RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13911
(183 letters)
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 52.8 bits (126), Expect = 2e-08
Identities = 52/167 (31%), Positives = 76/167 (45%), Gaps = 29/167 (17%)
Query: 12 KLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLNKCRQLNTLHVAYNAITSL 71
++ L + N LK LP N ++ LY SN LT I P + + ++ N IT L
Sbjct: 200 QITTLILDNNELKSLPE--NLQGNIKTLYANSNQLTSI-PATLPDTIQEMELSINRITEL 256
Query: 72 PDNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPTLYLSSSLRVL 131
P+ SA ++ L L N IS LP +P+ LR L ++ N + + P +L S + L
Sbjct: 257 PERLPSA---LQSLDLFHNKISCLPENLPEE---LRYLSVYDNSIRTLPA-HLPSGITHL 309
Query: 132 DLSYNHLERL------NLNTL-------------IPKQLQYLDVSGN 159
++ N L L L TL +P +LQ LDVS N
Sbjct: 310 NVQSNSLTALPETLPPGLKTLEAGENALTSLPASLPPELQVLDVSKN 356
Score = 50.9 bits (121), Expect = 8e-08
Identities = 43/129 (33%), Positives = 69/129 (53%), Gaps = 10/129 (7%)
Query: 13 LKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLNKCRQLNTLHVAYNAITSLP 72
L+ L++ N ++ LP+ + + L + SN+LT + P L TL NA+TSLP
Sbjct: 285 LRYLSVYDNSIRTLPA--HLPSGITHLNVQSNSLTAL-PETLPPGLKTLEAGENALTSLP 341
Query: 73 DNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPTLYLSSSLRVLD 132
S E++ L +S N I+ LP T+P P + L + N LT+ P L ++L+++
Sbjct: 342 A---SLPPELQVLDVSKNQITVLPETLP---PTITTLDVSRNALTNLPE-NLPAALQIMQ 394
Query: 133 LSYNHLERL 141
S N+L RL
Sbjct: 395 ASRNNLVRL 403
Score = 35.8 bits (82), Expect = 0.010
Identities = 34/109 (31%), Positives = 53/109 (48%), Gaps = 18/109 (16%)
Query: 4 ELFLQNSS----------KLKVLNISKNCLKMLP-SLNNENRYLEKLYLTSNALTDIGPL 52
L +Q++S LK L +N L LP SL E L+ L ++ N +T + P
Sbjct: 308 HLNVQSNSLTALPETLPPGLKTLEAGENALTSLPASLPPE---LQVLDVSKNQIT-VLPE 363
Query: 53 NKCRQLNTLHVAYNAITSLPDNCISAWSEMEELVLSGNGISSLPNTIPQ 101
+ TL V+ NA+T+LP+N +A M+ S N + LP ++P
Sbjct: 364 TLPPTITTLDVSRNALTNLPENLPAALQIMQA---SRNNLVRLPESLPH 409
>gnl|CDD|185285 PRK15387, PRK15387, E3 ubiquitin-protein ligase SspH2; Provisional.
