD+DL + + ++ F A LI L R
Sbjct: 23 IRFATEASYPP--FESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRR 80
Query: 103 YD-VLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
+ V+ + ITPER+K+ F+ PY + L V Q S L K V GT
Sbjct: 81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFV--GQQGKYTSVDQLKGKKVGVQNGTTHQ 138
Query: 162 RFAKELKSHLV-FSHNFEQSLQL-LLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM 219
+F + + ++ Q+ +L L + R DA +L+ P L + D++
Sbjct: 139 KFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNP---KLAAVGDKV 195
Query: 220 KDN----SAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK 263
D + + +R+GN +L + +N L + DGTY+ I++++F K
Sbjct: 196 TDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQK 243
>gnl|CDD|182785 PRK10859, PRK10859, membrane-bound lytic transglycosylase F;
Provisional.
Length = 482
Score = 73.8 bits (182), Expect = 5e-14
Identities = 62/241 (25%), Positives = 95/241 (39%), Gaps = 42/241 (17%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA-VSGLITGLDTN 101
LRVGT I P ++ G TGF+ +L K A L +K+E +S L LD
Sbjct: 45 LRVGT--INSPLTY-YIGNDGP-TGFEYELAKRFADYLGVKLEIKVRDNISQLFDALDKG 100
Query: 102 RYDVLV-NVAITPERQKKYDFSIPYIAHRVL--LVVRSDQQDIRSFKDLTDKTVAQILGT 158
+ D+ + TPER K++ F PY + V LV R Q RS DL T+ G+
Sbjct: 101 KADLAAAGLTYTPERLKQFRFGPPY--YSVSQQLVYRKGQPRPRSLGDLKGGTLTVAAGS 158
Query: 159 DLSRFAKELKSH---LVF--SHNFEQS--LQLLLSKRTDATMIPDIPFFNFLERRPHDGN 211
+ELK L + S + + L+ + + D T+ D
Sbjct: 159 SHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIA--------------DSV 204
Query: 212 LFKIADRMKDNSAVAF----------MMRKGN-NKLTRSINEILCAIHLDGTYKKIFDRY 260
+ R AVAF + + L ++ + I DGT ++ ++Y
Sbjct: 205 EISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARLEEKY 264
Query: 261 F 261
F
Sbjct: 265 F 265
>gnl|CDD|184972 PRK15010, PRK15010, ABC transporter lysine/arginine/ornithine
binding periplasmic protein; Provisional.
Length = 260
Score = 71.6 bits (175), Expect = 2e-13
Identities = 59/233 (25%), Positives = 104/233 (44%), Gaps = 11/233 (4%)
Query: 42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTN 101
+R+GTD Y P F ++D +G+ GFDIDL E+ R+ +K + + LI L
Sbjct: 27 TVRIGTDTTYAP--FSSKDAKGDFVGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAK 84
Query: 102 RYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDL 160
+ D ++ +++IT +RQ++ FS A L+ + L K V + G+
Sbjct: 85 KIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLDSLKGKHVGVLQGSTQ 144
Query: 161 SRFA----KELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA 216
+A + +V N + L + R DA + ++ ++P +
Sbjct: 145 EAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAG 204
Query: 217 DRMKDNS----AVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+KD +RK + +LT + N+ L + DGTY K+ +YFD N+
Sbjct: 205 PSVKDKKYFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFDFNV 257
>gnl|CDD|132040 TIGR02995, ectoine_ehuB, ectoine/hydroxyectoine ABC transporter
solute-binding protein. Members of this family are the
extracellular solute-binding proteins of ABC
transporters that closely resemble amino acid
transporters. The member from Sinorhizobium meliloti is
involved in ectoine uptake, both for osmoprotection and
for catabolism. All other members of the seed alignment
are found associated with ectoine catabolic genes.
