RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023476
(281 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 = 141 bits (357), Expect = 1e-40
Identities = 69/279 (24%), Positives = 135/279 (48%), Gaps = 15/279 (5%)
Query: 2 VLFAAKVYASVKSGSLAIIASTLDSLLDLLSGFILWFTAFSMQTPNPYQYPIGKKRMQPL 61
+L K+ A + +GSLA++A L SL+DLLS + P ++P G R++PL
Sbjct: 1 LLALVKLAAGLLTGSLALLADALHSLIDLLSSLLALLALRLSSRPPDKRHPFGHGRLEPL 60
Query: 62 GILVFASVMATLGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVYCR 121
L+ + ++ +G+ I+ ES+ L+S E+ ++ + L +V LLL +Y R
Sbjct: 61 AALIVSLLLLGVGVFILYESIERLISPEEIEPG------GILLVALISLVVNLLLALYLR 114
Query: 122 ------AFTNEIVKAYAQDHFFDVITNIIGLVAVLLANYIDD-WMDPVGAIILALYTIRT 174
+ ++A A DV+ ++ L+ +LL DP+ ++++AL + T
Sbjct: 115 RAGRKIGKKSSALRADALHALVDVLGSLAVLIGLLLILLTGLPIADPLASLLIALLILYT 174
Query: 175 WSMTVLENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYTFGSHYFVEVDIVLP 234
+ E+++ L+G S PE + ++ + + +R + G YFV++ I +
Sbjct: 175 GLRLLKESLSELLGASPDPELVDEIRDAL-EKLPGVLGVHDLRVWKSGPKYFVDIHIEVD 233
Query: 235 ASMPLQEAHDIGESLQEKL-ELLPEIERAFVHLDYEYTH 272
+ ++EAH+I + ++ L E P I +H++
Sbjct: 234 PDLTVEEAHEIADEIERALKEKFPGIADVTIHVEPAPEV 272
>gnl|CDD|223131 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 133 bits (338), Expect = 2e-37
Identities = 67/273 (24%), Positives = 142/273 (52%), Gaps = 13/273 (4%)
Query: 1 MVLFAAKVYASVKSGSLAIIASTLDSLLDLLSGFILWFT-AFSMQTPNPYQYPIGKKRMQ 59
+ L K+ A + +GS+A++A + SL D+++ I+ S + P+ +P G + +
Sbjct: 23 LALALLKLIAGILTGSVALLADAIHSLSDIVASLIVLIGLRISSKPPD-RDHPYGHGKAE 81
Query: 60 PLGILVFASVMATLGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVY 119
L L+ + ++ G +I+LE+++ L+S + E +G+ L ++K L Y
Sbjct: 82 TLASLIVSILIFAAGFEILLEAIKRLISPQ-----PVEPPLLALGVALISIVIKEALYRY 136
Query: 120 CR----AFTNEIVKAYAQDHFFDVITNIIGLVAVLLANYIDDWMDPVGAIILALYTIRTW 175
R ++ + A A H DV+T++ LV +L + W+DP+ A++++LY ++T
Sbjct: 137 LRRVGKKTNSQALIADALHHRSDVLTSLAVLVGLLGSLLGWPWLDPLAALLISLYILKTG 196
Query: 176 SMTVLENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYTFGSHYFVEVDIVLPA 235
E+VN L+ + PE L+K+ + + + +R GS F++V I +
Sbjct: 197 FRLFKESVNELMDAALDPEDLEKIRAIILSVPGVKG-VHDLRTRKSGSRIFIDVHIEVDP 255
Query: 236 SMPLQEAHDIGESLQEKL-ELLPEIERAFVHLD 267
+ L+EAH+I + +++++ + P++ +H++
Sbjct: 256 DLSLEEAHEIADEVEKRIKKEFPKVADVTIHVE 288
>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 = 94.2 bits (235), Expect = 7e-23
Identities = 62/281 (22%), Positives = 128/281 (45%), Gaps = 26/281 (9%)
Query: 2 VLFAAKVYASVKSGSLAIIASTLDSLLDLLSGFILWFTAFSMQTPNPYQYPIGKKRMQPL 61
+L K+ + SGSLA++A + SL D+ + I + P ++P G R + L
Sbjct: 1 LLMLIKIVGGLLSGSLALLADAIHSLSDVAASAIALLALRISRRPADERHPFGHGRAEIL 60
Query: 62 GILVFASVMATLGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVYCR 121
L+ + + L I+ E++ L++ E + ++ + + +V L+L +Y
Sbjct: 61 AALLNGLFLVVVALFILYEAIERLINPEPE-----IDGGTMLIVAIVGLIVNLILALYLH 115
