RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017001
(379 letters)
>gnl|CDD|223131 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 128 bits (324), Expect = 2e-34
Identities = 62/244 (25%), Positives = 123/244 (50%), Gaps = 11/244 (4%)
Query: 114 ERAMKISNYANIVLLACKIFATIKSGSIAIAASTLDSLLDLMAGGILWFT-HVAMKNINI 172
RA IS N+ L K+ A I +GS+A+ A + SL D++A I+ ++ K +
Sbjct: 12 RRAALISLAVNLALALLKLIAGILTGSVALLADAIHSLSDIVASLIVLIGLRISSKPPD- 70
Query: 173 YKYPIGKLRVQPVGIIIFAAIMATLGFQVLIEAVEKLVKDEPPKKMNTVQLEWLYSIMIG 232
+P G + + + +I + ++ GF++L+EA+++L+ +P + + +
Sbjct: 71 RDHPYGHGKAETLASLIVSILIFAAGFEILLEAIKRLISPQPVEPPLLA-----LGVALI 125
Query: 233 ATVVKLALWIY----CKSSGNKIVRAYAKDHYFDVVTNVVGLVAAVLGDSFYWWIDPAGA 288
+ V+K AL+ Y K + ++ + A A H DV+T++ LV + + W+DP A
Sbjct: 126 SIVIKEALYRYLRRVGKKTNSQALIADALHHRSDVLTSLAVLVGLLGSLLGWPWLDPLAA 185
Query: 289 ILLAVYTITNWSETVMENAVSLVGQSAPPEILQKLTYLVIRHPEVKRIDTVRAYTFGVLY 348
+L+++Y + E+ L+ + PE L+K+ +++ P VK + +R G
Sbjct: 186 LLISLYILKTGFRLFKESVNELMDAALDPEDLEKIRAIILSVPGVKGVHDLRTRKSGSRI 245
Query: 349 FVEV 352
F++V
Sbjct: 246 FIDV 249
>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 = 117 bits (296), Expect = 1e-30
Identities = 56/240 (23%), Positives = 115/240 (47%), Gaps = 13/240 (5%)
Query: 126 VLLACKIFATIKSGSIAIAASTLDSLLDLMAGGILWFTHVAMKNINIYKYPIGKLRVQPV 185
+L K+ A + +GS+A+ A L SL+DL++ + ++P G R++P+
Sbjct: 1 LLALVKLAAGLLTGSLALLADALHSLIDLLSSLLALLALRLSSRPPDKRHPFGHGRLEPL 60
Query: 186 GIIIFAAIMATLGFQVLIEAVEKLVKDEPPKKMNTVQLEWLYSIMIGATVVKLALWIYCK 245
+I + ++ +G +L E++E+L+ E ++ + + + + VV L L +Y +
Sbjct: 61 AALIVSLLLLGVGVFILYESIERLISPEE------IEPGGILLVALISLVVNLLLALYLR 114
Query: 246 SSGNKI------VRAYAKDHYFDVVTNVVGLVAAVLGDSFYW-WIDPAGAILLAVYTITN 298
+G KI +RA A DV+ ++ L+ +L DP ++L+A+ +
Sbjct: 115 RAGRKIGKKSSALRADALHALVDVLGSLAVLIGLLLILLTGLPIADPLASLLIALLILYT 174
Query: 299 WSETVMENAVSLVGQSAPPEILQKLTYLVIRHPEVKRIDTVRAYTFGVLYFVEVGCSVPS 358
+ E+ L+G S PE++ ++ + + P V + +R + G YFV++ V
