RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1891
(158 letters)
>gnl|CDD|216561 pfam01545, Cation_efflux, Cation efflux family. Members of this
family are integral membrane proteins, that are found to
increase tolerance to divalent metal ions such as
cadmium, zinc, and cobalt. These proteins are thought to
be efflux pumps that remove these ions from cells.
Length = 273
Score = 53.1 bits (128), Expect = 5e-09
Identities = 30/157 (19%), Positives = 57/157 (36%), Gaps = 38/157 (24%)
Query: 1 MGLTLYTGSHIPDAVGSFLVGGILGCVAYFIVSSNIEALVGRSIPDDYLDKINAELESDV 60
+ L L TG I D + S L+ ++ ++ ++ L+G S + +D+I LE
Sbjct: 148 LLLILLTGLPIADPLASLLIALLILYTGLRLLKESLSELLGASPDPELVDEIRDALEKLP 207
Query: 61 MIRAIYDVKGIQMGNSLIRYKAEVDFDGRELTRSYLDKQDLNTMLEEVQNMKTIDEMEAF 120
+ ++D++ + G ++ EV T++E
Sbjct: 208 GVLGVHDLRVWKSGPKYF---VDIHI--------------------EVDPDLTVEEAHEI 244
Query: 121 LLKHSENIVDMVGGEIDRIEMKLRKKYPDIRHVDLEV 157
D IE L++K+P I V + V
Sbjct: 245 ---------------ADEIERALKEKFPGIADVTIHV 266
>gnl|CDD|223131 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 38.8 bits (91), Expect = 5e-04
Identities = 12/75 (16%), Positives = 35/75 (46%)
Query: 3 LTLYTGSHIPDAVGSFLVGGILGCVAYFIVSSNIEALVGRSIPDDYLDKINAELESDVMI 62
L G D + + L+ + + + ++ L+ ++ + L+KI A + S +
Sbjct: 171 LGSLLGWPWLDPLAALLISLYILKTGFRLFKESVNELMDAALDPEDLEKIRAIILSVPGV 230
Query: 63 RAIYDVKGIQMGNSL 77
+ ++D++ + G+ +
Sbjct: 231 KGVHDLRTRKSGSRI 245
>gnl|CDD|182529 PRK10536, PRK10536, hypothetical protein; Provisional.
Length = 262
Score = 32.8 bits (75), Expect = 0.052
Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 19/90 (21%)
Query: 63 RAIYDVKGIQMGNSLIRY-------KAEV----DFDGRELTRSYLDKQDLNTMLEEVQNM 111
R +YDV ++G S ++Y K E+ GR + + +L+E QN+
Sbjct: 136 RPVYDVLVRRLGASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVV-------ILDEAQNV 188
Query: 112 KTIDEMEAFLLKHSENIVDMVGGEIDRIEM 141
T +M+ FL + EN+ +V G+I + ++
Sbjct: 189 -TAAQMKMFLTRLGENVTVIVNGDITQCDL 217
>gnl|CDD|220432 pfam09835, DUF2062, Uncharacterized protein conserved in bacteria
(DUF2062). This domain, found in various prokaryotic
proteins, has no known function.
Length = 148
Score = 29.8 bits (68), Expect = 0.31
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 15 VGSFLVGGILGCVAYFIV 32
+GS ++G +L + YF+V
Sbjct: 116 LGSLVLGLVLALLGYFLV 133
>gnl|CDD|148846 pfam07471, Phage_Nu1, Phage DNA packaging protein Nu1. Terminase,
the DNA packaging enzyme of bacteriophage lambda, is a
heteromultimer composed of subunits Nu1 and A. The
smaller Nu1 terminase subunit has a low-affinity ATPase
stimulated by non-specific DNA.
