RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17017
(442 letters)
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 225 bits (575), Expect = 4e-66
Identities = 132/369 (35%), Positives = 185/369 (50%), Gaps = 84/369 (22%)
Query: 85 PLIAVSKIPLFPKFIKIVDIFDQPLIDLIKRKVNLNQPYAGV---DHKVSLVKDLSEVYS 141
PL+ + + PLFP IK +D+ + I LIK + L QPY G+ + + ++YS
Sbjct: 1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEALRLKQPYLGLFLQKDDDNEEPEEDDIYS 60
Query: 142 VGSFVHIREVLTLPDR----LRLVLLAHRRIKIVAPYEDVDEGP----KVMNLKFPGVKD 193
VG I E+L LP ++V+ RRI+I E D+G +V NLK
Sbjct: 61 VGVVAQILEMLPLPSSGTATYKVVVEGLRRIRIK---ELSDKGGYLVVRVDNLK------ 111
Query: 194 GFDVLLEETNGGGARKKRSLRKRNGVKPAVPTESEEAPPVPGPGPDEPKPVTMVEVVNLK 253
P + ++ +E K +T
Sbjct: 112 ----------------------------EEPFDKDD---------EEIKALTR------- 127
Query: 254 HEKFKQSEEFKALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLGAAL 313
E K +E+I + L++EQ +L +D P LAD AA
Sbjct: 128 --------EIKETFRELISL-------SKLFREQPALLSA---LEDIDEPGRLADFVAAS 169
Query: 314 TG-AEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQ 372
E E Q +LE ++I KRL +L LLKKELEL KLQ KI ++VEEK+++ R+Y L+
Sbjct: 170 LQLKEKDELQEVLETVNIEKRLKKALELLKKELELLKLQNKITKKVEEKMEKTQREYYLR 229
Query: 373 EQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNV 432
EQLKAIKKELG+EKDDKD + EK +E++++ K+P V +V+ +EL KL LE SSEF V
Sbjct: 230 EQLKAIKKELGIEKDDKDEL-EKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTV 288
Query: 433 TRNYLDWLT 441
TRNYLDWLT
Sbjct: 289 TRNYLDWLT 297
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 169 bits (430), Expect = 7e-46
Identities = 74/204 (36%), Positives = 119/204 (58%), Gaps = 8/204 (3%)
Query: 240 EPKPVTMVEVVNLKHEKFKQSEEFKALMQEVIKTVRDIISMNP-LYKEQLMILLQQENSP 298
+ + E+ L E + E +AL++ ++ + +N + E+L L
Sbjct: 105 DEEEFFEAEIELLPDEPIDEEREIEALVRSILSEFEEYAKLNKKIPPEELQSLNS----- 159
Query: 299 VVDNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREV 358
+D+P LAD AA + E+Q ILE +D+ +RL L LL+KE++L +L+++I ++V
Sbjct: 160 -IDDPGKLADTIAAHLPLKLEEKQEILETLDVKERLEKLLDLLEKEIDLLQLEKRIRKKV 218
Query: 359 EEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELA 418
+E++++ R+Y L+EQLKAI+KELG + DDKD +EE RE+I+ K+P E +EL
Sbjct: 219 KEQMEKSQREYYLREQLKAIQKELGEDDDDKDEVEE-LREKIEKLKLPKEAKEKAEKELK 277
Query: 419 KLGFLESHSSEFNVTRNYLDWLTK 442
KL + S+E V RNYLDWL
Sbjct: 278 KLETMSPMSAEATVIRNYLDWLLD 301
Score = 39.5 bits (93), Expect = 0.004
Identities = 20/105 (19%), Positives = 50/105 (47%), Gaps = 12/105 (11%)
Query: 82 PHLPLIAVSKIPLFPKFIKIVDIFDQPLIDLIKRKVNLNQPYAGVDHKVSLVKDLS---- 137
LP++ + + +FP + + + + I ++ + +Q Y + KD S
Sbjct: 8 IELPVLPLRDVVVFPGMVIPLFVGREKSIKALEEAMKNDQKYIL----LVTQKDASTDEP 63
Query: 138 ---EVYSVGSFVHIREVLTLPD-RLRLVLLAHRRIKIVAPYEDVD 178
++Y VG+ I ++L LPD +++++ +R++I ++ +
Sbjct: 64 TEDDLYEVGTLAKILQILKLPDGTVKVLVEGLQRVRISKLSDEEE 108
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 85.8 bits (212), Expect = 7e-18
Identities = 48/143 (33%), Positives = 86/143 (60%), Gaps = 1/143 (0%)
Query: 300 VDNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVE 359
+D+P LAD AA + ++Q++LE D+ +RL +++++ E++L +++++I V+
Sbjct: 159 IDDPARLADTIAAHMPLKLADKQSVLEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVK 218
Query: 360 EKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK 419
+++++ R+Y L EQ+KAI+KELG E DD E + +I K+P E EL K
Sbjct: 219 KQMEKSQREYYLNEQMKAIQKELG-EMDDAPDENEALKRKIDAAKMPKEAKEKAEAELQK 277
Query: 420 LGFLESHSSEFNVTRNYLDWLTK 442
L + S+E V R Y+DW+ +
Sbjct: 278 LKMMSPMSAEATVVRGYIDWMVQ 300
>gnl|CDD|216923 pfam02190, LON, ATP-dependent protease La (LON) domain. This
domain has been shown to be part of the PUA superfamily.
