RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3378
(239 letters)
>gnl|CDD|133004 cd02510, pp-GalNAc-T, pp-GalNAc-T initiates the formation of
mucin-type O-linked glycans. UDP-GalNAc: polypeptide
alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T)
initiate the formation of mucin-type, O-linked glycans
by catalyzing the transfer of
alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to
hydroxyl groups of Ser or Thr residues of core proteins
to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These
enzymes are type II membrane proteins with a GT-A type
catalytic domain and a lectin domain located on the
lumen side of the Golgi apparatus. In human, there are
15 isozymes of pp-GalNAc-Ts, representing the largest of
all glycosyltransferase families. Each isozyme has
unique but partially redundant substrate specificity for
glycosylation sites on acceptor proteins.
Length = 299
Score = 97.3 bits (243), Expect = 3e-24
Identities = 32/41 (78%), Positives = 36/41 (87%)
Query: 194 SVIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYSD 234
SVII FHNEA S LLRTVHSV++R+P LLKEIILVDD+SD
Sbjct: 1 SVIIIFHNEALSTLLRTVHSVINRTPPELLKEIILVDDFSD 41
>gnl|CDD|215980 pfam00535, Glycos_transf_2, Glycosyl transferase family 2. Diverse
family, transferring sugar from UDP-glucose,
UDP-N-acetyl- galactosamine, GDP-mannose or
CDP-abequose, to a range of substrates including
cellulose, dolichol phosphate and teichoic acids.
Length = 168
Score = 43.2 bits (102), Expect = 2e-05
Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 194 SVIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYS 233
SVII +NE L T+ S+L+++ + EII+VDD S
Sbjct: 1 SVIIPTYNEE-KYLEETLESLLNQT--YKNFEIIVVDDGS 37
>gnl|CDD|133035 cd04192, GT_2_like_e, Subfamily of Glycosyltransferase Family GT2
of unknown function. GT-2 includes diverse families of
glycosyltransferases with a common GT-A type structural
fold, which has two tightly associated beta/alpha/beta
domains that tend to form a continuous central sheet of
at least eight beta-strands. These are enzymes that
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. Glycosyltransferases have been
classified into more than 90 distinct sequence based
families.
Length = 229
Score = 34.6 bits (80), Expect = 0.029
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 195 VIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYS 233
V+I NEA + L R + S+ E+ILVDD+S
Sbjct: 1 VVIAARNEAEN-LPRLLQSLSALDYPKEKFEVILVDDHS 38
>gnl|CDD|223539 COG0463, WcaA, Glycosyltransferases involved in cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 291
Score = 33.9 bits (76), Expect = 0.058
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 194 SVIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYSD 234
SV+I +NE L + S+L+++ EII+VDD S
Sbjct: 6 SVVIPTYNEE-EYLPEALESLLNQTYKDF--EIIVVDDGST 43
>gnl|CDD|132997 cd00761, Glyco_tranf_GTA_type, Glycosyltransferase family A (GT-A)
includes diverse families of glycosyl transferases with
a common GT-A type structural fold.
Glycosyltransferases (GTs) are enzymes that synthesize
oligosaccharides, polysaccharides, and glycoconjugates
by transferring the sugar moiety from an activated
nucleotide-sugar donor to an acceptor molecule, which
may be a growing oligosaccharide, a lipid, or a protein.
Based on the stereochemistry of the donor and acceptor
molecules, GTs are classified as either retaining or
inverting enzymes. To date, all GT structures adopt one
of two possible folds, termed GT-A fold and GT-B fold.
This hierarchy includes diverse families of glycosyl
transferases with a common GT-A type structural fold,
which has two tightly associated beta/alpha/beta domains
that tend to form a continuous central sheet of at least
eight beta-strands. The majority of the proteins in this
superfamily are Glycosyltransferase family 2 (GT-2)
proteins. But it also includes families GT-43, GT-6,
GT-8, GT13 and GT-7; which are evolutionarily related to
GT-2 and share structure similarities.
Length = 156
Score = 32.5 bits (74), Expect = 0.084
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 195 VIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYSD 234
VII +NE L R + S+L ++ + E+I+VDD S
Sbjct: 1 VIIPAYNEE-PYLERCLESLLAQTYPNF--EVIVVDDGST 37
>gnl|CDD|133061 cd06439, CESA_like_1, CESA_like_1 is a member of the cellulose
synthase (CESA) superfamily. This is a subfamily of
cellulose synthase (CESA) superfamily. CESA superfamily
includes a wide variety of glycosyltransferase family 2
enzymes that share the common characteristic of
catalyzing the elongation of polysaccharide chains. The
members of the superfamily include cellulose synthase
catalytic subunit, chitin synthase, glucan biosynthesis
protein and other families of CESA-like proteins.
