RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11919
(453 letters)
>gnl|CDD|214514 smart00094, TR_FER, Transferrin.
Length = 332
Score = 167 bits (424), Expect = 6e-48
Identities = 83/258 (32%), Positives = 120/258 (46%), Gaps = 32/258 (12%)
Query: 199 QCRNL-----EKYGNEKD----LLAVAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAP 249
+ NL E YG+E++ AVAVVKK S + + LRG KSCH+G ++GW P
Sbjct: 64 KPYNLVPVFAENYGSEEEPETGYYAVAVVKKGSAIFTWNQLRGKKSCHTGVGRTAGWNIP 123
Query: 250 VYHLLEKGLIKNDVCPYYKGVEQFFSGGSCVPGLEEKEKSESPSLEKIC-HNITTIFATN 308
+ L K +I+ CP+ K V +FFS SC PG + + +L +C + +++
Sbjct: 124 MGLLYNKLVIRPPNCPFEKAVSKFFS-ASCAPG--ADKPDPNSNLCALCAGDNKCACSSH 180
Query: 309 --------TLQCLKMGDADVAFTNQVKVNE-------AIEEGIFKVDEIEFLCSKGGRAP 353
+CL G DVAF V E A K D+ E LC G R P
Sbjct: 181 EPYYGYSGAFRCLAEGAGDVAFVKHSTVFENTDGKNGADWAKNLKRDDYELLCLDGTRKP 240
Query: 354 VSKAADCNLGVVPPHMVVTSNSKSNMEIDIIKHAIITAADLFSKKPEIFKLFGSFMGKPD 413
V++ +C+L VP H VV K I + + KP +F+LFGS GK D
Sbjct: 241 VTEYKNCHLARVPSHAVVARKDKKEDVIWELLN---QQQKFGKDKPSLFQLFGSPTGK-D 296
Query: 414 VLFLNPATGVESLPDQAT 431
+LF + A + +P +
Sbjct: 297 LLFKDSAKCLAKIPPKTD 314
>gnl|CDD|215903 pfam00405, Transferrin, Transferrin.
Length = 328
Score = 127 bits (322), Expect = 2e-33
Identities = 84/249 (33%), Positives = 115/249 (46%), Gaps = 29/249 (11%)
Query: 204 EKYGNEKD----LLAVAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGLI 259
E YG++++ AVAVVKK S Q L+G KSCH+G S+GW P+ L + +
Sbjct: 75 EVYGSKEEPQTHYYAVAVVKKGSNFQ-LNQLQGKKSCHTGLGRSAGWNIPIG--LLRPQL 131
Query: 260 K--NDVCPYYKGVEQFFSGGSCVPGLEEKEKSESPSLEKICHNITTI---FATN------ 308
P K V +FFS SCVPG +E P L ++C + N
Sbjct: 132 PWAIPREPLEKAVSKFFSA-SCVPGADE---GAFPKLCQLCAGDGENKCACSNNEPYFGY 187
Query: 309 --TLQCLKMGDADVAFTNQVKVNEAIEEGIFKVDEIEFLCSKGGRAPVSKAADCNLGVVP 366
+CLK G DVAF V E + + + D+ E LC R PV + DC+L VP
Sbjct: 188 SGAFKCLKDGAGDVAFVKHSTVFENLPDKADR-DQYELLCPDNTRKPVDEYKDCHLARVP 246
Query: 367 PHMVVTSNSKSNMEIDIIKHAIITAADLFSK-KPEIFKLFGSFMGKPDVLFLNPATGVES 425
H VV + S E I + + A + F K K F+LF S G+ D+LF + A G
Sbjct: 247 SHAVV-ARSVDGKEDLIWE-LLNQAQEKFGKDKSSDFQLFSSPHGQKDLLFKDSAIGFVR 304
Query: 426 LPDQATDVE 434
+P D
Sbjct: 305 VP-SKMDSF 312
>gnl|CDD|221878 pfam12974, Phosphonate-bd, ABC transporter, phosphonate,
periplasmic substrate-binding protein. This is a family
of periplasmic proteins which are part of the transport
system for alkylphosphonate uptake.
Length = 242
Score = 44.1 bits (105), Expect = 6e-05
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 214 AVAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGL 258
+V +V+KDS +++ EDL+G +SG++ P L E G+
Sbjct: 87 SVIIVRKDSPIKSLEDLKGKTFAFGDPNSTSGYLVPRALLKEAGI 131
>gnl|CDD|233271 TIGR01098, 3A0109s03R, phosphate/phosphite/phosphonate ABC
transporters, periplasmic binding protein. Phosphonates
are a varied class of phosphorus-containing organic
compound in which a direct C-P bond is found, rather
than a C-O-P linkage of the phosphorus through an oxygen
atom. They may be toxic but also may be used as sources
of phosphorus and energy by various bacteria.
Phosphonate utilization systems typically are encoded in
14 or more genes, including a three gene ABC
transporter. This family includes the periplasmic
binding protein component of ABC transporters for
phosphonates as well as other, related binding
components for closely related substances such as
phosphate and phosphite. A number of members of this
family are found in genomic contexts with components of
selenium metabolic processes suggestive of a role in
selenate or other selenium-compound transport. A subset
of this model in which nearly all members exhibit
genomic context with elements of phosphonate metabolism,
particularly the C-P lyase system (GenProp0232) has been
built (TIGR03431) as an equivalog. Nevertheless, there
are members of this subfamily (TIGR01098) which show up
sporadically on a phylogenetic tree that also show
phosphonate context and are most likely competent to
transport phosphonates [Transport and binding proteins,
Anions].