Length = 191
Score = 60.1 bits (146), Expect = 1e-10
Identities = 22/89 (24%), Positives = 47/89 (52%), Gaps = 1/89 (1%)
Query: 84 LPLIAVSKIPLFPKFIKIVDIFDQPLIDLIKRKVNLNQPYAGVDHKVSLVKDLSEVYSVG 143
LPL+ + + LFP + + +F+ I I+ + ++P+ V + ++Y VG
Sbjct: 2 LPLLPLRNVVLFPGMVLPLHVFEPRYIAAIEEALESDRPFGLVLVSQKDPPSIDDLYEVG 61
Query: 144 SFVHIREVLTLPD-RLRLVLLAHRRIKIV 171
+ I +++ LPD RL++++ R +I+
Sbjct: 62 TLARIIQIVKLPDGRLKILVEGLERFRIL 90
Score = 54.7 bits (132), Expect = 9e-09
Identities = 30/103 (29%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 242 KPVTMVEVVNLKHEKFK-QSEEFKALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVV 300
+P + EV +L E+ + E +AL++E+I+ +++++ + + L I +
Sbjct: 96 EPYLVAEVEDLPEEELEELLEALEALVKELIEKIKELLPLLLPLELLLKIDD-------I 148
Query: 301 DNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSLLKK 343
++P LADL A+L E+Q +LE +D+ +RL L LLK+
Sbjct: 149 EDPGRLADLIASLLPLSPEEKQELLETLDVKERLEKLLELLKR 191
>gnl|CDD|197740 smart00464, LON, Found in ATP-dependent protease La (LON).
N-terminal domain of the ATP-dependent protease La
(LON), present also in other bacterial ORFs.
Length = 92
Score = 37.8 bits (88), Expect = 0.001
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 83 HLPLIAVSKIPLFPKFIKIVDIFDQPLIDLIKRKVNLNQPYAGVDHKVSLVKDLSEVYSV 142
LPL+ + + PLFP F+ + + + IK + +QPY V L D +E
Sbjct: 1 TLPLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRRSQPYVIV---FLLQDDPTETPEP 57
Query: 143 GSF 145
S
Sbjct: 58 LSD 60
Score = 33.6 bits (77), Expect = 0.031
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 290 ILLQQENSPVVDNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSL 340
LLQ + + + P L+D AAL E E+Q +LE KRL + L
Sbjct: 45 FLLQDDPT---ETPEPLSDTIAALMPLELHEKQELLELEGTNKRLEKVIKL 92
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 37.3 bits (86), Expect = 0.017
Identities = 30/182 (16%), Positives = 70/182 (38%), Gaps = 3/182 (1%)
Query: 251 NLKHEKFKQSEEFKALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLG 310
K EK + E+ + E +I +E+ + LQ++ + + + L
Sbjct: 324 LKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLE 383
Query: 311 AALTGAEGTEQQAILEEMDIPKRLMLSLSLL--KKELELNKLQQKIGREVEEKVK-QQHR 367
+ + ++ LE + ++ L L ++E L + +++ + VEE + + +
Sbjct: 384 SERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETK 443
Query: 368 KYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHS 427
+ L E+ + ++K+ DK +++ + K V L KL
Sbjct: 444 QGKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKLEEASQKE 503
Query: 428 SE 429
S+
Sbjct: 504 SK 505
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 33.3 bits (76), Expect = 0.25
Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 316 AEGTEQQAILE---EMDIPKRLMLSLS--LLKKELELNKLQQKIGREVEEKVKQQHRKYI 370
E EQQ + + ++ + SLS L KK +L + Q++I + + V Q +
Sbjct: 194 YEEKEQQLVNDCVKQLREANDQIASLSEELAKKTEDLERQQEEITHLLSQIVDLQKKCKS 253
Query: 371 LQEQLKAIKKELGLEKDDKDAIEEKFRE 398
+ + +++ L KD + ++ + +E
Sbjct: 254 YALENEELQQHLAAAKDAQRQLQAELQE 281
>gnl|CDD|119417 cd00891, PI3Kc, Phosphoinositide 3-kinase (PI3K), catalytic domain;
The PI3K catalytic domain family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as the typical serine/threonine/tyrosine
protein kinases (PKs), aminoglycoside
phosphotransferase, choline kinase, and RIO kinases.