Length = 251
Score = 32.6 bits (75), Expect = 0.14
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 188 KNLPATSVIICFHNEAWSVLLRTVHSVLDRS-PAHLLKEIILVDDYSD 234
LP ++II +NE +V+ + ++L P L EII+V D S
Sbjct: 26 AYLPTVTIIIPAYNEE-AVIEAKLENLLALDYPRDRL-EIIVVSDGST 71
>gnl|CDD|197912 smart00844, GA, GA module. The protein G-related albumin-binding
(GA) module is composed of three alpha helices. This
module is found in a range of bacterial cell surface
proteins. The GA module from the Peptostreptococcus
magnus albumin-binding protein (PAB) shows a strong
affinity for albumin.
Length = 60
Score = 29.8 bits (68), Expect = 0.18
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 61 IESLDNLNNVDRQSLKNVDDNDNLIQPVAQAQ 92
I +L +LNN +Q+LKN + V Q
Sbjct: 25 INNLTHLNNAQKQALKNQINQATTRAEVNQIL 56
>gnl|CDD|224136 COG1215, COG1215, Glycosyltransferases, probably involved in cell
wall biogenesis [Cell envelope biogenesis, outer
membrane].
Length = 439
Score = 30.7 bits (69), Expect = 0.61
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 188 KNLPATSVIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYSDMR 236
K LP SVII +NE VL T+ S+L + + E+I+VDD S
Sbjct: 51 KLLPKVSVIIPAYNEEPEVLEETLESLLSQ--DYPRYEVIVVDDGSTDE 97
>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal. This model
describes archaeal transcription factor S, a protein
related in size and sequence to certain eukaryotic RNA
polymerase small subunits, and in sequence and function
to the much larger eukaryotic transcription factor IIS
(TFIIS). Although originally suggested to be a subunit
of the archaeal RNA polymerase, it elutes separately
from active polymerase in gel filtration experiments and
acts, like TFIIs, as an induction factor for RNA
cleavage by RNA polymerase. There has been an apparent
duplication event in the Halobacteriaceae lineage
(Haloarcula, Haloferax, Haloquadratum, Halobacterium and
Natromonas). There appears to be a separate duplication
in Methanosphaera stadtmanae [Transcription,
Transcription factors].
Length = 104
Score = 29.0 bits (65), Expect = 0.80
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 164 DLISVKRKLPDPRDEWCKVPGRYLKNLPATSVII--CFHNEAWSVLLRT 210
D V K+ E + + LP T V C H EA+ LL+T
Sbjct: 32 DDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYWLLQT 80
>gnl|CDD|237563 PRK13928, PRK13928, rod shape-determining protein Mbl; Provisional.
Length = 336
Score = 29.9 bits (68), Expect = 1.0
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 173 PDPRDEWCKVPGRYL-----KNLPATSVIICFH-NEAWSVLLRTVHSVLDRSPAHLLKEI 226
P R+E ++ GR L K + TS I E S +++ V SVL+R+P L +I
Sbjct: 215 PGAREEEMEIRGRDLVTGLPKTITVTSEEIREALKEPVSAIVQAVKSVLERTPPELSADI 274
Query: 227 I 227
I
Sbjct: 275 I 275
>gnl|CDD|233363 TIGR01341, aconitase_1, aconitate hydratase 1. This model
represents one form of the TCA cycle enzyme aconitate
hydratase, also known as aconitase and citrate
hydro-lyase. It is found in bacteria, archaea, and
eukaryotic cytosol. It has been shown to act also as an
iron-responsive element binding protein in animals and
may have the same role in other eukaryotes [Energy
metabolism, TCA cycle].
Length = 876
Score = 30.2 bits (68), Expect = 1.1
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 72 RQSLKNVDDNDNLIQPVAQAQIAETPSAETVDKNADKMVLHAPEKGEFDEDKNKMQYGEW 131
R+++KN+ + I P+ + S VD + L + EF+ + + Q+ +W
Sbjct: 87 REAMKNLGGDPKKINPLVPVDLVIDHSV-QVDYYGTEYALEFNMELEFERNLERYQFLKW 145
Query: 132 GK 133
+
Sbjct: 146 AQ 147
>gnl|CDD|223759 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
[Amino acid transport and metabolism].