Length = 164
Score = 29.9 bits (67), Expect = 0.36
Identities = 15/73 (20%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 84 VDFDGRELTRSYLDKQDLNTMLEEVQNMKTIDEMEAFLLKHSENIVDMVGGEIDRIEMKL 143
+D++ LTR+ D Q+L + + ++T F + + +D I + +
Sbjct: 82 IDYERHRLTRAQADAQELKNARDSAEVVET-----EFCTFVLSRVAAEIASILDGIPLSV 136
Query: 144 RKKYPDI--RHVD 154
++++P++ RH+D
Sbjct: 137 QRRFPELENRHID 149
>gnl|CDD|235870 PRK06834, PRK06834, hypothetical protein; Provisional.
Length = 488
Score = 30.4 bits (69), Expect = 0.41
Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 55 ELESDVMIRAIYDVKGIQMGNSLIRYKAEVDFDGRELTRSYL 96
EL +RA Y V G G SL+R A +DF G + T SYL
Sbjct: 136 ELSDGRTLRAQYLV-GCDGGRSLVRKAAGIDFPGWDPTTSYL 176
>gnl|CDD|131901 TIGR02854, spore_II_GA, sigma-E processing peptidase SpoIIGA.
Members of this protein family are the stage II
sporulation protein SpoIIGA. This protein acts as an
activating protease for Sigma-E, one of several
specialized sigma factors of the sporulation process in
Bacillus subtilis and related endospore-forming bacteria
[Cellular processes, Sporulation and germination].
Length = 288
Score = 29.2 bits (66), Expect = 0.71
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 15 VGSFLVGGILGCVAYFIVSSNIEALVGRSIPDDYLDK---INAELESDVMIRAIYDVKGI 71
SF GG L + +F+ ++N AL I D K I + + R + ++
Sbjct: 93 FVSFATGGGLFALHFFL-ATNEPALFNAFIGDGVSWKFILIGFPILYYFVKRRMDAIRDR 151
Query: 72 QMGNSLIRYKAEVDFDGRELT-RSYLD 97
+ + I Y+ E+ DG+++T + +LD
Sbjct: 152 AILDKQI-YELEICLDGKKVTIKGFLD 177
>gnl|CDD|172710 PRK14222, PRK14222, camphor resistance protein CrcB; Provisional.
Length = 124
Score = 28.5 bits (64), Expect = 0.73
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 22 GILGCVAYFIVSSNIEALVGRSIP 45
G LGC+A + +S + AL GR+ P
Sbjct: 11 GALGCLARYYLSGWVYALFGRAFP 34
>gnl|CDD|129272 TIGR00168, infC, translation initiation factor IF-3. infC uses
abnormal initiation codons such as AUA, AUC, and CUG
which render its expression particularly sensitive to
excess of its gene product IF-3 thereby regulating its
own expression [Protein synthesis, Translation factors].
Length = 165
Score = 28.9 bits (65), Expect = 0.86
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 81 KAEVDFDGRELTRSYLDKQDLNTMLEEVQNMKTIDE 116
K V F GRE T L ++ L+ +V ++ +++
Sbjct: 111 KFTVRFRGRESTHIELGEKVLDRFYTDVADVAEVEK 146
>gnl|CDD|216577 pfam01569, PAP2, PAP2 superfamily. This family includes the enzyme
type 2 phosphatidic acid phosphatase (PAP2),
Glucose-6-phosphatase EC:3.1.3.9,
Phosphatidylglycerophosphatase B EC:3.1.3.27 and
bacterial acid phosphatase EC:3.1.3.2. The family also
includes a variety of haloperoxidases that function by
oxidising halides in the presence of hydrogen peroxide
to form the corresponding hypohalous acids.
Length = 123
Score = 28.2 bits (63), Expect = 1.1
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 1 MGLT-LYTGSHIP-DAVGSFLVGGILGCVAYFIVSSNIE 37
+GL+ +Y G+H P D + L+G ++ + Y ++ E
Sbjct: 85 VGLSRVYLGAHFPSDVLAGALLGALVALLVYRLLKKLRE 123
>gnl|CDD|233348 TIGR01297, CDF, cation diffusion facilitator family transporter.