PI3Ks catalyze the transfer of the gamma-phosphoryl
group from ATP to the 3-hydroxyl of the inositol ring of
D-myo-phosphatidylinositol (PtdIns) or its derivatives.
PI3Ks play an important role in a variety of fundamental
cellular processes, including cell motility, the Ras
pathway, vesicle trafficking and secretion, immune cell
activation and apoptosis. They can be divided into three
main classes (I, II, and III), defined by their
substrate specificity, regulation, and domain structure.
Class I PI3Ks are the only enzymes capable of converting
PtdIns(4,5)P2 to the critical second messenger
PtdIns(3,4,5)P3. Class I enzymes are heterodimers and
exist in multiple isoforms consisting of one catalytic
subunit (out of four isoforms) and one of several
regulatory subunits. Class II PI3Ks comprise three
catalytic isoforms that do not associate with any
regulatory subunits. They selectively use PtdIns as a
susbtrate to produce PtsIns(3)P.
Length = 352
Score = 32.2 bits (74), Expect = 0.48
Identities = 12/46 (26%), Positives = 27/46 (58%)
Query: 338 LSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELG 383
S L K++E+ + + ++V+ + + RK +L+E+LK ++ L
Sbjct: 1 RSELLKQVEVINELKTLAKKVKREKSKSQRKELLREELKKLENNLP 46
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 29.9 bits (68), Expect = 0.54
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 346 ELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKV 405
EL L +K+ +E+E K + + +++ + E GL ++ K + + K V
Sbjct: 2 ELEALIEKLEKEIEAARKAERAAAL--AEIRELAAEYGLTLEELLGGAAKKKAKKKRAPV 59
Query: 406 PP 407
P
Sbjct: 60 PA 61
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 31.2 bits (71), Expect = 0.88
Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 322 QAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKE 381
QA+ E +D +L+L LKK+L + ++ + + + L+E+L+ +
Sbjct: 103 QAVKETLDDRADALLTLQSLKKDL--ASKKAQLEKLKAAPGIKPAKVEELEEELEEAESA 160
Query: 382 LGLEKDDKDAIEEKFRERIK 401
L + + I E+ +E +K
Sbjct: 161 LEEARKRYEEISERLKEELK 180
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 31.7 bits (72), Expect = 0.94
Identities = 23/122 (18%), Positives = 53/122 (43%), Gaps = 9/122 (7%)
Query: 322 QAILEEMDIPKRLMLSLSLLKKELE------LNKLQQKIGREVEEKVKQQHRKYILQEQL 375
+ + E+++ + + L+ K EL L +L++++ +E K R L+E +
Sbjct: 332 EKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAI 391
Query: 376 KAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRN 435
+ +K+EL + I+E+ E K+ + + L E ++ LE ++
Sbjct: 392 QELKEELAELSAALEEIQEELEELEKELE---ELERELEELEEEIKKLEEQINQLESKEL 448
Query: 436 YL 437
+
Sbjct: 449 MI 450
Score = 29.7 bits (67), Expect = 4.0
Identities = 21/106 (19%), Positives = 47/106 (44%), Gaps = 8/106 (7%)
Query: 332 KRLMLSLSLLKKELE-----LNKLQQKIGR---EVEEKVKQQHRKYILQEQLKAIKKELG 383
+ + L L++ELE L +L +K+G +EE ++ L+++L+ ++K L
Sbjct: 684 EEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALE 743
Query: 384 LEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSE 429
L ++ ++ + + + + + NE L+KL
Sbjct: 744 LLEELREKLGKAGLRADILRNLLAQIEAEANEILSKLSLNRYDLRR 789
Score = 29.3 bits (66), Expect = 5.5
Identities = 17/78 (21%), Positives = 42/78 (53%), Gaps = 10/78 (12%)
Query: 325 LEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGL 384
E ++ + L L L++EL K + ++ E+EE L+++L+ +++EL
Sbjct: 470 EHEKELLELYELELEELEEELSREKEEAELREEIEE----------LEKELRELEEELIE 519
Query: 385 EKDDKDAIEEKFRERIKD 402
+ ++A++E+ E+++
Sbjct: 520 LLELEEALKEELEEKLEK 537
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 31.6 bits (72), Expect = 0.95
Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 9/107 (8%)
Query: 334 LMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE 393
L + S + +L ++Q++I ++ +QQ ++ L++QLK+++ E+ ++E
Sbjct: 27 LAAAFSAAADDKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEI-------ASLE 79
Query: 394 EKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWL 440
+ E D K + LN L L + L L
Sbjct: 80 AQLIETADDLKKLRKQIADLNARLNAL--EVQEREQRRRLAEQLAAL 124
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 30.6 bits (70), Expect = 1.1
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 341 LKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERI 400
L+ E ++L+Q+I + EEK + + R L+ +L+AI+K E++++ E++ + I
Sbjct: 116 LQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKR---EEEERQIEEKRHADEI 172
>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
protein; Provisional.