Length = 788
Score = 48.2 bits (114), Expect = 7e-07
Identities = 51/137 (37%), Positives = 71/137 (51%), Gaps = 14/137 (10%)
Query: 11 SKLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLNKCRQLNTLHVAYNAITS 70
S L+ L++S N L LP+L +E L KL+ +N LT + L L L V+ N +TS
Sbjct: 342 SGLQELSVSDNQLASLPTLPSE---LYKLWAYNNRLTSLPALPS--GLKELIVSGNRLTS 396
Query: 71 LPDNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCP-TLYLSSSLR 129
LP SE++EL++SGN ++SLP +P L V R N LT P +L SS
Sbjct: 397 LP----VLPSELKELMVSGNRLTSLP-MLPSGLLSLSVYR---NQLTRLPESLIHLSSET 448
Query: 130 VLDLSYNHLERLNLNTL 146
++L N L L L
Sbjct: 449 TVNLEGNPLSERTLQAL 465
Score = 38.2 bits (88), Expect = 0.002
Identities = 48/136 (35%), Positives = 62/136 (45%), Gaps = 17/136 (12%)
Query: 24 KMLPSLNNENRYLEKLYLTSNALTDIGPLNKCRQLNTLHVAYNAITSLPDNCISAWSEME 83
KM LNN N L L D P + + TL + N +TSLP + E+
Sbjct: 194 KMRACLNNGNAVLNVGESGLTTLPDCLPAH----ITTLVIPDNNLTSLP----ALPPELR 245
Query: 84 ELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPTLYLSSSLRVLDLSYNHLERLNL 143
L +SGN ++SLP +P P L L + SN LT P L S L L + N L L
Sbjct: 246 TLEVSGNQLTSLP-VLP---PGLLELSIFSNPLTHLPA--LPSGLCKLWIFGNQLTSL-- 297
Query: 144 NTLIPKQLQYLDVSGN 159
++P LQ L VS N
Sbjct: 298 -PVLPPGLQELSVSDN 312
>gnl|CDD|238064 cd00116, LRR_RI, Leucine-rich repeats (LRRs), ribonuclease
inhibitor (RI)-like subfamily. LRRs are 20-29 residue
sequence motifs present in many proteins that
participate in protein-protein interactions and have
different functions and cellular locations. LRRs
correspond to structural units consisting of a beta
strand (LxxLxLxxN/CxL conserved pattern) and an alpha
helix. This alignment contains 12 strands corresponding
to 11 full repeats, consistent with the extent observed
in the subfamily acting as Ran GTPase Activating
Proteins (RanGAP1).
Length = 319
Score = 45.4 bits (108), Expect = 4e-06
Identities = 46/156 (29%), Positives = 57/156 (36%), Gaps = 38/156 (24%)
Query: 36 LEKLYLTSNALTDIG------PLNKCRQLNTLHVAYNAIT---------SLPDNCISAWS 80
LEKL L N L L R L L++A N I L NC
Sbjct: 139 LEKLVLGRNRLEGASCEALAKALRANRDLKELNLANNGIGDAGIRALAEGLKANC----- 193
Query: 81 EMEELVLSGN-----GISSLPNTIPQSWPHLRVLRLHSNHLTSCPTLYLSS-------SL 128
+E L L+ N G S+L T+ L VL L N+LT L+S SL
Sbjct: 194 NLEVLDLNNNGLTDEGASALAETLAS-LKSLEVLNLGDNNLTDAGAAALASALLSPNISL 252
Query: 129 RVLDLSYNHLERLNLNTLIP-----KQLQYLDVSGN 159
L LS N + L + L LD+ GN
Sbjct: 253 LTLSLSCNDITDDGAKDLAEVLAEKESLLELDLRGN 288
Score = 33.9 bits (78), Expect = 0.033
Identities = 38/154 (24%), Positives = 54/154 (35%), Gaps = 36/154 (23%)
Query: 2 ALELFLQNSSKLKVLNISKNCL------KMLPSLNNENRYLEKLYLTSNALTDIGPLNKC 55
AL L+ + LK LN++ N + + L N LE L L +N LTD G
Sbjct: 156 ALAKALRANRDLKELNLANNGIGDAGIRALAEGLK-ANCNLEVLDLNNNGLTDEG----A 210
Query: 56 RQLNTLHVAYNAITSLPDNCISAWSEMEELVLSGN-----GISSLPNTIPQSWPHLRVLR 110
L +++ +E L L N G ++L + + L L
Sbjct: 211 SALA--------------ETLASLKSLEVLNLGDNNLTDAGAAALASALLSPNISLLTLS 256
Query: 111 LHSNHLTS------CPTLYLSSSLRVLDLSYNHL 138
L N +T L SL LDL N
Sbjct: 257 LSCNDITDDGAKDLAEVLAEKESLLELDLRGNKF 290
>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat.