This model describes a broadly distributed family of
transporters, a number of which have been shown to
transport divalent cations of cobalt, cadmium and/or
zinc. The family has six predicted transmembrane
domains. Members of the family are variable in length
because of variably sized inserts, often containing
low-complexity sequence [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 268
Score = 28.7 bits (65), Expect = 1.1
Identities = 15/83 (18%), Positives = 39/83 (46%)
Query: 6 YTGSHIPDAVGSFLVGGILGCVAYFIVSSNIEALVGRSIPDDYLDKINAELESDVMIRAI 65
Y G H D + + L+ ++ A+ ++ +I L+ + ++ L++I + S ++ +
Sbjct: 151 YFGWHWADPIAALLISLLILYTAFRLLKESINVLLDAAPDEEDLEEIKKAILSIPGVKGV 210
Query: 66 YDVKGIQMGNSLIRYKAEVDFDG 88
+D+ ++G + V D
Sbjct: 211 HDLHIWRIGPGKLFLDVHVVVDP 233
>gnl|CDD|237643 PRK14228, PRK14228, camphor resistance protein CrcB; Provisional.
Length = 122
Score = 27.8 bits (62), Expect = 1.4
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 15 VGSFLVGGILGCVAYFIVSSNIEALVGRSIP 45
+G L+GG +G V F+V + + R+ P
Sbjct: 8 IGVMLIGG-IGSVLRFLVDRTVARRLARTFP 37
>gnl|CDD|144565 pfam01024, Colicin, Colicin pore forming domain.
Length = 187
Score = 28.1 bits (63), Expect = 1.7
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 9 SHIPDAVGSFLVGGILGCVAYFIVSSNIEALVGRSIPDDYLDKINAEL 56
S + V S +G LG + I+ + + AL+ D+++DK+N E+
Sbjct: 144 SAVVALVFSATLGTALGIIGIAIIMAIVGALID----DNFVDKLNNEI 187
>gnl|CDD|239489 cd03395, PAP2_like_4, PAP2_like_4 proteins. PAP2 is a super-family
of phosphatases and haloperoxidases. This subgroup,
which is specific to bacteria, lacks functional
characterization and may act as a membrane-associated
lipid phosphatase.
Length = 177
Score = 28.0 bits (63), Expect = 1.9
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 5 LYTGSHIP-DAVGSFLVGGILGCVAYFI 31
+Y G H P D + L+G I G + Y +
Sbjct: 146 VYVGVHYPGDVIAGALIGIISGLLFYLL 173
>gnl|CDD|147296 pfam05038, Cytochrom_B558a, Cytochrome Cytochrome b558
alpha-subunit. Cytochrome b-245 light chain (p22-phox)
is one of the key electron transfer elements of the
NADPH oxidase in phagocytes.
Length = 186
Score = 27.6 bits (61), Expect = 2.5
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 5 LYTGSHIPDAVGSFLVGGILGCVAYFIVSS 34
L+ +P FL+ ILG V FI S
Sbjct: 92 LHLALCVP---AGFLLATILGTVCLFIASI 118
>gnl|CDD|234058 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase.
Members of this protein family have a novel N-terminal
domain, a single predicted membrane-spanning helix, and
a predicted cystosolic histidine kinase domain. We
designate this protein PrsK, and its companion
DNA-binding response regulator protein (TIGR02915) PrsR.
These predicted signal-transducing proteins appear to
enable enhancer-dependent transcriptional activation.
The prsK gene is often associated with exopolysaccharide
biosynthesis genes [Protein fate, Protein and peptide
secretion and trafficking, Signal transduction,
Two-component systems].
Length = 679
Score = 27.8 bits (62), Expect = 3.3
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 79 RYKAEVDFDGRELTR-------SYLDKQDLNTMLEEVQNMKTIDEMEAFLLKHSENIV 129
R E +++ R+L + SYL + + + L E + + + M AF++ +N+V
Sbjct: 433 RTAGEFNWEVRDLLKTAGRQAASYLAQMEASEALAEARQFEAFNRMSAFVVHDLKNLV 490
>gnl|CDD|118668 pfam10140, YukC, WXG100 protein secretion system (Wss), protein
YukC. Members of this family of proteins include
predicted membrane proteins homologous to YukC in B.
subtilis. The YukC protein family would participate to
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria, the
WXG100 protein secretion system (Wss). This family
includes EssB in Staphylococcus aureus.