Length = 311
Score = 30.8 bits (69), Expect = 1.3
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 8/82 (9%)
Query: 214 RKRNGVKPAVPTESEEAPPVPGPGPDEPKPVTMVEVVNLKHEKFKQSEEFKALMQEVIKT 273
+K P P E V P E KPV E N+ E K+ ++ ++++
Sbjct: 125 KKSKKPLPVEPKAKVETKKVAKPSKVEVKPVEKDE--NVDPELLKREQQVLKVVEKTASQ 182
Query: 274 VRD------IISMNPLYKEQLM 289
+ +IS +P + L
Sbjct: 183 KEEETTETIMISTSPKNAQVLF 204
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 30.3 bits (69), Expect = 1.4
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 329 DIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 382
D+ +R+ + + E E+ KL++K+ +E KQ +RK L ++K +KKEL
Sbjct: 173 DLKERVERLEQIEELEKEIAKLKKKLKKE-----KQFNRKVELNLEIKKLKKEL 221
>gnl|CDD|235958 PRK07194, fliG, flagellar motor switch protein G; Reviewed.
Length = 334
Score = 30.7 bits (70), Expect = 1.5
Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 26/88 (29%)
Query: 271 IKTVRDIISMNPLYKEQLMILLQQENSPVVDN------------------------PIYL 306
+K DII+ P ++QLM +L++ + VV+ + +
Sbjct: 199 VKQAADIINRFPGDRQQLMEMLKEHDEEVVNEIEDNMYDFFILSRQSEETLQRLMDEVPM 258
Query: 307 ADLGAALTGAEGTEQQAILEEMDIPKRL 334
AL G E +QAIL M PKR
Sbjct: 259 ELWAVALKGTEPALRQAILRVM--PKRQ 284
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 28.7 bits (65), Expect = 1.5
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 356 REVEEKVKQQHRKYI-LQEQLKAIKKELGLEKDDKDAIEEKFRER 399
++ +++ + L+ + + ++ E+ K D D IEE+ R
Sbjct: 20 YQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYIEERARSE 64
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 30.8 bits (70), Expect = 1.5
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 25/85 (29%)
Query: 214 RKRNGVKPAVPTESEEAPPVPGPGPDEPKPVTMVEVVNLKHEKFKQSEEFKALMQEVIKT 273
R+R P P E EE P+E E+ ++ EE + +EV T
Sbjct: 292 RRRRRRPPPSPPEPEEEEEEEEEVPEE--------------EEEEEEEEERTFEEEVRAT 337
Query: 274 VRDIISMNPLYKEQLMILLQQENSP 298
V + I LL++E +
Sbjct: 338 VAEAIR-----------LLEEELTV 351
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 29.9 bits (68), Expect = 1.7
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 332 KRLMLSLSLLKKELELNKLQQKI------------GREVEEKV-KQQHRKYILQEQLKAI 378
+L L LKKELE +L+Q+I GRE E+ + L+++LK +
Sbjct: 65 NKLKTRLEKLKKELE--ELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKL 122
Query: 379 KKELG-LEKDDKDAIEEKFRERIKDKK 404
K EL EK+D + IE+ +E K K
Sbjct: 123 KAELEKYEKNDPERIEKL-KEETKVAK 148
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 30.8 bits (70), Expect = 1.8
Identities = 16/72 (22%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 332 KRLMLSLSLLKKELE-----LNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEK 386
++L L L++ELE L +LQ+++ EE + L+E+++ ++++ +
Sbjct: 733 EQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQ 792
Query: 387 DDKDAIEEKFRE 398
++ + +EE+ E
Sbjct: 793 EELEELEEELEE 804
Score = 28.5 bits (64), Expect = 9.1
Identities = 26/119 (21%), Positives = 51/119 (42%), Gaps = 12/119 (10%)
Query: 336 LSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEK 395
L L + EL +LQ+++ EE + + +L+E+L+ ++ EL ++ + ++EK
Sbjct: 272 LKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEK 331
Query: 396 FRERIKDKKVPPPVMEVLNEELAKL------------GFLESHSSEFNVTRNYLDWLTK 442
++ + ++E L + LA+L LE F R L L