Length = 60
Score = 38.7 bits (91), Expect = 7e-05
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 57 QLNTLHVAYNAITSLPDNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHL 116
L +L ++ N +T +PD ++ L LSGN ++S+ P LR L L N+L
Sbjct: 1 NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNNL 60
Score = 35.2 bits (82), Expect = 0.001
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 83 EELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCP--TLYLSSSLRVLDLSYNHL 138
+ L LS N ++ +P+ + P+L+VL L N+LTS SLR LDLS N+L
Sbjct: 3 KSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNNL 60
Score = 35.2 bits (82), Expect = 0.002
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 105 HLRVLRLHSNHLTSCPTLYLS--SSLRVLDLSYNHLERLNLNTLI-PKQLQYLDVSGNP 160
+L+ L L +N LT P +L+VLDLS N+L ++ L+ LD+SGN
Sbjct: 1 NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNN 59
Score = 34.1 bits (79), Expect = 0.004
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 36 LEKLYLTSNALTDIGP--LNKCRQLNTLHVAYNAITSLPDNCISAWSEMEELVLSGNGI 92
L+ L L++N LT I L L ++ N +TS+ S + L LSGN +
Sbjct: 2 LKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNNL 60
Score = 26.4 bits (59), Expect = 2.2
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 12 KLKVLNISKNCLKMLP--SLNNENRYLEKLYLTSNALTDIGP--LNKCRQLNTLHVAYNA 67
LK L++S N L ++P + L+ L L+ N LT I P + L +L ++ N
Sbjct: 1 NLKSLDLSNNRLTVIPDGAFKGLPN-LKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNN 59
Query: 68 I 68
+
Sbjct: 60 L 60
Score = 25.2 bits (56), Expect = 5.3
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 127 SLRVLDLSYNHLERLNLNTLI-PKQLQYLDVSGNPRLHVDPNHFK 170
+L+ LDLS N L + L+ LD+SGN + P F
Sbjct: 1 NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFS 45
>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function
unknown].
Length = 394
Score = 40.7 bits (95), Expect = 2e-04
Identities = 53/164 (32%), Positives = 79/164 (48%), Gaps = 5/164 (3%)
Query: 9 NSSKLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLN-KCRQLNTLHVAYNA 67
S LK L++S N ++ LPS L+ L L+ N L+D+ L LN L ++ N
Sbjct: 138 LKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNNLDLSGNK 197
Query: 68 ITSLPDNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPT-LYLSS 126
I+ LP I S +EEL LS N I L +++ +L L L +N L P + S
Sbjct: 198 ISDLPPE-IELLSALEELDLSNNSIIELLSSLSNL-KNLSGLELSNNKLEDLPESIGNLS 255
Query: 127 SLRVLDLSYNHLERLNLNTLIPKQLQYLDVSGNPRLHVDPNHFK 170
+L LDLS N + ++ + L+ LD+SGN + P
Sbjct: 256 NLETLDLSNNQISSISSLGSLTN-LRELDLSGNSLSNALPLIAL 298
Score = 35.7 bits (82), Expect = 0.009
Identities = 50/163 (30%), Positives = 73/163 (44%), Gaps = 5/163 (3%)
Query: 1 MALELFLQNSSKLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPL--NKCRQL 58
+ L N L L+++ N L+ S E L L L +N +TDI PL L
Sbjct: 83 LDGSENLLNLLPLPSLDLNLNRLRSNISELLELTNLTSLDLDNNNITDIPPLIGLLKSNL 142
Query: 59 NTLHVAYNAITSLPDNCISAWSEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTS 118
L ++ N I SLP + ++ L LS N +S LP + +L L L N ++
Sbjct: 143 KELDLSDNKIESLPS-PLRNLPNLKNLDLSFNDLSDLPKLLSNL-SNLNNLDLSGNKISD 200
Query: 119 CP-TLYLSSSLRVLDLSYNHLERLNLNTLIPKQLQYLDVSGNP 160
P + L S+L LDLS N + L + K L L++S N
Sbjct: 201 LPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNK 243
Score = 28.4 bits (63), Expect = 2.2
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 82 MEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPTL--YLSSSLRVLDLSYNHLE 139
+ L L+ N + S + + + +L L L +N++T P L L S+L+ LDLS N +E
Sbjct: 95 LPSLDLNLNRLRSNISELLEL-TNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIE 153
Query: 140 RLNLNTLIPKQLQYLDVSGNPRLHVDPNHFKS 171
L L+ LD+S N +
Sbjct: 154 SLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNL 185
Score = 26.9 bits (59), Expect = 7.9
Identities = 19/75 (25%), Positives = 31/75 (41%)
Query: 5 LFLQNSSKLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLNKCRQLNTLHVA 64
L N L L +S N L+ LP LE L L++N ++ I L L L ++
Sbjct: 226 SSLSNLKNLSGLELSNNKLEDLPESIGNLSNLETLDLSNNQISSISSLGSLTNLRELDLS 285
Query: 65 YNAITSLPDNCISAW 79
N++++
Sbjct: 286 GNSLSNALPLIALLL 300
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number
of proteins with diverse functions and cellular
locations. These repeats are usually involved in
protein-protein interactions. Each Leucine Rich Repeat
is composed of a beta-alpha unit. These units form
elongated non-globular structures. Leucine Rich Repeats
are often flanked by cysteine rich domains.