Query: 122 AFT----NEIVKAYAQDHFFDVITNIIGLVAVLLANYIDDWMDPVGAIILALYTIRTWSM 177
+ ++A A D ++++ L+ LL + W DP+ A++++L + +
Sbjct: 116 RVGHRLGSLALRAAALHVLSDALSSVGVLIGALLIYFGWHWADPIAALLISLLILY-TAF 174
Query: 178 TVL-ENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYTF-------GSHYFVEV 229
+L E++N L+ + E L+++ K+I I V+ F++V
Sbjct: 175 RLLKESINVLLDAAPDEEDLEEIK-------KAILSIPGVKGVHDLHIWRIGPGKLFLDV 227
Query: 230 DIVLPASMPLQEAHDIG-ESLQEKLELLPEIERAFVHLDYE 269
+V+ + L++AHDI E +E L+ P IE + ++
Sbjct: 228 HVVVDPDLDLKQAHDIALEIEREILKRHPGIEHVTIQVEPC 268
>gnl|CDD|181919 PRK09509, fieF, ferrous iron efflux protein F; Reviewed.
Length = 299
Score = 48.5 bits (116), Expect = 1e-06
Identities = 57/257 (22%), Positives = 120/257 (46%), Gaps = 12/257 (4%)
Query: 2 VLFAAKVYASVKSGSLAIIASTLDSLLDLLSGFI-LWFTAFSMQTPNPYQYPIGKKRMQP 60
+L K++A +GS++++A+ +DSL+D+ + L +S+Q P ++ G + +
Sbjct: 22 LLLLIKIFAWWYTGSVSLLAALVDSLVDIAASLTNLLVVRYSLQ-PADDEHTFGHGKAES 80
Query: 61 LGILVFASVMATLGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVYC 120
L L + ++ L + L ++ L+S + V + L TL+ LV +
Sbjct: 81 LAALAQSMFISGSALFLFLTGIQHLISPTPMND--PGVGIIVTLVALICTLI---LVTFQ 135
Query: 121 RAFTNEI-VKAYAQD--HF-FDVITNIIGLVAVLLANYIDDWMDPVGAIILALYTIRTWS 176
R + +A D H+ DV+ N L+A+ L+ Y D + A+ + +Y + +
Sbjct: 136 RWVVRKTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSAL 195
Query: 177 MTVLENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYTFGSHYFVEVDIVLPAS 236
E V SL+ R+ E Q++ + + + +R G F+++ + + +
Sbjct: 196 RMGYEAVQSLLDRALPDEERQEIIDIVTS-WPGVSGAHDLRTRQSGPTRFIQLHLEMEDN 254
Query: 237 MPLQEAHDIGESLQEKL 253
+PL +AH I + +++ L
Sbjct: 255 LPLVQAHMIADQVEQAL 271
>gnl|CDD|226474 COG3965, COG3965, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 314
Score = 45.1 bits (107), Expect = 1e-05
Identities = 42/256 (16%), Positives = 88/256 (34%), Gaps = 40/256 (15%)
Query: 14 SGSLAIIASTLDSLLDL-LSGFILWFTAFSMQTPNPYQYPIGKKRMQPLGILVFASVMAT 72
SGS++II + SL+D ++ L + + P ++P G ++PL + + +++A
Sbjct: 43 SGSMSIIFDGVYSLIDAGMTLLSLLVSRLIAKDPRDARFPYGFWHLEPLVLAINGTLLAL 102
Query: 73 LGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVY----CRAFTNEIV 128
L L ++ +L +L+ + + L + R + ++
Sbjct: 103 LCLYALINALGSLLDGGREVEPG-----HAIAYTLVSVTGCAAIAWKLRRLNRRLKSPLI 157
Query: 129 KAYAQDHFFDVITNIIGLVAVLLANYID----DWM----DPVGAIILALYTIRTWSMTVL 180
+ + VA A + + DP+ ++ L I TV
Sbjct: 158 ALDTKQWLMSTCLSAALFVAFAAAWLLAGTKFAHLVVYADPMVLALVCLVFIPLPLGTVK 217
Query: 181 ENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHID-TVRAYTFGSHY----------FVEV 229
+ ++ P LQ+ H V Y F S++ F+E+
Sbjct: 218 SALREIL--LMTPNELQQ---------SIESHAHEIVEKYGFPSYHVYVARVGRGLFIEI 266
Query: 230 DIVLPASMPLQEAHDI 245
++P + D
Sbjct: 267 HFIIPRESDARNVEDW 282
>gnl|CDD|224151 COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion
transport and metabolism].