Sbjct: 175 GLRLLKESLSELLGASPDPELVDEIRDALEKLPGVLGVHDLRVWKSGPKYFVDIHIEVDP 234
>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 = 92.3 bits (230), Expect = 2e-21
Identities = 50/225 (22%), Positives = 102/225 (45%), Gaps = 11/225 (4%)
Query: 126 VLLACKIFATIKSGSIAIAASTLDSLLDLMAGGILWFT-HVAMKNINIYKYPIGKLRVQP 184
+L+ KI + SGS+A+ A + SL D+ A I ++ + + ++P G R +
Sbjct: 1 LLMLIKIVGGLLSGSLALLADAIHSLSDVAASAIALLALRISRRPAD-ERHPFGHGRAEI 59
Query: 185 VGIIIFAAIMATLGFQVLIEAVEKLVKDEPPKKMNTVQLEWLYSIMIGATVVKLALWIYC 244
+ ++ + + +L EA+E+L+ EP + + I +V L L +Y
Sbjct: 60 LAALLNGLFLVVVALFILYEAIERLINPEPEIDGG-----TMLIVAIVGLIVNLILALYL 114
Query: 245 KSSG----NKIVRAYAKDHYFDVVTNVVGLVAAVLGDSFYWWIDPAGAILLAVYTITNWS 300
G + +RA A D +++V L+ A+L + W DP A+L+++ +
Sbjct: 115 HRVGHRLGSLALRAAALHVLSDALSSVGVLIGALLIYFGWHWADPIAALLISLLILYTAF 174
Query: 301 ETVMENAVSLVGQSAPPEILQKLTYLVIRHPEVKRIDTVRAYTFG 345
+ E+ L+ + E L+++ ++ P VK + + + G
Sbjct: 175 RLLKESINVLLDAAPDEEDLEEIKKAILSIPGVKGVHDLHIWRIG 219
>gnl|CDD|224151 COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion
transport and metabolism].
Length = 296
Score = 52.3 bits (126), Expect = 1e-07
Identities = 47/232 (20%), Positives = 106/232 (45%), Gaps = 21/232 (9%)
Query: 114 ERAMKISNYANIVLLACKIFATIKSGSIAIAASTLDSLLDLMAGGILWFTHVAMKNINIY 173
ER + I+ N+ + +I + +GS+A+ A L L D +A + +
Sbjct: 21 ERRLLIALLLNLAFMLIEIIGGLLTGSLALLADALHMLSDALALLLALIAIKLARRPATK 80
Query: 174 KYPIGKLRVQPVGIIIFAAIMATLGFQVLIEAVEKLVKDEPPKKMNTVQLEWLYSIMIGA 233
++ G R++ + + A ++ + +L EA+++L+ P YS M+
Sbjct: 81 RFTFGYKRLEILAAFLNALLLIVVSLLILWEAIQRLLAPPPIH----------YSGMLVV 130
Query: 234 TVVKL-----ALWIYCK-SSGNKIVRAYAKDHYF-DVVTNVVGLVAAVLGDSFYW-WIDP 285
++ L + + K N +R A H D + +V ++AA++ W W+DP
Sbjct: 131 AIIGLVVNLVSALLLHKGHEENLNMRG-AYLHVLGDALGSVGVIIAAIVIRFTGWSWLDP 189
Query: 286 AGAILLAVYTITNWSETVMENAVSLVGQSAPPEI-LQKLTYLVIRHPEVKRI 336
+I++A+ I + + +++ +++++ + P I + K+ ++R P V +