Length = 43
Score = 35.5 bits (83), Expect = 9e-04
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 36 LEKLYLTSNALTDIGPLNKCRQLNTLHVAYNAITSLP 72
LE L L++N +TD+ PL+ L TL ++ N IT L
Sbjct: 3 LETLDLSNNQITDLPPLSNLPNLETLDLSGNKITDLS 39
Score = 32.8 bits (76), Expect = 0.008
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 12 KLKVLNISKNCLKMLPSLNNENRYLEKLYLTSNALTDIGPLNK 54
L+ L++S N + LP L+N LE L L+ N +TD+ PL+
Sbjct: 2 NLETLDLSNNQITDLPPLSN-LPNLETLDLSGNKITDLSPLSN 43
Score = 30.2 bits (69), Expect = 0.065
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 104 PHLRVLRLHSNHLTSCPTLYLSSSLRVLDLSYNHLERLN 142
+L L L +N +T P L +L LDLS N + L+
Sbjct: 1 TNLETLDLSNNQITDLPPLSNLPNLETLDLSGNKITDLS 39
Score = 26.3 bits (59), Expect = 1.8
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 83 EELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSCPTL 122
E L LS N I+ LP + P+L L L N +T L
Sbjct: 4 ETLDLSNNQITDLPP--LSNLPNLETLDLSGNKITDLSPL 41
Score = 25.5 bits (57), Expect = 3.2
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 57 QLNTLHVAYNAITSLPDNCISAWSEMEELVLSGNGISSLPN 97
L TL ++ N IT LP +S +E L LSGN I+ L
Sbjct: 2 NLETLDLSNNQITDLPP--LSNLPNLETLDLSGNKITDLSP 40
Score = 25.5 bits (57), Expect = 3.6
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 127 SLRVLDLSYNHLERLN-LNTLIPKQLQYLDVSGNP 160
+L LDLS N + L L+ L L+ LD+SGN
Sbjct: 2 NLETLDLSNNQITDLPPLSNL--PNLETLDLSGNK 34
>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional.
Length = 623
Score = 37.1 bits (86), Expect = 0.004
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 73 DNCISAWSEMEELVLSGNGISS-LPNTIPQSWPHLRVLRLHSNHLTSC--PTLYLSSSLR 129
D+ W ++ L L G+ +PN I + HL+ + L N + P+L +SL
Sbjct: 412 DSTKGKWF-IDGLGLDNQGLRGFIPNDISK-LRHLQSINLSGNSIRGNIPPSLGSITSLE 469
Query: 130 VLDLSYNHLERLNLNTLIPK------QLQYLDVSGN 159
VLDLSYN + N IP+ L+ L+++GN
Sbjct: 470 VLDLSYN-----SFNGSIPESLGQLTSLRILNLNGN 500
>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein
kinase; Provisional.