Length = 296
Score = 44.6 bits (106), Expect = 2e-05
Identities = 51/283 (18%), Positives = 114/283 (40%), Gaps = 34/283 (12%)
Query: 1 MVLFAAKVYASVKSGSLAIIASTLDSLLDLLS-GFILWFTAFSMQTPNPYQYPIGKKRMQ 59
+ ++ + +GSLA++A L L D L+ L + + ++ G KR++
Sbjct: 32 LAFMLIEIIGGLLTGSLALLADALHMLSDALALLLALIAIKLARRPATK-RFTFGYKRLE 90
Query: 60 PLGILVFASVMATLGLQIILESLRTLVSNEDQFNLTKEQEQWVVGIM---LSVTLVKLLL 116
L + A ++ + L I+ E+++ L ++ + L V LV LL
Sbjct: 91 ILAAFLNALLLIVVSLLILWEAIQRL------LAPPPIHYSGMLVVAIIGLVVNLVSALL 144
Query: 117 VVYCRAFTNEIVKAYAQDHFF-DVITNIIGLVAVLLANYID-DWMDPVGAIILALYTI-R 173
+ + AY H D + ++ ++A ++ + W+DP+ +I++AL +
Sbjct: 145 LHKGHEENLNMRGAYL--HVLGDALGSVGVIIAAIVIRFTGWSWLDPILSIVIALLILSS 202
Query: 174 TWSMTVLENVNSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYT-------FGSHYF 226
W + E++N L+ + K+ +++ I V + G +
Sbjct: 203 AWPLLK-ESLNILLEGVPEGIDIDKV-------REALLRIPGVASVHDLHVWSITGGEHA 254
Query: 227 VEVDIVLPASMPLQEAHDIGESLQEKLELLPEIERAFVHLDYE 269
+ + +V+ + +A + + +L IE + L+ E
Sbjct: 255 LTLHVVVD---EVADADAALDQIVRRLLEKYGIEHVTIQLETE 294
>gnl|CDD|213771 TIGR03076, near_not_gcvH, Chlamydial GcvH-like protein upstream
region protein. The H protein (GcvH) of the glycine
cleavage system shuttles the methylamine group of
glycine from the P protein to the T protein. Most
Chlamydia but lack the P and T proteins, and have a
single homolog of GcvH that appears deeply split from
canonical GcvH in molecular phylogenetic trees. The
protein family modeled here is observed so far only in
the Chlamydiae, always as part of a two-gene operon,
upstream of the homolog of GcvH. Its function is unknown
[Unknown function, General].
Length = 686
Score = 31.4 bits (71), Expect = 0.60
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 9/70 (12%)
Query: 75 LQIILESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKLLLVVYCRAFTNEIVKAYAQD 134
IL L ++ L+ ++ + GI V L K+LL NE++ Y+QD
Sbjct: 464 PGRILSELAQQEQKSEEVFLSAGKDSLLPGIQDGVRLAKVLL-------QNEVLDYYSQD 516
Query: 135 --HFFDVITN 142
+++ +I
Sbjct: 517 DEYYYTIIVK 526
>gnl|CDD|235798 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
Length = 462
Score = 29.0 bits (66), Expect = 3.0
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 66 FASVMATLGLQI-ILESLRTLVSNED 90
FAS A+LG ++ I+E+L ++ ED
Sbjct: 187 FASAYASLGAEVTIVEALPRILPGED 212
>gnl|CDD|237123 PRK12511, PRK12511, RNA polymerase sigma factor; Provisional.