Sbjct: 332 IEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEA 390
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 30.2 bits (68), Expect = 1.9
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 339 SLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 398
S +KK E N L V++K K+ K LQ++L+ +KKEL E +D+ I+ +
Sbjct: 90 SHIKKHKERNTLPDL--NNVDKKTKKLINK--LQKELEELKKELDNEMNDELTIQPIHDK 145
Query: 399 RIKDKKVPPPVMEVLNEELAKL 420
I K V E +E+ +L
Sbjct: 146 IIIKKDENNSVSE--HEDFKQL 165
>gnl|CDD|179392 PRK02249, PRK02249, DNA primase large subunit; Validated.
Length = 343
Score = 30.3 bits (69), Expect = 1.9
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 392 IEEKFRERIKDK---KVPPPVMEVLNEELAKL 420
+ E RERI D VP + E L L ++
Sbjct: 170 LREAIRERILDGLPLAVPEEIAEALLPLLEEI 201
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 30.0 bits (68), Expect = 2.0
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 6/97 (6%)
Query: 308 DLGAALTGAEGTEQQAILEEMDIPK------RLMLSLSLLKKELELNKLQQKIGREVEEK 361
L A E E Q E +I + R LS +K E EL L +I E
Sbjct: 46 ALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERI 105
Query: 362 VKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 398
+ L E+++ ++KE+ K+ + +E+ E
Sbjct: 106 NSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAE 142
>gnl|CDD|225471 COG2919, COG2919, Septum formation initiator [Cell division and
chromosome partitioning].
Length = 117
Score = 28.8 bits (65), Expect = 2.0
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 13/91 (14%)
Query: 319 TEQQAILEEMDIPKR--LMLSLSLLKKELELNKLQQKIG----REVEEKVKQQHRKYILQ 372
++ E + +R L L L L + K G +++ ++ Q +
Sbjct: 10 KQKATRQGERRVRRRRILTLVLLALLALFQYLAWFGKNGAADVLQLQRQIAAQQAEL--- 66
Query: 373 EQLKA----IKKELGLEKDDKDAIEEKFRER 399
E+L A ++ E+ KD +D IEE+ R
Sbjct: 67 EKLSARNTALEAEIKDLKDGRDYIEERARSE 97
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 30.3 bits (69), Expect = 2.3
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 356 REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNE 415
E+EE++++++ + +LK + E + + +K +E+K ++ IK K + E L E
Sbjct: 64 EEIEEELREEYEE-----ELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLE 118
Query: 416 ELA 418
A
Sbjct: 119 LEA 121
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 30.0 bits (68), Expect = 2.5
Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 342 KKELELNKLQQKIG---REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE----- 393
EL++ ++K+ +E+ KVK+ L+E+L+ ++ ++ + K +
Sbjct: 201 CDPTELDRAKEKLKKLLQEIMIKVKKLE---ELEEELQELESKIEDLTNKKSELNTEIAE 257
Query: 394 -EKFRERIKD 402
EK E+ +
Sbjct: 258 AEKKLEQCRG 267
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly related
to archaeal Holliday junction resolvase [Nucleotide
transport and metabolism].
Length = 175
Score = 29.3 bits (66), Expect = 2.6
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 334 LMLSLSLLKKELELNKLQQKI---GREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKD 390
+L+L L + LQ K+ RE+EE +++ R+ ++ E ++E L++ +
Sbjct: 11 FILALVLYLLRAYIRSLQGKVESKARELEETLQKAERERLVNEAQARKEEEWKLKEWIEK 70
Query: 391 AIEEKFRERIK 401
IEE + ++
Sbjct: 71 KIEEAREDAVR 81
>gnl|CDD|237937 PRK15304, PRK15304, putative fimbrial outer membrane usher protein;
Provisional.