Length = 968
Score = 30.2 bits (68), Expect = 0.58
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 80 SEMEELVLSGNGISSLPNTIPQSWPHLRVLRLHSNHLTSC---PTLYLSSSLRVLDLSYN 136
S + + LSG IS ++ P+++ + L +N L+ SSSLR L+LS N
Sbjct: 69 SRVVSIDLSGKNISGKISSAIFRLPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLSNN 128
Query: 137 HLERLNLNTLIPKQLQYLDVSGN 159
+ IP L+ LD+S N
Sbjct: 129 NFTGSIPRGSIP-NLETLDLSNN 150
Score = 27.5 bits (61), Expect = 4.5
Identities = 35/119 (29%), Positives = 56/119 (47%), Gaps = 11/119 (9%)
Query: 27 PSLNNENRYLEKLYLTSNALTDIGP--LNKCRQLNTLHVAYNAITSLPDNCISAWSEMEE 84
SL N L+ L+L N L+ P + ++L +L ++ N+++ + +E
Sbjct: 254 SSLGNLKN-LQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNSLSGEIPELVIQLQNLEI 312
Query: 85 LVLSGNGISSLPNTIPQ---SWPHLRVLRLHSNHLTS--CPTLYLSSSLRVLDLSYNHL 138
L L N + IP S P L+VL+L SN + L ++L VLDLS N+L
Sbjct: 313 LHLFSN---NFTGKIPVALTSLPRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLSTNNL 368
>gnl|CDD|176127 cd08436, PBP2_LTTR_like_3, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 194
Score = 29.5 bits (67), Expect = 0.70
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 82 MEELVLSGNGISSLPNTIPQSWPHLRVLRLH 112
+ +LV G G++ LP ++ P L L L
Sbjct: 137 LLDLVARGLGVALLPASVAARLPGLAALPLE 167
>gnl|CDD|176129 cd08438, PBP2_CidR, The C-terminal substrate binding domain of
LysR-like transcriptional regulator CidR, contains the
type 2 periplasmic binding fold. This CD includes the
substrate binding domain of CidR which positively
up-regulates the expression of cidABC operon in the
presence of acetic acid produced by the metabolism of
excess glucose. The CidR affects the control of murein
hydrolase activity by enhancing cidABC expression in the
presence of acetic acid. Thus, up-regulation of cidABC
expression results in increased murein hydrolase
activity. This substrate binding domain has significant
homology to the type 2 periplasmic binding proteins
(PBP2), which are responsible for the uptake of a
variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 29.1 bits (66), Expect = 1.0
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 11/62 (17%)
Query: 39 LYLTSNALTDIGPLNKCRQLN-TLHVAYNAITSLPDNCISAWSEMEELVLSGNGISSLPN 97
L+ AL D ++ C+Q T ++A S W + ELV +G G++ LP
Sbjct: 102 LFNEDFALHDR-IIDACQQAGFTPNIAA---------RSSQWDFIAELVAAGLGVALLPR 151
Query: 98 TI 99
+I
Sbjct: 152 SI 153
>gnl|CDD|176140 cd08449, PBP2_XapR, The C-terminal substrate binding domain of
LysR-type transcriptional regulator XapR involved in
xanthosine catabolism, contains the type 2 periplasmic
binding fold. In Escherichia coli, XapR is a positive
regulator for the expression of xapA gene, encoding
xanthosine phosphorylase, and xapB gene, encoding a
polypeptide similar to the nucleotide transport protein
NupG. As an operon, the expression of both xapA and xapB
is fully dependent on the presence of both XapR and the
inducer xanthosine. Expression of the xapR is
constitutive but not auto-regulated, unlike many other
LysR family proteins. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 29.2 bits (66), Expect = 1.1
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 85 LVLSGNGISSLPNTIPQ-SWPHLRVLRL 111
LV +G G++ +P + + WP +R + L
Sbjct: 142 LVAAGFGVALVPESYARLPWPGVRFIPL 169
>gnl|CDD|234245 TIGR03528, 2_3_DAP_am_ly, diaminopropionate ammonia-lyase. Members
of this protein family are the homodimeric, pyridoxal
phosphate enzyme diaminopropionate ammonia-lyase, which
adds water to remove two amino groups, leaving pyruvate.