Length = 182
Score = 28.2 bits (63), Expect = 3.2
Identities = 24/97 (24%), Positives = 35/97 (36%), Gaps = 31/97 (31%)
Query: 172 IRTWSMTVLENV--NSLVGRSAAPEYLQKLTYLCWNHHKSIRHIDTVRAYTFGSHYFVEV 229
+RTW M++L N + L R R D + V
Sbjct: 55 LRTWLMSILHNAFIDELRRRRVEA-----------------RRADELA---------VLA 88
Query: 230 DIVLPASMPLQEAHDIGESLQEKLELLPEIERAFVHL 266
D LPA+ QE +++ LPE +RA +HL
Sbjct: 89 DASLPAA---QEHAVRLAQIRDAFFDLPEEQRAALHL 122
>gnl|CDD|238756 cd01479, Sec24-like, Sec24-like: Protein and membrane traffic in
eukaryotes is mediated by at least in part by the
budding and fusion of intracellular transport vesicles
that selectively carry cargo proteins and lipids from
donor to acceptor organelles. The two main classes of
vesicular carriers within the endocytic and the
biosynthetic pathways are COP- and clathrin-coated
vesicles. Formation of COPII vesicles requires the
ordered assembly of the coat built from several
cytosolic components GTPase Sar1, complexes of
Sec23-Sec24 and Sec13-Sec31. The process is initiated
by the conversion of GDP to GTP by the GTPase Sar1
which then recruits the heterodimeric complex of Sec23
and Sec24. This heterodimeric complex generates the
pre-budding complex. The final step leading to membrane
deformation and budding of COPII-coated vesicles is
carried by the heterodimeric complex Sec13-Sec31. The
members of this CD belong to the Sec23-like family. Sec
24 is very similar to Sec23. The Sec23 and Sec24
polypeptides fold into five distinct domains: a
beta-barrel, a zinc finger, a vWA or trunk, an all
helical region and a carboxy Gelsolin domain. The
members of this subgroup carry a partial MIDAS motif
and have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 244
Score = 28.4 bits (64), Expect = 4.0
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 9 YASVKSGSLAIIASTLDSLLDLLSGF 34
Y ++KSG LA L S LD L G
Sbjct: 14 YNAIKSGLLATACEALLSNLDNLPGD 39
>gnl|CDD|212083 cd11514, SLC6sbd_DAT1, Na(+)- and Cl(-)-dependent dopamine
transporter 1; solute-binding domain. DAT1 (also called
DAT), is a plasma membrane transport protein that
functions at the dopaminergic synapses to transport
dopamine from the extracellular space back into the
presynaptic nerve terminal. Human DAT1 is encoded by the
SLC6A3 gene, and is expressed in the brain. DAT1 may
play a role in diseases or disorders related to
dopaminergic neurons, including attention-deficit
hyperactivity disorder (ADHD), Tourette syndrome,
Parkinson's disease, alcoholism, drug abuse,
schizophrenia, extraversion, and risky behavior. This
subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 555
Score = 28.7 bits (64), Expect = 4.2
Identities = 32/123 (26%), Positives = 57/123 (46%), Gaps = 27/123 (21%)
Query: 18 AIIASTLDSLLDLLSGFILW-FTAFSMQTPNPYQYPIGKKRMQPLGI--LVFASVMATLG 74
AII ++++SL SGF+++ F + Q N PIG G+ +++ +ATL
Sbjct: 287 AIITTSINSLTSFFSGFVVFSFLGYMAQKHN---VPIGDVAKDGPGLIFIIYPEAIATLP 343
Query: 75 LQII--------------------LESLRTLVSNEDQFNLTKEQEQWVVGIMLSVTLVKL 114
L + +ES+ T + +E +F L + +E + + I+LS L+ L
Sbjct: 344 LSSVWAVIFFIMLLTLGIDSAMGGMESVITGLIDEFKF-LHRHRELFTLFIVLSTFLISL 402
Query: 115 LLV 117
V
Sbjct: 403 FCV 405
>gnl|CDD|224511 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma
subunit, sigma24 homolog [Transcription].