Sbjct: 190 ILSIVIALL-ILSSAWPLLKESLNILLEGVPEGIDIDKVREALLRIPGVASV 240
>gnl|CDD|226474 COG3965, COG3965, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 314
Score = 37.8 bits (88), Expect = 0.007
Identities = 51/271 (18%), Positives = 95/271 (35%), Gaps = 25/271 (9%)
Query: 107 LQEQVQHERAMKISNYANIVLLACKIFATIKSGSIAIAASTLDSLLDL-MAGGILWFTHV 165
Q+ + ++IS ++ A I + SGS++I + SL+D M L + +
Sbjct: 12 SQDSSNEQLYLRISIAGTVIFAAFGIIWGLLSGSMSIIFDGVYSLIDAGMTLLSLLVSRL 71
Query: 166 AMKNINIYKYPIGKLRVQPVGIIIFAAIMATLGFQVLIEAVEKLVKDEPPKKMNTVQLEW 225
K+ ++P G ++P+ + I ++A L LI A+ L+ ++E
Sbjct: 72 IAKDPRDARFPYGFWHLEPLVLAINGTLLALLCLYALINALGSLLD-------GGREVEP 124
Query: 226 LYSIMIGATVVKLALWIYCKSSG------NKIVRAYAKDHYFDVVTNVVGLVA-----AV 274
++I V I K + ++ K + VA +
Sbjct: 125 GHAIAYTLVSVTGCAAIAWKLRRLNRRLKSPLIALDTKQWLMSTCLSAALFVAFAAAWLL 184
Query: 275 LGDSFYW---WIDPAGAILLAVYTITNWSETVMENAVSLVGQSAPPEILQKLTYLVIRHP 331
G F + DP L+ + I TV A+ + P E+ Q +
Sbjct: 185 AGTKFAHLVVYADPMVLALVCLVFIPLPLGTVKS-ALREILLMTPNELQQSIESHAHEIV 243
Query: 332 EVKRIDTVRAYT--FGVLYFVEVGCSVPSLW 360
E + Y G F+E+ +P
Sbjct: 244 EKYGFPSYHVYVARVGRGLFIEIHFIIPRES 274
>gnl|CDD|181919 PRK09509, fieF, ferrous iron efflux protein F; Reviewed.
Length = 299
Score = 33.9 bits (78), Expect = 0.12
Identities = 14/31 (45%), Positives = 23/31 (74%)
Query: 126 VLLACKIFATIKSGSIAIAASTLDSLLDLMA 156
+LL KIFA +GS+++ A+ +DSL+D+ A
Sbjct: 22 LLLLIKIFAWWYTGSVSLLAALVDSLVDIAA 52
>gnl|CDD|181462 PRK08537, PRK08537, 2-oxoglutarate ferredoxin oxidoreductase
subunit gamma; Validated.
Length = 177
Score = 32.3 bits (74), Expect = 0.20
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 168 KNINIYKYPIGKLRVQPVGIIIFAAIMATLGFQVLI------EAVEKLVKDEPPK---KM 218
K + +YK P ++ + +G+ I A I+ LG + EA+EK + D PK +
Sbjct: 108 KKVKVYKVPFTEIAEEEIGLSIVANIV-MLGALTKLTGIVSKEAIEKAILDSVPKGTEEK 166
Query: 219 NTVQLE 224
N + E
Sbjct: 167 NLMAFE 172
>gnl|CDD|227102 COG4760, COG4760, Predicted membrane protein [Function unknown].