Length = 396
Score = 28.9 bits (65), Expect = 1.6
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 96 PNTIPQSWPHLRVLRLHSNHLTSCPTLYLSSSLRVL 131
PNTI W +LR +++ SCP + +R+L
Sbjct: 298 PNTI--GWE---ILRDYASQFISCPDWVAAKGMRIL 328
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 29.0 bits (64), Expect = 1.7
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 14/63 (22%)
Query: 55 CRQLNT--LHVAYNAITSLPDN--CISAWSEMEELV---------LSGNGISSLPNTIPQ 101
C+ LN L A NA++ PDN C +A S + E + L G+SS+ N + +
Sbjct: 325 CKALNARGLSTALNALSKWPDNPVCAAAVSALAERLVADPELRKDLEPQGVSSVLNALSK 384
Query: 102 SWP 104
WP
Sbjct: 385 -WP 386
>gnl|CDD|133162 cd06098, phytepsin, Phytepsin, a plant homolog of mammalian
lysosomal pepsins. Phytepsin, a plant homolog of
mammalian lysosomal pepsins, resides in grains, roots,
stems, leaves and flowers. Phytepsin may participate in
metabolic turnover and in protein processing events. In
addition, it highly expressed in several plant tissues
undergoing apoptosis. Phytepsin contains an internal
region consisting of about 100 residues not present in
animal or microbial pepsins. This region is thus called
a plant specific insert. The insert is highly similar to
saponins, which are lysosomal sphingolipid-activating
proteins in mammalian cells. The saponin-like domain may
have a role in the vacuolar targeting of phytepsin.
Phytepsin, as its animal counterparts, possesses a
topology typical of all aspartic proteases. They are
bilobal enzymes, each lobe contributing a catalytic Asp
residue, with an extended active site cleft localized
between the two lobes of the molecule. One lobe has
probably evolved from the other through a gene
duplication event in the distant past. This family of
aspartate proteases is classified by MEROPS as the
peptidase family A1 (pepsin A, clan AA).
Length = 317
Score = 28.5 bits (64), Expect = 1.7
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 164 VDPNHFKSYRSYVRV 178
VDP HFK +YV V
Sbjct: 170 VDPKHFKGEHTYVPV 184
>gnl|CDD|129876 TIGR00794, kup, potassium uptake protein. Proteins of the KUP
family include the KUP (TrkD) protein of E. coli, a
partially sequenced ORF from Lactococcus lactis, high
affinity K+ uptake systems (Hak1) of the yeast
Debaryomyces occidentalis as well as the fungus,
Neurospora crassa, and several homologues in plants.
While the E. coli KUP protein is assumed to be a
secondary transporter, and uptake is blocked by
protonophores such as CCCP (but not arsenate), the
energy coupling mechanism has not been defined. However,
the N. crassa protein has been shown to be a K+:H+
symporter, establishing that the KUP family consists of
secondary carriers. The plant high affinity (20mM) K+
transporter can complement K+ uptake defects in E. coli
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 688
Score = 27.4 bits (61), Expect = 4.7
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 87 LSGNGI--SSLPNTIPQSWPHLRVLRLHSNHLTSCPTLYLSSSLRVLDLSYNH-LERLNL 143
+ G GI S+L N IP + HL S +++ SLR LD H ER+ +
Sbjct: 500 VPGIGIYYSNLVNGIPAVFGHL------VTKFPSIHEVFIFLSLRTLDAPTVHNEERVQI 553
Query: 144 NTLIPKQLQY 153
+ + P + Y
Sbjct: 554 SQVGPTEGMY 563
>gnl|CDD|217281 pfam02910, Succ_DH_flav_C, Fumarate reductase flavoprotein C-term.
This family contains fumarate reductases, succinate
dehydrogenases and L-aspartate oxidases.
Length = 127
Score = 26.4 bits (59), Expect = 5.6
Identities = 10/29 (34%), Positives = 11/29 (37%)
Query: 151 LQYLDVSGNPRLHVDPNHFKSYRSYVRVY 179
L Y D G PRL +P R Y
Sbjct: 99 LAYYDGDGGPRLDYEPVVITRIPPKERSY 127
>gnl|CDD|197688 smart00370, LRR, Leucine-rich repeats, outliers.
Length = 24
Score = 24.2 bits (54), Expect = 7.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 126 SSLRVLDLSYNHLERL 141
+LR LDLS N L L
Sbjct: 2 PNLRELDLSNNQLSSL 17
>gnl|CDD|197687 smart00369, LRR_TYP, Leucine-rich repeats, typical (most populated)
subfamily.
Length = 24
Score = 24.2 bits (54), Expect = 7.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 126 SSLRVLDLSYNHLERL 141
+LR LDLS N L L
Sbjct: 2 PNLRELDLSNNQLSSL 17
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.395
Gapped
Lambda K H
0.267 0.0925 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,010,628
Number of extensions: 788929
Number of successful extensions: 705
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 64
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.7 bits)
S2: 56 (25.0 bits)