Length = 275
Score = 59.5 bits (144), Expect = 9e-10
Identities = 56/244 (22%), Positives = 102/244 (41%), Gaps = 18/244 (7%)
Query: 38 EDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLK-VEFFETAVSGLIT 96
++Q R+ PP ++ DG+ ++G D+ + + RL + V T LI
Sbjct: 30 KEQGFARIAIAN-EPPFTYVGADGK--VSGAAPDVARAIFKRLGIADVNASITEYGALIP 86
Query: 97 GLDTNRYD-VLVNVAITPERQKKYDFSIPYIAH-RVLLVVRSDQQDIRSFKDLTDK---T 151
GL R+D + + I PER K+ F+ P + LLV + + + ++S+KD+
Sbjct: 87 GLQAGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPKGLKSYKDIAKNPDAK 146
Query: 152 VAQILGTDLSRFAKEL---KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPH 208
+A G + A+E + ++ + + L+++ R DA + + N L +
Sbjct: 147 IAAPGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLTVLTI-NDLASKAG 205
Query: 209 DGNLFKIADRMKDNSAV---AFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRY-FDKN 264
D N+ +A KD R + +L + N L + G + KI Y F
Sbjct: 206 DPNVEVLAP-FKDAPVRYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPYGFSAK 264
Query: 265 IISS 268
S
Sbjct: 265 AAMS 268
>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
aspartate/glutamate-binding protein; Reviewed.
Length = 259
Score = 49.5 bits (118), Expect = 9e-07
Identities = 43/139 (30%), Positives = 67/139 (48%), Gaps = 11/139 (7%)
Query: 63 GELTGFDIDLIKEVA-HRLNLKVEFFETAVSGLITG--LDTNRYD-VLVNVAITPERQKK 118
GE+ GF+ID+ K +A L + AV+ G LD D V+ ITPER++
Sbjct: 59 GEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRI 118
Query: 119 YDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKT--VAQILGTD--LSRFAKELKSHLVFS 174
Y+FS PY + L+V + ++ +S D+ VAQ T + AK++ + FS
Sbjct: 119 YNFSEPYYQDAIGLLVLKE-KNYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFS 177
Query: 175 H--NFEQSLQLLLSKRTDA 191
++ L +KR DA
Sbjct: 178 EFPDYPSIKAALDAKRVDA 196
>gnl|CDD|182740 PRK10797, PRK10797, glutamate and aspartate transporter subunit;
Provisional.
Length = 302
Score = 43.3 bits (102), Expect = 7e-05
Identities = 39/161 (24%), Positives = 72/161 (44%), Gaps = 14/161 (8%)
Query: 114 ERQKKYDFS--IPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD----LSRF--AK 165
ERQK+ FS I + R L+ + DI+ F DL K V GT L++ +
Sbjct: 119 ERQKQAAFSDTIFVVGTR--LLTKKGG-DIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQ 175
Query: 166 ELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLER-RPHDGNLFKIADRMKDNSA 224
++ ++ + + S + L S R A M+ D ER + + ++I + + A
Sbjct: 176 KMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAG--ERAKAKKPDNWEIVGKPQSQEA 233
Query: 225 VAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
M+RK + + + +++ + G +K FD++F I
Sbjct: 234 YGCMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNPI 274
>gnl|CDD|131338 TIGR02285, TIGR02285, conserved hypothetical protein. Members of
this family are found in several Proteobacteria,
including Pseudomonas putida KT2440, Bdellovibrio
bacteriovorus HD100 (three members), Aeromonas
hydrophila, and Chromobacterium violaceum ATCC 12472.
The function is unknown.