Length = 254
Score = 40.8 bits (96), Expect = 7e-04
Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 32/122 (26%)
Query: 214 AVAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGLIKNDVCPYYKGVEQF 273
+V +VK DS +++ +DL+G +SG++ P Y L ++G + D E
Sbjct: 123 SVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFS----EVV 178
Query: 274 FSGGSCVPGLEEKEKSESPSLEKICHNITTIFATNTLQCLKMGDADVAFTNQVKVNEAIE 333
FSG H+ + + N G D A N + +
Sbjct: 179 FSGS---------------------HDASALAVAN-------GKVDAATNNSSAIGRLKK 210
Query: 334 EG 335
G
Sbjct: 211 RG 212
>gnl|CDD|225762 COG3221, PhnD, ABC-type phosphate/phosphonate transport system,
periplasmic component [Inorganic ion transport and
metabolism].
Length = 299
Score = 37.3 bits (87), Expect = 0.010
Identities = 25/130 (19%), Positives = 44/130 (33%), Gaps = 38/130 (29%)
Query: 209 EKDLLAVAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGLIKNDVCPYYK 268
+V +V+ DS +++ EDL+G + +SG++ P+Y+L ++G I D
Sbjct: 121 SPGYYSVIIVRADSPIKSLEDLKGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPD------ 174
Query: 269 GVEQFFSGGSCVPGLEEKEKSESPSLEKICHNITTIFATNTLQCLKM---GDADVAFTNQ 325
+FF IF+ + G DVA N
Sbjct: 175 ---KFFG--------------------------EVIFSGGHDAAVLAVANGQVDVAAVNS 205
Query: 326 VKVNEAIEEG 335
+
Sbjct: 206 SARGLLKKAA 215
>gnl|CDD|132472 TIGR03431, PhnD, phosphonate ABC transporter, periplasmic
phosphonate binding protein. This model is a subset of
the broader subfamily of phosphate/phosphonate binding
protein ABC transporter components, TIGR01098. In this
model all members of the seed have support from genomic
context for association with pathways for the metabolims
of phosphonates, particularly the C-P lyase system,
GenProp0232. This model includes the characterized phnD
gene from E. coli. Note that this model does not
identify all phnD-subfamily genes with evident
phosphonate context, but all sequences above the trusted
context may be inferred to bind phosphonate compounds
even in the absence of such context. Furthermore, there
is ample evidence to suggest that many other members of
the TIGR01098 subfamily have a different primary
function.
Length = 288
Score = 32.3 bits (74), Expect = 0.44
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 215 VAVVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGLIKNDVCPYYKGVEQFF 274
V +VKKDS +++ EDL+G +SG++ P Y+L +K IK Y+K V F
Sbjct: 118 VLIVKKDSPIKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPK--EYFKKVT--F 173
Query: 275 SGG 277
SG
Sbjct: 174 SGS 176
>gnl|CDD|236644 PRK10049, pgaA, outer membrane protein PgaA; Provisional.
Length = 765
Score = 31.2 bits (71), Expect = 1.3
Identities = 17/93 (18%), Positives = 26/93 (27%), Gaps = 13/93 (13%)
Query: 87 KAGGCIKSFKLGLVAGFSSEVSSKVYGLRPTIYRSILPKVVLTADWRQYLPV-------Y 139
G I + VA S+ + +P +SIL ++ + L Y
Sbjct: 265 AEGQIIPPWAQRWVA------SAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFY 318
Query: 140 SNLASCKLRSATHYQVDLTDISHWRRSSRNSSV 172
S L S A + S S
Sbjct: 319 SLLESENYPGALTVTAHTINNSPPFLRLYGSPT 351
>gnl|CDD|173007 PRK14541, PRK14541, nucleoside diphosphate kinase; Provisional.
Length = 140
Score = 28.8 bits (64), Expect = 3.2
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 265 PYYKGVEQFFSGGSCVPGLEEKEKS 289
P+Y + +F S G CVP + EKE +
Sbjct: 56 PFYGELVEFMSSGPCVPMILEKENA 80
>gnl|CDD|184851 PRK14849, PRK14849, putative lipoprotein/autotransporter
domain-containing protein; Provisional.
Length = 1806
Score = 29.7 bits (66), Expect = 4.3
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 64 FKLGLVAGFSSEVSSKSSKTLNYKAGGCIKSFKLGLVAGFSSEVSSK 110
+ LG++AG++++ S+ S + YK+ G I + GL A + ++K
Sbjct: 1569 WHLGVMAGYANQHSNTQSNRVGYKSDGRISGYSAGLYATWYQNDANK 1615
>gnl|CDD|224274 COG1355, COG1355, Predicted dioxygenase [General function
prediction only].
Length = 279
Score = 28.4 bits (64), Expect = 7.9
Identities = 10/44 (22%), Positives = 15/44 (34%)
Query: 217 VVKKDSKVQNFEDLRGLKSCHSGYMDSSGWVAPVYHLLEKGLIK 260
+ G+ H+GY S A VY L++G
Sbjct: 33 GPGTLPETGFDRKAIGIVVPHAGYRYSGPTAAHVYSALDEGEPD 76
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
0.318 0.133 0.394
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,059,630
Number of extensions: 2056528
Number of successful extensions: 1380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1368
Number of HSP's successfully gapped: 12
Length of query: 453
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 353
Effective length of database: 6,502,202
Effective search space: 2295277306
Effective search space used: 2295277306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.3 bits)