Length = 363
Score = 29.7 bits (67), Expect = 1.1
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 5/72 (6%)
Query: 84 LIQPVAQAQIAETPSAETVDKNADKMVLHAPEKGEFDEDKNKMQYGEWGKPVILPQNLSS 143
L+ P A++AE +K A K++ E +D E K + ++L
Sbjct: 292 LLDPEVAAKLAEFVGYAPPNKAARKLL-----PKEIKDDPAIYPTAEILKKLFGQKDLGP 346
Query: 144 DIKKLVEEGWQR 155
+ +L + WQ
Sbjct: 347 EALRLYTKAWQE 358
>gnl|CDD|133030 cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to
eukaryotic DPM1. A family of bacterial enzymes related
to eukaryotic DPM1; Although the mechanism of eukaryotic
enzyme is well studied, the mechanism of the bacterial
enzymes is not well understood. The eukaryotic DPM1 is
the catalytic subunit of eukaryotic Dolichol-phosphate
mannose (DPM) synthase. DPM synthase is required for
synthesis of the glycosylphosphatidylinositol (GPI)
anchor, N-glycan precursor, protein O-mannose, and
C-mannose. The enzyme has three subunits, DPM1, DPM2 and
DPM3. DPM is synthesized from dolichol phosphate and
GDP-Man on the cytosolic surface of the ER membrane by
DPM synthase and then is flipped onto the luminal side
and used as a donor substrate. This protein family
belongs to Glycosyltransferase 2 superfamily.
Length = 181
Score = 29.0 bits (66), Expect = 1.7
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 195 VIICFHNEAWSV--LLRTVHSVLDRSPAHLLKEIILVDDYS 233
+++ +NE ++ L + +VL+ EII VDD S
Sbjct: 1 IVVPVYNEEENLPELYERLKAVLESLGYDY--EIIFVDDGS 39
>gnl|CDD|213815 TIGR03469, HpnB, hopene-associated glycosyltransferase HpnB. This
family of genes include a glycosyl transferase, group 2
domain (pfam00535) which are responsible, generally for
the transfer of nucleotide-diphosphate sugars to
substrates such as polysaccharides and lipids. The genes
of this family are often found in the same genetic locus
with squalene-hopene cyclase genes, and are never
associated with genes for the metabolism of phytoene.
Indeed, the members of this family appear to never be
found in a genome lacking squalene-hopene cyclase (SHC),
although not all genomes encoding SHC have this glycosyl
transferase. In the organism Zymomonas mobilis the
linkage of this gene to hopanoid biosynthesis has been
noted and the gene named HpnB. Hopanoids are known to
feature polar glycosyl head groups in many organisms.
Length = 384
Score = 28.9 bits (65), Expect = 2.2
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 190 LPATSVIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIILVDDYSD 234
PA ++ NEA V+ V S+L++ L +ILVDD+S
Sbjct: 39 WPAVVAVVPARNEA-DVIGECVTSLLEQDYPGKLH-VILVDDHST 81
>gnl|CDD|227742 COG5455, COG5455, Predicted integral membrane protein [Function
unknown].
Length = 129
Score = 27.8 bits (62), Expect = 2.3
Identities = 21/121 (17%), Positives = 40/121 (33%), Gaps = 27/121 (22%)
Query: 87 PVAQAQIAET---------PSAETVDKNADKMVLHAPEKGEFDEDKNKMQYGEWGKPVIL 137
P+A AQ A +D++ E+ ++ ++ W + L
Sbjct: 18 PMALAQQDGEFMDIKRKMPQGARHLDRDRAWDRPRTVERRSYELKSVIAKFNRWKRGDRL 77
Query: 138 PQNLSSDIKKLVEEGWQRNAFNQYVSDLISVKRKLPDPR--DEWCKVPGRYLKNLPATSV 195
P ++R+ +N + D + L P W +V G Y+ T +
Sbjct: 78 PP------------MYRRHQYN--IRDY--RRYNLRAPPRGQHWVRVGGDYVLISDTTGL 121
Query: 196 I 196
I
Sbjct: 122 I 122
>gnl|CDD|220329 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8).
Clusters of short DNA repeats with nonhomologous
spacers, which are found at regular intervals in the
genomes of phylogenetically distinct prokaryotic
species, comprise a family with recognisable features.