Length = 801
Score = 30.1 bits (68), Expect = 2.9
Identities = 16/58 (27%), Positives = 20/58 (34%), Gaps = 7/58 (12%)
Query: 2 SIPSRINLGYSNYYRDNGGIHSARICLNQCKANFKPFS------SQGGSGDRGSKDDD 53
S+ +LGY +G S I + K FK S D S DDD
Sbjct: 471 SLLGTFSLGYYYNQATDGDNDSRYINASWGKT-FKYASVSVNWQHAVSQDDENSNDDD 527
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.0 bits (68), Expect = 3.2
Identities = 21/119 (17%), Positives = 52/119 (43%), Gaps = 15/119 (12%)
Query: 326 EEMDIPKRLMLSLSLLKKELELNK---------LQQKIGREVEEKVKQQHRKYILQEQLK 376
EE++ ++ + +L+ LE K L++++ + + + + L E+L
Sbjct: 281 EEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELA 340
Query: 377 AIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRN 435
++++L K++ +++E + E + +E EEL + LE+ S+
Sbjct: 341 ELEEKLEELKEELESLEAELEELEAEL----EELESRLEELEEQ--LETLRSKVAQLEL 393
>gnl|CDD|204827 pfam12120, Arr-ms, Rifampin ADP-ribosyl transferase. This protein
is found in bacteria. Proteins in this family are
typically between 136 to 150 amino acids in length. The
opportunistic pathogen Mycobacterium smegmatis is
resistant to rifampin because of the presence of a
chromosomally encoded rifampin ADP-ribosyltransferase
(Arr-ms). Arr-ms is a small enzyme whose activity thus
renders rifamycin antibiotics ineffective.
Length = 100
Score = 28.1 bits (63), Expect = 3.3
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 167 RIKIVAPYEDVDEGPKVMNLKFPG 190
RI IV P ++ P + + KFPG
Sbjct: 56 RIYIVEPTGPFEDDPNLTDKKFPG 79
>gnl|CDD|240348 PTZ00294, PTZ00294, glycerol kinase-like protein; Provisional.
Length = 504
Score = 29.6 bits (67), Expect = 3.7
Identities = 13/51 (25%), Positives = 26/51 (50%)
Query: 336 LSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEK 386
L++ + K E+ KL ++ ++ + RK I +E KA+++ L K
Sbjct: 453 LAVGVWKSLEEVKKLIRRSNSTFSPQMSAEERKAIYKEWNKAVERSLKWAK 503
>gnl|CDD|187827 cd09696, Cas3_I, CRISPR/Cas system-associated protein Cas3;
Distinct Cas3 family with HD domain fused to C-termus of
Helicase domain. 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; DNA helicase Cas3; This protein includes
both DEAH and HD motifs; signature gene for Type I.
Length = 843
Score = 29.6 bits (66), Expect = 3.8
Identities = 36/146 (24%), Positives = 52/146 (35%), Gaps = 16/146 (10%)
Query: 182 KVMNLKFPGVKDGFDVLLEETNGGGARKKRSLRKRNGVKPAVPTESEEAPPVPGPGPDEP 241
+V+ L DG D K L+KR K V P DE
Sbjct: 206 RVVELTATSRTDGPDRTT--LLSAEDYKHPVLKKRLAAKKIVKLV---------PPSDEK 254
Query: 242 KPVTMVEVVNLKHEKFKQSEEFKALMQEVIKTVRDIISMNPLYKEQLMI--LLQQENSPV 299
TMV+ +NL K S + +K VR + + P K +L+ L E +
Sbjct: 255 FLSTMVKELNLLM---KDSGGAILVFCRTVKHVRKVFAKLPKEKFELLTGTLRGAERDDL 311
Query: 300 VDNPIYLADLGAALTGAEGTEQQAIL 325
V I+ L L+G+ QQ +
Sbjct: 312 VKKEIFNRFLPQMLSGSRARPQQGTV 337
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 29.7 bits (67), Expect = 3.8
Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 28/133 (21%)
Query: 322 QAILEEMDIPKRLMLSLSLLKKELELN---------KLQQKIGREVEEKVKQQHRKYI-- 370
+ LEE I K L + KE L+ Q + G E +E+VK++ K +
Sbjct: 440 KKFLEEEAILKSLEEFKQSIVKEAALSILEEIREKVLEQAEQGCENQEEVKKEVPKKVKK 499
Query: 371 -LQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEE---------LAKL 420
+ + +ELG+ ++ + +E + KK + V+ E+ LAKL
Sbjct: 500 IPEVDTYLLLEELGINEETYEKLEA-----LLAKKNNFTL--VVGEDLYAHKNAKNLAKL 552
Query: 421 GFLESHSSEFNVT 433
L + F V
Sbjct: 553 LGLIQKYTAFKVI 565
>gnl|CDD|173302 PRK14841, PRK14841, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 233
Score = 29.2 bits (65), Expect = 4.0
Identities = 25/98 (25%), Positives = 46/98 (46%), Gaps = 12/98 (12%)
Query: 322 QAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKE 381
Q I EM++ +R + + +L ++ L + K +EVEEK K+ R ++ I
Sbjct: 77 QMIDREMELLRRERVRVRILGRKEGLPEKVLKKWQEVEEKTKEFDRMTLV------IAFN 130
Query: 382 LGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK 419
G ++ DA+E ++ + KK+ L EE +
Sbjct: 131 YGGRREILDAVESILKDVSQGKKI------ELTEETFR 162
>gnl|CDD|178173 PLN02559, PLN02559, chalcone--flavonone isomerase.