Length = 276
Score = 31.0 bits (70), Expect = 0.98
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 184 PVGII--IFAAIMATLGFQVLIEAVEKLVKDEPPKKMN-------TVQLEWLY 227
P GII +F +A F + +A +++V+ P+KM TV L WLY
Sbjct: 211 PFGIIFSLFCIGIAAFSFLLDFDAADQMVRAGAPEKMAWGVALGLTVTLVWLY 263
>gnl|CDD|187619 cd05361, haloalcohol_DH_SDR_c-like, haloalcohol dehalogenase,
classical (c) SDRs. Dehalogenases cleave carbon-halogen
bonds. Haloalcohol dehalogenase show low sequence
similarity to short-chain dehydrogenases/reductases
(SDRs). Like the SDRs, haloalcohol dehalogenases have a
conserved catalytic triad (Ser-Tyr-Lys/Arg), and form a
Rossmann fold. However, the normal classical SDR
NAD(P)-binding motif (TGXXGXG) and NAD-binding function
is replaced with a halide binding site, allowing the
enzyme to catalyze a dehalogenation reaction. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 242
Score = 29.5 bits (66), Expect = 2.8
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 57 DAEAPFDVDTSKTIALSEGEKEYYESQFATLKSFEEVDVLVDSDCF 102
F+ + T ALSE + E E A L++ +DVLV +D
Sbjct: 39 AERQAFESENPGTKALSEQKPE--ELVDAVLQAGGAIDVLVSNDYI 82
>gnl|CDD|233883 TIGR02475, CobW, cobalamin biosynthesis protein CobW. The family
of proteins identified by this model is generally found
proximal to the trimeric cobaltochelatase subunit CobN
which is essential for vitamin B12 (cobalamin)
biosynthesis. The protein contains an P-loop
nucleotide-binding loop in the N-terminal domain and a
histidine-rich region in the C-terminal portion
suggesting a role in metal binding, possibly as an
intermediary between the cobalt transport and chelation
systems. A broader CobW family is delineated by two PFAM
models which identify the N- and C-terminal domains
(pfam02492 and pfam07683) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 341
Score = 29.3 bits (66), Expect = 3.1
Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 14/99 (14%)
Query: 31 LSRRNSVNALRHEFVSKLPEKVLAGIDAEAPFDVDTSKTIALSEGEKEYYESQFAT---- 86
L R + H ++ +VL G+ A A D+D + EG +E+ +F +
Sbjct: 202 LPRAVKIVEASH---GEVDARVLLGLGAAAEDDLDNRPSHHDFEGGEEHDHDEFDSVVVD 258
Query: 87 LKSFEEVDVLVDSDCFIEEDLQEQVQHERAMKISNYANI 125
L + L L+ + ++I +A +
Sbjct: 259 LGEVADPAALRQR-------LERLAEEHDVLRIKGFAAV 290
>gnl|CDD|220373 pfam09738, DUF2051, Double stranded RNA binding protein (DUF2051).
This is a novel protein identified as interacting with
the leucine-rich repeat domain of human flightless-I,
FliI protein.
Length = 294
Score = 28.7 bits (64), Expect = 4.5
Identities = 25/89 (28%), Positives = 36/89 (40%), Gaps = 18/89 (20%)
Query: 13 RTSSSSRERKRSGSGRLSLSRRNSVNALRHEFVSKLPEKVLAGIDAEAPFD--------- 63
SSS R+ SG S+ S+ L+ + ++ EKV + + A D
Sbjct: 57 GGSSS---RRSSGDTSSSVDTEASIRELKDS-LIEVEEKVKKAMVSNAQLDNEKTNLMYE 112
Query: 64 VDTSKTIALSEGEKEYYESQFATLKSFEE 92
VD K L E E+ E Q + FEE
Sbjct: 113 VDLLKD-KLEELEESLAELQ----REFEE 136
>gnl|CDD|224931 COG2020, STE14, Putative protein-S-isoprenylcysteine
methyltransferase [Posttranslational modification,
protein turnover, chaperones].
Length = 187
Score = 28.2 bits (63), Expect = 5.7
Identities = 22/114 (19%), Positives = 46/114 (40%), Gaps = 14/114 (12%)
Query: 267 VVGLVAAVLGDSFYWWIDPAGAILLAV-YTITNWSETVMENAVSLVGQSAPPEILQK-LT 324
VVG+ + WI G +L+ + + W+ + + ++ ++ L
Sbjct: 53 VVGVSFPLPWSLIPSWIVGLGLLLVGLGLALRLWAMRTLGRSWTVSVKARKGHELVTTGP 112
Query: 325 YLVIRHPEVKRIDTVRAYTFGVLYFVEVGCSVPSLWLILKMIFILPIITTLFSF 378
Y ++RHP Y +L+ + G + SLW ++ + ++ LF F
Sbjct: 113 YSIVRHPI---------YLGLLLFALGTGLLLGSLWA---LLIFVVLVALLFLF 154
>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
reductase subunit; Provisional.