Length = 359
Score = 27.2 bits (61), Expect = 4.0
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 10/56 (17%)
Query: 77 LIRYKA--------EVDFDGRELTRSYLDKQDLNTMLEEVQNMKTIDEMEAFLLKH 124
L YKA + F+ EL L+ L+ +E+ +T++E+ AF+ +
Sbjct: 118 LKEYKAFIIALFDGKYSFE--ELYLGSLETLKLSPFEKEILEAETLEELLAFIDES 171
>gnl|CDD|235957 PRK07193, fliF, flagellar MS-ring protein; Reviewed.
Length = 552
Score = 27.3 bits (61), Expect = 4.8
Identities = 22/88 (25%), Positives = 32/88 (36%), Gaps = 6/88 (6%)
Query: 33 SSNIEALVGRSIPDDYLDKINAELESDVMIRA---IYDVKGIQMGNSLIRYKAEVDFDGR 89
S+ I A S + ELE + A + V G GN + A+VDF
Sbjct: 225 SAGINANGDGSQASKKQLEYAQELEQSTIKNAASMLTPVLGP--GNFRVSVAADVDFSRV 282
Query: 90 ELTRSYLDKQDLNTMLEEVQNMKTIDEM 117
E TR + + E + D+M
Sbjct: 283 EETREHYGPAPV-VTNENTSQENSNDDM 309
>gnl|CDD|132234 TIGR03190, benz_CoA_bzdN, benzoyl-CoA reductase, bzd-type, N
subunit. Members of this family are the N subunit of
one of two related types of four-subunit ATP-dependent
benzoyl-CoA reductase. This enzyme system catalyzes the
dearomatization of benzoyl-CoA, a common intermediate in
pathways for the degradation for a number of different
aromatic compounds, such as phenol and toluene.
Length = 377
Score = 26.9 bits (59), Expect = 5.0
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 16/79 (20%)
Query: 36 IEALVGRSIPDDYL-DKINAELESDVMIRAIYDVKGIQMGNSLIRYKAEVDFDGRE---- 90
++ L G+ I DD L D + E+ ++R ++D R +A+ G E
Sbjct: 147 LQTLTGKEITDDMLRDALAVCDENRRLLRELFDY----------RKEADPKVTGVEALYA 196
Query: 91 -LTRSYLDKQDLNTMLEEV 108
LT ++DK++ N ML++V
Sbjct: 197 SLTAQFIDKREHNEMLKKV 215
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 26.9 bits (60), Expect = 5.3
Identities = 25/121 (20%), Positives = 44/121 (36%), Gaps = 19/121 (15%)
Query: 14 AVG-SFLVGGI--LGCVAYFIVSSNIEALVGRSIPD----DYLD----------KINAEL 56
VG SFL L +A F+V N+ LV + + LD ++ L
Sbjct: 466 GVGFSFLFSWFLMLVVLALFLVGGNVYTLVCEPLANNELFQVLDTPGNLNPGYLNLSGTL 525
Query: 57 ESDVMIRAIYDVKGIQMGNSLIR-YKAEVDFDGRELTRSYLDKQDLNTMLEEVQ-NMKTI 114
E + + + + L + +D EL +++ LE ++ N+ TI
Sbjct: 526 ELKINLTISEVYRDCEQNEPLYTVLQLNNSYDLNELLDIKQYTPEIDQELESLKVNLSTI 585
Query: 115 D 115
Sbjct: 586 T 586
>gnl|CDD|239480 cd03385, PAP2_BcrC_like, PAP2_like proteins, BcrC_like subfamily.
Several members of this family have been annotated as
bacitracin transport permeases, as it was suspected that
they form the permease component of an ABC transporter
system. It was shown, however, that BcrC from Bacillus
subtilis posesses undecaprenyl pyrophosphate (UPP)
phospatase activity, and it is hypothesized that it
competes with bacitracin for UPP, increasing the cell's
resistance to bacitracin.