This family is known as CRISPR (short for Clustered,
Regularly Interspaced Short Palindromic Repeats). A
number of protein families appear only in association
with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry describes
proteins of unknown function which are encoded in the
midst of a cas gene operon.
Length = 441
Score = 28.7 bits (64), Expect = 2.6
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 19 RFYIYFLRRRF-VVLKLILLVCLIWLTVAALLFMEDRNRSGVVIESLDNLNNVDRQSLKN 77
++Y L F +L L LL I ++D+N I L +N + R K
Sbjct: 304 KYYFNLLDEVFSAILNLSLLDNSI------EYLLKDKNSYSYAINELIKINQLIRNGGKE 357
Query: 78 VDDN 81
+D+N
Sbjct: 358 MDEN 361
>gnl|CDD|187875 cd09744, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as Csx8 family.
Length = 441
Score = 28.7 bits (64), Expect = 2.6
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 19 RFYIYFLRRRF-VVLKLILLVCLIWLTVAALLFMEDRNRSGVVIESLDNLNNVDRQSLKN 77
++Y L F +L L LL I ++D+N I L +N + R K
Sbjct: 304 KYYFNLLDEVFSAILNLSLLDNSI------EYLLKDKNSFSYAINELIKINQLIRNGGKE 357
Query: 78 VDDN 81
+D+N
Sbjct: 358 MDEN 361
>gnl|CDD|227423 COG5092, NMT1, N-myristoyl transferase [Lipid metabolism].
Length = 451
Score = 28.4 bits (63), Expect = 3.5
Identities = 22/128 (17%), Positives = 48/128 (37%), Gaps = 12/128 (9%)
Query: 63 SLDNLNNVDRQSLKNVDDNDNLIQPVAQAQIAETPSAETVDKNADKMVLHAP-EKGEFDE 121
L+NL + L N D + + + + S + VD+ ++ + P +K
Sbjct: 9 KLENL--LKLLQLNNDDTSKFTQEQKKMGKDHKFWSTQPVDRFDEEAMPEGPIDKHTISI 66
Query: 122 DKNKMQYG-----EWGKPVILPQNLSSDIKKLVEEGWQRNAFN----QYVSDLISVKRKL 172
++ K+ G EW + + D+ L+EE + + + +Y + +
Sbjct: 67 EQPKLPDGLLFEFEWCVIDVANKKQLEDVFVLLEENYVEDIYAGHRFRYSVEFLQWALDG 126
Query: 173 PDPRDEWC 180
P + W
Sbjct: 127 PGGKKRWH 134
>gnl|CDD|218334 pfam04932, Wzy_C, O-Antigen ligase. This group of bacterial
proteins is involved in the synthesis of O-antigen, a
lipopolysaccharide found in the outer membrane in
gram-negative bacteria. This family includes O-antigen
ligases such as E. coli RfaL.
Length = 152
Score = 27.8 bits (62), Expect = 3.6
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 20 FYIYFLRRRFVVLKLILLVCLIWLTVAALLF 50
+ RR +L+ L+ L+ L + LL
Sbjct: 28 LLLLLRLRRRRKKRLLALLLLVVLLLVVLLA 58
>gnl|CDD|151328 pfam10879, DUF2674, Protein of unknown function (DUF2674). This
family of proteins with unknown function appears to be
conserved to Rickettsia spp.
Length = 67
Score = 26.5 bits (58), Expect = 3.6
Identities = 13/41 (31%), Positives = 17/41 (41%)
Query: 145 IKKLVEEGWQRNAFNQYVSDLISVKRKLPDPRDEWCKVPGR 185
IKK +EEGW I + K+ DE +P R
Sbjct: 21 IKKAIEEGWAIVKLVPNKDRFIGLLEKISHAEDETIYIPPR 61
>gnl|CDD|181598 PRK08965, PRK08965, putative monovalent cation/H+ antiporter
subunit E; Reviewed.