Length = 268
Score = 32.1 bits (73), Expect = 0.17
Identities = 37/185 (20%), Positives = 63/185 (34%), Gaps = 44/185 (23%)
Query: 112 TPERQKKYDFSIPYIAHRVL---LVVRSDQQDIRSFKDLTDKTVAQILGTDLSRF--AKE 166
TPER+K FS P R L LV+R + Q DL + +K+
Sbjct: 87 TPEREKFLIFSDP--TLRALPVGLVLRK--------ELTAGVRDEQDGDVDLKKLLASKK 136
Query: 167 LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIP------FFNFLERRPHDGNL---FKIAD 217
+ ++ S ++ Q + +LS I F LE+ + L +
Sbjct: 137 KRLGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGRVNYTLAYPPEKTY 196
Query: 218 RMKDNSA----VAFMMRKGNNKL----------------TRSINEILCAIHLDGTYKKIF 257
+ N+ + F+ G I++ L +++D Y K F
Sbjct: 197 YEELNNGALPPLKFLPVAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYF 256
Query: 258 DRYFD 262
DR+
Sbjct: 257 DRWLS 261
>gnl|CDD|151136 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called
the S1 domain, is the luminal domain just upstream of
the first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 29.1 bits (66), Expect = 1.3
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 60 DGRGELTGFDIDLIKEVAHRLNLKVEF 86
G G+ IDL+ E+A L E
Sbjct: 13 TGNERFEGYCIDLLDELAKILGFNYEI 39
>gnl|CDD|132611 TIGR03572, WbuZ, glycosyl amidation-associated protein WbuZ. This
clade of sequences is highly similar to the HisF
protein, but generally represents the second HisF
homolog in the genome where the other is an authentic
HisF observed in the context of a complete histidine
biosynthesis operon. The similarity between these WbuZ
sequences and true HisFs is such that often the closest
match by BLAST of a WbuZ is a HisF. Only by making a
multiple sequence alignment is the homology relationship
among the WbuZ sequences made apparent. WbuZ genes are
invariably observed in the presence of a homolog of the
HisH protein (designated WbuY) and a proposed N-acetyl
sugar amidotransferase designated in WbuX in E. coli,
IfnA in P. aeriginosa and PseA in C. jejuni. Similarly,
this trio of genes is invariably found in the context of
saccharide biosynthesis loci. It has been shown that the
WbuYZ homologs are not essential components of the
activity expressed by WbuX, leading to the proposal that
these to proteins provide ammonium ions to the
amidotransferase when these are in low concentration.
WbuY (like HisH) is proposed to act as a glutaminase to
release ammonium. In histidine biosynthesis this is also
dispensible in the presence of exogenous ammonium ion.
HisH and HisF form a complex such that the ammonium ion
is passed directly to HisF where it is used in an
amidation reaction causing a subsequent cleavage and
cyclization. In the case of WbuYZ, the ammonium ion
would be passed from WbuY to WbuZ. WbuZ, being
non-essential and so similar to HisF that a sugar
substrate is unlikely, would function instead as a
amoonium channel to the WbuX protein which does the
enzymatic work.
Length = 232
Score = 28.8 bits (65), Expect = 1.8
Identities = 9/26 (34%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 59 QDGRGELTGFDIDLIKEVAHRLNLKV 84
+DG G+D++LIK V+ +++ V
Sbjct: 177 RDGTM--KGYDLELIKTVSDAVSIPV 200
>gnl|CDD|182636 PRK10672, PRK10672, rare lipoprotein A; Provisional.
Length = 361
Score = 28.5 bits (64), Expect = 2.0
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 62 RGELT-GFDIDLIKEVAHRLNL------KVEFFETAVSGLITGLDT 100
RG G IDL + A RLN +++ A G ++G T
Sbjct: 137 RGPYGPGRVIDLSRAAADRLNTSNNTKVRIDPIIVAPDGSLSGPGT 182
>gnl|CDD|135656 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed.