Length = 144
Score = 26.1 bits (58), Expect = 6.0
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 5 LYTGSHIP-DAVGSFLVGGILGCVAYFI 31
+Y G H P D +G+ LV +L + F
Sbjct: 118 IYLGVHYPLDMLGAALV-AVLSALLVFQ 144
>gnl|CDD|237726 PRK14488, PRK14488, cbb3-type cytochrome c oxidase subunit I;
Provisional.
Length = 473
Score = 26.8 bits (60), Expect = 6.5
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 14 AVGSFLVGGILGCVAYFI 31
AVG FL G LG + YF+
Sbjct: 208 AVGFFLTAGFLGMMYYFV 225
>gnl|CDD|219689 pfam07995, GSDH, Glucose / Sorbosone dehydrogenase. Members of
this family are glucose/sorbosone dehydrogenases that
possess a beta-propeller fold.
Length = 324
Score = 26.3 bits (59), Expect = 6.6
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 2 GLTLYTGSHIPDAVGSFLVGG 22
G+ YTG P+ G VG
Sbjct: 254 GMAFYTGDAFPEWKGDLFVGA 274
>gnl|CDD|218030 pfam04332, DUF475, Protein of unknown function (DUF475). Predicted
to be an integral membrane protein with multiple
membrane spans.
Length = 294
Score = 26.6 bits (59), Expect = 6.8
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 13 DAVGSFLVGGILGCVAYFIVSS 34
+ + L G+LG + Y +V
Sbjct: 138 EQFQTVLFAGLLGLLTYLLVDG 159
>gnl|CDD|216788 pfam01923, Cob_adeno_trans, Cobalamin adenosyltransferase.
Cobalamin adenosyltransferase This family contains the
gene products of PduO and EutT which are both cobalamin
adenosyltransferases. PduO is a protein with
ATP:cob(I)alamin adenosyltransferase activity. The main
role of this protein is the conversion of inactive
cobalamins to AdoCbl for 1,2-propanediol degradation.The
EutT enzyme appears to be an adenosyl transferase,
converting CNB12 to AdoB12.
Length = 162
Score = 25.9 bits (58), Expect = 7.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 91 LTRSYLDKQDLNTMLEEVQNM 111
L R+ L +DL +LE +QN
Sbjct: 41 LARALLPDEDLRELLERIQND 61
>gnl|CDD|237814 PRK14777, PRK14777, lipoprotein signal peptidase; Provisional.
Length = 184
Score = 26.0 bits (57), Expect = 7.8
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 4 TLYTGSHIPDAVGSFLVGGILGCVAYFI 31
+L++GS +P A+ LVG LG + Y +
Sbjct: 78 SLFSGSALPLALMRLLVG--LGLLVYLL 103
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 26.3 bits (59), Expect = 8.1
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 24 LGCVAYFIVSSNIEALVGRSIPDDYLDKINAELESDVMIRAIYDVK 69
LG VA+F + P+ + +NA L D+ + +V
Sbjct: 58 LGQVAHFDTPAPRP-------PEKWRRALNALLPDDIAVLWAEEVP 96
>gnl|CDD|129862 TIGR00780, ccoN, cytochrome c oxidase, cbb3-type, subunit I. This
model represents the largest subunit, I, of the
ccb3-type cytochrome c oxidase, with two protohemes and
copper. It shows strong homology to subunits of other
types of cytochrome oxidases. Species with this type,
all from the Proteobacteria so far, include Neisseria
meningitidis, Helicobacter pylori, Campylobacter jejuni,
Rhodobacter sphaeroides, Rhizobium leguminosarum, and
others. Gene symbols ccoN and fixN are synonymous
[Energy metabolism, Electron transport].
Length = 474
Score = 26.4 bits (58), Expect = 9.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 13 DAVGSFLVGGILGCVAYFI 31
+AVG FL G LG + YF+
Sbjct: 207 NAVGFFLTAGFLGMMYYFL 225
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
0.320 0.140 0.390
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,430,035
Number of extensions: 805625
Number of successful extensions: 1041
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1039
Number of HSP's successfully gapped: 61
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
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 (21.8 bits)
S2: 55 (25.0 bits)