Length = 182
Score = 27.7 bits (62), Expect = 5.1
Identities = 16/95 (16%), Positives = 32/95 (33%), Gaps = 5/95 (5%)
Query: 177 MTVLENVNSLVGRSAAPEYLQK-LTYLCWNHHKSIRHIDTVRAYTFGSHYFVEVDIVLPA 235
+ ++S GRS+ +L + L + + + + L
Sbjct: 51 LRAWRAIDSFRGRSSFKAWLYRIARNLAIDRLRKRKRRRARVEEADLLPEEADPAPDLAE 110
Query: 236 SMPLQEAHDIGESLQEKLELLPEIER-AFVHLDYE 269
+ +E + L+ L LP +R AF+ E
Sbjct: 111 LLLAEEELER---LRRALARLPPRQREAFLLRYLE 142
>gnl|CDD|233061 TIGR00629, uvde, UV damage endonuclease UvdE. All proteins in this
family for which functions are known are UV dimer
endonucleases that function in an alternative nucleotide
excision repair process. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 312
Score = 28.0 bits (62), Expect = 6.6
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 202 LCWNHHKSIRHID-TVRAYTFGSHYFVEVDIVLPASMPLQEAHDIGESLQEKLELLP 257
L WN I + + F SH V D+V A L+E ++ ++ Q +L P
Sbjct: 58 LHWNIGHGIPFYRFSSSIFPFASHPDVGYDLVTFAQKELREIGELAKTHQHRLTFHP 114
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 27.7 bits (62), Expect = 7.9
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 162 VGAIILALYTIRTWSMTV----LENVNSLVGRSAAPEYLQKLTYLC 203
V A+ L + T ++ + + N++V A E L + +C
Sbjct: 307 VAAVPEGLPAVVTIALALGAQRMAKDNAIVRSLNAIETLGSVDVIC 352
>gnl|CDD|217357 pfam03079, ARD, ARD/ARD' family. The two acireductone dioxygenase
enzymes (ARD and ARD', previously known as E-2 and E-2')
from Klebsiella pneumoniae share the same amino acid
sequence, but bind different metal ions: ARD binds Ni2+,
ARD' binds Fe2+. ARD and ARD' can be experimentally
interconverted by removal of the bound metal ion and
reconstitution with the appropriate metal ion. The two
enzymes share the same substrate,
1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield
different products. ARD' yields the alpha-keto precursor
of methionine (and formate), thus forming part of the
ubiquitous methionine salvage pathway that converts
5'-methylthioadenosine (MTA) to methionine. This pathway
is responsible for the tight control of the
concentration of MTA, which is a powerful inhibitor of
polyamine biosynthesis and transmethylation reactions.
ARD yields methylthiopropanoate, carbon monoxide and
formate, and thus prevents the conversion of MTA to
methionine. The role of the ARD catalyzed reaction is
unclear: methylthiopropanoate is cytotoxic, and carbon
monoxide can activate guanylyl cyclase, leading to
increased intracellular cGMP levels. This family also
contains other members, whose functions are not well
characterized.
Length = 157
Score = 26.9 bits (60), Expect = 8.5
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 5/53 (9%)
Query: 190 SAAPEYLQKLTYLCWNH----HKSIRHIDTVRAYTFGSHYFVEVDIVLPASMP 238
A + L KL L W ++ + +R Y V P + P
Sbjct: 24 KAETDELAKLGVLYWKLDADDEETAEELLRIRKY-KHYDDVDIDVTVCPETTP 75
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
0.324 0.137 0.409
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,500,348
Number of extensions: 1404622
Number of successful extensions: 2027
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2001
Number of HSP's successfully gapped: 51
Length of query: 281
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 185
Effective length of database: 6,679,618
Effective search space: 1235729330
Effective search space used: 1235729330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.0 bits)