Length = 230
Score = 29.0 bits (65), Expect = 4.3
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 355 GREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPP 407
G + EKV E AI K LG+ D + EKF+E K++ PP
Sbjct: 102 GEQYSEKVT---------ENCVAIWKSLGIYTDAEAKAVEKFKEAFKEETFPP 145
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 29.5 bits (67), Expect = 4.4
Identities = 15/101 (14%), Positives = 36/101 (35%), Gaps = 13/101 (12%)
Query: 333 RLMLSLSLLKKELELNKLQQKIGREVEEKV---------KQQHRKYILQEQLKAIKKELG 383
L L L E E ++ E + ++ + ++ + + LG
Sbjct: 307 HLFLLYLLWLDEPEDTDQWVELADENNNLIALEHPLEALALAAEAELILDAMEDLVQHLG 366
Query: 384 LEKDDKDAIEEKFRERIKDKKVPPP---VMEVLNEELAKLG 421
L + +D I++ +E++ D + + ++ E G
Sbjct: 367 LPDEYQDLIKQL-KEQLTDPEKTLSGRLLKQIKQESYVAFG 406
>gnl|CDD|191179 pfam05053, Menin, Menin. MEN1, the gene responsible for multiple
endocrine neoplasia type 1, is a tumour suppressor gene
that encodes a protein called Menin which may be an
atypical GTPase stimulated by nm23.
Length = 618
Score = 29.6 bits (66), Expect = 4.5
Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 3/61 (4%)
Query: 203 NGGGARKKRSLRKRNGVKPAVPTESEEAPPVPGPGPDEPKPVTMVEVVNLKHEKFKQSEE 262
N GA +K + A T + VP P EP V+ EK K +E
Sbjct: 515 NNNGADRKEAAATTGN---ATTTSNGSGTSVPLPVSSEPPQHKEGPVITFYSEKMKGMKE 571
Query: 263 F 263
Sbjct: 572 L 572
>gnl|CDD|191851 pfam07798, DUF1640, Protein of unknown function (DUF1640). This
family consists of sequences derived from hypothetical
eukaryotic proteins. A region approximately 100 residues
in length is featured.