Length = 257
Score = 28.0 bits (62), Expect = 2.9
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 17/66 (25%)
Query: 62 RGELTGFDIDLIKEVAHRL------NLKVE-FFETAVSGLITGLDTNRYDVLVNVAITPE 114
R L F + L+K VAHRL ++K E + + V GL+ ++ R+D PE
Sbjct: 25 RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVE--RFD--------PE 74
Query: 115 RQKKYD 120
+ ++++
Sbjct: 75 KSRRFE 80
>gnl|CDD|185585 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 27.6 bits (62), Expect = 3.5
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 181 LQLLLSKRTDATMIPDIP 198
LQLL+ +D MIP IP
Sbjct: 155 LQLLIGDPSDGVMIP-IP 171
>gnl|CDD|165355 PHA03066, PHA03066, Hypothetical protein; Provisional.
Length = 110
Score = 27.4 bits (61), Expect = 4.1
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 16 YLFFAPFFILFSYYFVIYP 34
YL F F+ SYYF YP
Sbjct: 6 YLLFFIIFLCISYYFNYYP 24
>gnl|CDD|162686 TIGR02074, PBP_1a_fam, penicillin-binding protein, 1A family.
Bacterial that synthesize a cell wall of peptidoglycan
(murein) generally have several transglycosylases and
transpeptidases for the task. This family consists of
bifunctional transglycosylase/transpeptidase
penicillin-binding proteins (PBP). In the
Proteobacteria, this family includes PBP 1A but not the
paralogous PBP 1B (TIGR02071). This family also includes
related proteins, often designated PBP 1A, from other
bacterial lineages.
Length = 530
Score = 27.2 bits (61), Expect = 4.4
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 236 LTRSINEILCAIHLDGTYKK--IFDRYFDK 263
+TR I E L A+ L+ K I + Y ++
Sbjct: 73 ITRKIQEALLALKLEQKLSKDEILELYLNR 102
>gnl|CDD|177374 PHA02539, 18, tail sheath protein; Provisional.
Length = 648
Score = 27.0 bits (60), Expect = 5.4
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 249 LDGTYKKIFDRYFDKN 264
+DG YK +D+Y D N
Sbjct: 441 IDGNYKYQYDKYNDVN 456
>gnl|CDD|178226 PLN02617, PLN02617, imidazole glycerol phosphate synthase hisHF.
Length = 538
Score = 27.0 bits (60), Expect = 5.5
Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 60 DGRGELTGFDIDLIKEVAHRLNLKV 84
DG+G+ GFDI+L+K V+ + + V
Sbjct: 463 DGQGK--GFDIELVKLVSDAVTIPV 485
>gnl|CDD|178178 PLN02564, PLN02564, 6-phosphofructokinase.
Length = 484
Score = 26.6 bits (59), Expect = 6.8
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 184 LLSKRTDATMIPDIPFFNFLERRPHDGNLFK-IADRMKDNSAVAFMMRKG 232
L S+ D +IP+ PF +LE + G LF+ I R+K+N + ++ +G
Sbjct: 272 LASRDVDCCLIPESPF--YLEGK---GGLFEFIEKRLKENGHMVIVVAEG 316
>gnl|CDD|161830 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP).
Length = 851
Score = 26.2 bits (58), Expect = 8.6
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 67 GFDIDLIKEVAHRLNLKVEF--FETAV 91
GF ++L KE+A L V+ FET +
Sbjct: 396 GFPVELTKEIAEERGLTVDIPGFETLM 422
>gnl|CDD|171443 PRK12369, PRK12369, putative transporter; Reviewed.
Length = 326
Score = 26.2 bits (58), Expect = 9.7
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 1 MRRLLRDLRKIFFS---KYLFFAPFFILFSYYFVIYPF 35
+ L LR +F Y +F + I FS VI P+
Sbjct: 227 LIELFTGLRFNYFRLFLHYGYFNIWLISFSQMMVIVPY 264
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
0.327 0.142 0.417
Gapped
Lambda K H
0.267 0.0600 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,602,711
Number of extensions: 294539
Number of successful extensions: 899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 875
Number of HSP's successfully gapped: 38
Length of query: 274
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 182
Effective length of database: 4,006,537
Effective search space: 729189734
Effective search space used: 729189734
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.6 bits)