Length = 162
Score = 27.8 bits (63), Expect = 3.7
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 15 LFPSRFYIYFLRRRFVVLKLILLVCLIWLTVAAL------LFMEDRNRSGVV 60
L P + RR +L+L+L+V L L V+ + L R R G V
Sbjct: 48 LVPLEGRL---RRPLALLRLLLVV-LYDLVVSNIQVAWLILRPGPRPRPGFV 95
>gnl|CDD|133022 cd04179, DPM_DPG-synthase_like, DPM_DPG-synthase_like is a member
of the Glycosyltransferase 2 superfamily. DPM1 is the
catalytic subunit of eukaryotic dolichol-phosphate
mannose (DPM) synthase. DPM synthase is required for
synthesis of the glycosylphosphatidylinositol (GPI)
anchor, N-glycan precursor, protein O-mannose, and
C-mannose. In higher eukaryotes,the enzyme has three
subunits, DPM1, DPM2 and DPM3. DPM is synthesized from
dolichol phosphate and GDP-Man on the cytosolic surface
of the ER membrane by DPM synthase and then is flipped
onto the luminal side and used as a donor substrate. In
lower eukaryotes, such as Saccharomyces cerevisiae and
Trypanosoma brucei, DPM synthase consists of a single
component (Dpm1p and TbDpm1, respectively) that
possesses one predicted transmembrane region near the C
terminus for anchoring to the ER membrane. In contrast,
the Dpm1 homologues of higher eukaryotes, namely fission
yeast, fungi, and animals, have no transmembrane region,
suggesting the existence of adapter molecules for
membrane anchoring. This family also includes bacteria
and archaea DPM1_like enzymes. However, the enzyme
structure and mechanism of function are not well
understood. The UDP-glucose:dolichyl-phosphate
glucosyltransferase (DPG_synthase) is a
transmembrane-bound enzyme of the endoplasmic reticulum
involved in protein N-linked glycosylation. This enzyme
catalyzes the transfer of glucose from UDP-glucose to
dolichyl phosphate. This protein family belongs to
Glycosyltransferase 2 superfamily.
Length = 185
Score = 27.5 bits (62), Expect = 4.5
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 9/43 (20%)
Query: 195 VIICFHNEAWSVLLRTVHSVLDRSPAHLLK----EIILVDDYS 233
V+I +NE + +++R A L + EII+VDD S
Sbjct: 1 VVIPAYNEE-----ENIPELVERLLAVLEEGYDYEIIVVDDGS 38
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease.
Length = 286
Score = 27.8 bits (62), Expect = 5.4
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 195 VIICFHNEAWSVLLRTVHSVLDRSPAHLLKEIIL--VDDYSDMRK 237
+ C H +A +L ++ S R A I+L D + RK
Sbjct: 36 TLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTDSV-NWRK 79
>gnl|CDD|216066 pfam00695, vMSA, Major surface antigen from hepadnavirus.
Length = 364
Score = 27.7 bits (61), Expect = 5.8
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 21 YIYFLRRRFVVLKLILLVCLIWLTV 45
+ + RRF++ LILL+ L +L V
Sbjct: 217 FRWMYLRRFIIFLLILLLALGFLLV 241
>gnl|CDD|187828 cd09697, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as Csx8 family.
Length = 441
Score = 27.6 bits (61), Expect = 6.0
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 19 RFYIYFLRRRF-VVLKLILLVCLIWLTVAALLFMEDRNRSGVVIESLDNLNNVDRQSLKN 77
++Y L F +L L LL I ++D+N I L +N + R K
Sbjct: 304 KYYFNLLDEVFSAILNLSLLDNSI------EYLLKDKNSYSYAINELIKINQLIRNGGKE 357
Query: 78 VDDN 81
+D+N
Sbjct: 358 MDEN 361
>gnl|CDD|233970 TIGR02670, cas_csx8, CRISPR-associated protein Cas8a1/Csx8, subtype
I. In three genomes so far, a member of this protein
appears in the midst of a CRISPR-associated (cas) gene
operon, immediately upstream of a member of family
TIGR01875 (CRISPR-associated autoregulator, DevR
family). The genomes so far are Nocardia farcinica
IFM10152, Clostridium perfringens SM101, and Clostridium
tetani E88 [Mobile and extrachromosomal element
functions, Other].