Length = 396
Score = 28.4 bits (63), Expect = 7.2
Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 3/31 (9%)
Query: 302 TVMENAVSLVGQSAPPEILQKLTYLVIRHPE 332
TV+E A +++G++APP +Q+ YL+ RH +
Sbjct: 171 TVIELAATVMGRNAPP-PVQR--YLLQRHQQ 198
>gnl|CDD|212068 cd11499, SLC6sbd_GlyT2, Na(+)- and Cl(-)-dependent glycine
transporter GlyT2; solute-binding domain. GlyT2 (also
called NET1) is a membrane-bound transporter that
re-uptakes glycine from the synaptic cleft. Human GlyT2
is encoded by the SLC6A5 gene. GlyT2 is expressed in
brain and spinal cord. GlyT2 may play a role in pain,
and in spasticity. This subgroup belongs to the solute
carrier 6 (SLC6) transporter family.
Length = 606
Score = 28.4 bits (63), Expect = 7.8
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 172 IYKYPIGKLRVQPVGIIIFAAIMATLGFQVLIEAVEKLV---KDEPPKKMNT 220
+Y + +L + P IIF ++ TLG + +E +V DE PK + T
Sbjct: 359 VYPEALTRLPLSPFWAIIFFLMLLTLGLDTMFATIETIVTSVSDEFPKYLRT 410
>gnl|CDD|217489 pfam03315, SDH_beta, Serine dehydratase beta chain. L-serine
dehydratase (EC:4.2.1.13) is a found as a heterodimer of
alpha and beta chain or as a fusion of the two chains in
a single protein. This enzyme catalyzes the deamination
of serine to form pyruvate. This enzyme is part of the
gluconeogenesis pathway.
Length = 155
Score = 27.5 bits (62), Expect = 8.1
Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 10/97 (10%)
Query: 52 VLAGIDAEAPFDVDTSKTIALSEGEKEYYESQFATLKSF---EEVDVLVDSDCFIEEDLQ 108
V+ G+ P DVD A +E + A S E D++ +
Sbjct: 62 VILGLLGFDPDDVDIDSIEARLARIREEGKLNLAGEHSIPFAPERDIVFHFKEILPF--- 118
Query: 109 EQVQHERAMKISNYANIVLLACKIFATIKSGSIAIAA 145
H M+ + + + L + + +I G I I
Sbjct: 119 ----HPNGMRFTAFDDGGELLEETYYSIGGGFIVIEE 151
>gnl|CDD|223383 COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion
transport and metabolism].
Length = 326
Score = 27.9 bits (63), Expect = 9.2
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 264 VTNVVGLVAAVLGDSF-YWWIDPAGAILLAVYTITNWS---ETVMENAVSL 310
V N +G + AVL S +W+ G I LA+ T+T ETV + L
Sbjct: 194 VANAIGPLVAVLISSLPPFWVLVLGGIALALGTLTGGPRVIETVGKKITEL 244
>gnl|CDD|184699 PRK14478, PRK14478, nitrogenase molybdenum-cofactor biosynthesis
protein NifE; Provisional.
Length = 475
Score = 28.1 bits (63), Expect = 9.5
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 294 YTITNWSETVMENAVSLVGQSAPPEILQKLTYLVIRHPEVKRIDTVRAYT 343
Y I + S+++ + A LV + A E++++ T +I E K + Y
Sbjct: 271 YGIEDTSDSLRQIARLLVERGADAELVER-TEALIAEEEAKAWAALEPYR 319
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
0.322 0.136 0.396
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,580,475
Number of extensions: 1949481
Number of successful extensions: 2216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2202
Number of HSP's successfully gapped: 37
Length of query: 379
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 280
Effective length of database: 6,546,556
Effective search space: 1833035680
Effective search space used: 1833035680
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: 60 (26.6 bits)