Length = 441
Score = 27.6 bits (61), Expect = 6.0
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 19 RFYIYFLRRRF-VVLKLILLVCLIWLTVAALLFMEDRNRSGVVIESLDNLNNVDRQSLKN 77
++Y L F +L L LL I ++D+N I L +N + R K
Sbjct: 304 KYYFNLLDEVFSAILNLSLLDNSI------EYLLKDKNSYSYAINELIKINQLIRNGGKE 357
Query: 78 VDDN 81
+D+N
Sbjct: 358 MDEN 361
>gnl|CDD|233850 TIGR02402, trehalose_TreZ, malto-oligosyltrehalose
trehalohydrolase. Members of this family are the
trehalose biosynthetic enzyme malto-oligosyltrehalose
trehalohydrolase, formally known as
4-alpha-D-{(1->4)-alpha-D-glucano}trehalose
trehalohydrolase (EC 3.2.1.141). It is the TreZ protein
of the TreYZ pathway for trehalose biosynthesis, and
alternative to the OtsAB system [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 544
Score = 27.7 bits (62), Expect = 6.9
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 128 YGEWGKPVILPQN----LSSDIK-KLVEEGWQRNAFNQYVSDLISVKRKLPDPRDEWCKV 182
+G + V PQ+ L S + E G + DL++++R+LP P +
Sbjct: 449 FGWDPEDVPDPQDPETFLRSKLDWAEAESGEHARWLA-FYRDLLALRRELPVPLLPGARA 507
Query: 183 PG 184
Sbjct: 508 LE 509
>gnl|CDD|225126 COG2216, KdpB, High-affinity K+ transport system, ATPase chain B
[Inorganic ion transport and metabolism].
Length = 681
Score = 27.6 bits (62), Expect = 8.0
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 15 LFPSRFYIYFLRRRFVVLKLI-LLVCLIWLTVAALL 49
L+P F IY V L+ LLVCLI T+ LL
Sbjct: 236 LYP--FAIYSGGGAASVTVLVALLVCLIPTTIGGLL 269
>gnl|CDD|212034 cd10324, SLC6sbd, Solute carrier 6 family, neurotransmitter
transporters; solute-binding domain. This family
represents the solute-binding domain of SLC6 proteins
(also called the sodium- and chloride-dependent
neurotransmitter transporter family or Na+/Cl--dependent
transporter family). These use sodium and chloride
electrochemical gradients to catalyze the
thermodynamically uphill movement of a variety of
substrates, and include neurotransmitter transporters
(NTTs). The latter are Na+/Cl--dependent plasma membrane
transporters for the monoamine neurotransmitters
serotonin (5-hydroxytryptamine), dopamine, and
norepinephrine, and the amino acid neurotransmitters
GABA and glycine. NTTs are widely expressed in the
mammalian brain, and are involved in regulating
neurotransmitter signaling and homeostasis, through
facilitating the uptake of released neurotransmitters
from the extracellular space into neurons and glial
cells. NTTs are the target of a range of therapeutic
drugs for the treatment of psychiatric diseases, such as
major depression, anxiety disorders, attention deficit
hyperactivity disorder and epilepsy. In addition, they
are the primary targets of cocaine, amphetamines and
other psychostimulants. This family also includes
Drosophila Blot which is expressed primarily in
epithelial tissues of ectodermal origin and in the
nervous system of the embryo and larvae, but in addition
found in the developing oocyte and the freshly laid egg.
A lack or reduction of Blot function during oogenesis
results in early arrest of embryonic development. 12
transmembrane helices (TMs) appears to be common for
eukaryotic and some prokaryotic and archaeal SLC6s, (a
core inverted topology repeat, TM1-5 and TM6-10, plus
TMs11-12; TMs numbered to conform to the SLC6 Aquifex
aeolicus LeuT), although a majority of bacterial, and
some archaeal SLC6s lack TM12, for example the
functional Fusobacterium nucleatum tyrosine transporter
Tyt1.
Length = 417
Score = 27.1 bits (61), Expect = 8.5
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 22 IYFLRRRFVVLKLILLVCLIWLTVAALLF 50
+Y+L F+ +L L + L W+ V +F
Sbjct: 105 LYYLFASFINWELALCLLLAWILVYLCIF 133
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 27.4 bits (61), Expect = 8.8
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 15/85 (17%)
Query: 24 FLRRRFVVLKLILLVCLIWLTVA----------ALLFMEDRNRSGVVIESLDNLNNVDRQ 73
RRR+++L + LV + + A A L ++ R+ S +V+E + D
Sbjct: 21 LRRRRWLILLVAALVVGLAVLYAFLAPPIYEADAQLLVDPRSSSVLVLEDGQSGLPNDSS 80
Query: 74 SLKNVDDNDNLIQ--PVAQAQIAET 96
SL + ++Q V + I +
Sbjct: 81 SL---ETEIEILQSRSVLEKVIDKL 102
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
0.321 0.137 0.414
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,512,604
Number of extensions: 1181592
Number of successful extensions: 1173
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1169
Number of HSP's successfully gapped: 47
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
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: 57 (25.6 bits)