Length = 177
Score = 28.7 bits (65), Expect = 4.6
Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 14/107 (13%)
Query: 249 VVNLKHEKF--KQSEEFKALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYL 306
V +L+ F +Q+E + + +VI + +S + + KEQ Q+
Sbjct: 8 VQSLEENGFTEEQAEAIVSALTDVINDSIENVSKDMVTKEQQEKTEYQQKV-------DF 60
Query: 307 ADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSLLKKEL--ELNKLQ 351
A L + L E +E + E ++L L LK L E+ K+
Sbjct: 61 AKLKSELQSLEKSEFANLQAEN---EKLKNDLEKLKNRLRDEITKVT 104
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 28.8 bits (65), Expect = 4.7
Identities = 8/47 (17%), Positives = 22/47 (46%)
Query: 356 REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKD 402
E E +++Q + + +L+A ++ L K+ + + + + I
Sbjct: 49 AEAEREIEQLREQELSSAKLEAKRERLNARKEVLEDVRNQVEDEIAS 95
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.9 bits (65), Expect = 4.8
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 7/72 (9%)
Query: 343 KELELNKLQQKIGREVEE----KVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 398
+ E N Q++ + ++E K+KQQ +K +E+ + +K+ E++ K EE +++
Sbjct: 169 AKPERNVSQEEAKKRLQEWELKKLKQQQQKR--EEERRKQRKKQQEEEERKQKAEEAWQK 226
Query: 399 RIKD-KKVPPPV 409
+K+ K+ P PV
Sbjct: 227 WMKNVKQRPKPV 238
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 29.3 bits (66), Expect = 5.3
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 337 SLSLLKKELELNKLQQKIGREVEEKVKQ-QHRKYILQEQLKAIKKELGLEKDDKDAIEEK 395
S L E E+ L+ +I +EVEE ++ + L+E L + +E ++ + + E
Sbjct: 66 SKEFLDLEEEILDLEAEI-KEVEENLESLEKEINELEEWLNVLDEEKSFLDENLEELSEL 124
Query: 396 FR 397
Sbjct: 125 SN 126
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 28.1 bits (62), Expect = 5.6
Identities = 19/64 (29%), Positives = 36/64 (56%)
Query: 341 LKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERI 400
L++E E + +++ RE EEK K++ + QEQ + + + E+ + A EE R R+
Sbjct: 69 LRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRL 128
Query: 401 KDKK 404
+ +K
Sbjct: 129 EREK 132
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. 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 = 1042
Score = 29.2 bits (65), Expect = 5.8
Identities = 28/181 (15%), Positives = 59/181 (32%), Gaps = 23/181 (12%)
Query: 258 KQSEEFKALMQEVIKTVRDIISMNPLYKEQLMILLQ--QENSPVVDNPIYLADLGAALTG 315
KQ K MQE+ ++ + + KE + L + + D+ A
Sbjct: 556 KQRASLKEQMQEIQQSFSILTQCDNRSKEDIPNLQNITVRLQDLTEKLSEAEDMLACEQH 615
Query: 316 AEGTE-------QQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRK 368
A + Q L + L L L+ L +L Q+++ RE ++ ++
Sbjct: 616 ALLRKLQPEQDLQDVRLHLQQCSQELALKLTALHAL-QLTLTQERV-REHALSIRVLPKE 673
Query: 369 YILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSS 428
+ QL ++ + + K++ +L E + + +
Sbjct: 674 LLASRQLA------------LQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFN 721
Query: 429 E 429
E
Sbjct: 722 E 722
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 28.9 bits (65), Expect = 6.0
Identities = 30/115 (26%), Positives = 53/115 (46%), Gaps = 12/115 (10%)
Query: 325 LEEMDIPKRLMLSL-SLLKKE---LELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKK 380
L E+ IP L L+L +K+ ++ KL++++G V ++ AI+K
Sbjct: 95 LLELGIPMILALNLVDEAEKKGIRIDEEKLEERLGVPVVPTSAT--EGRGIERLKDAIRK 152
Query: 381 ELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK-----LGFLESHSSEF 430
+GL++ K AIE E + +V ++E++ + LG LE S E
Sbjct: 153 AIGLKELKKRAIEI-VPEAYQVVEVVEGLIEIIYSISKRGLEILLGLLEDLSLEI 206
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 28.8 bits (65), Expect = 6.2
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 353 KIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE--EKFRERIKDKKVP 406
+I E+EE++K++ K I +E+L+ +EKD ++ E +R RI+ K P
Sbjct: 38 EIASEIEEELKKEGIKEITKEELRRRVYYKLIEKDYEEVAEKYLLWR-RIRKSKEP 92
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 28.6 bits (64), Expect = 6.3
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 24/105 (22%)
Query: 314 TGAEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQE 373
T E T+Q+ + L+ +KELE + Q EE +K Q + QE
Sbjct: 97 TLQEQTQQEQQRAQYQDE----LARKRYQKELEQQRRQN------EELLKMQEESVLRQE 146
Query: 374 QL-------------KAIKKELGLE-KDDKDAIEEKFRERIKDKK 404
+ + I++E LE ++ + IE + R R K+++
Sbjct: 147 AMRRATEEEILEMRRETIEEEAELERENIRAKIEAEARGRAKEER 191
>gnl|CDD|235718 PRK06154, PRK06154, hypothetical protein; Provisional.
Length = 565
Score = 29.0 bits (65), Expect = 6.5
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 11/72 (15%)
Query: 162 LLAHRRI-KIVAPYEDVDEGPKVMNLKFPGVKDG----------FDVLLEETNGGGARKK 210
L +R I K DE P++M F +++G DVL EE + +
Sbjct: 131 LRNYRHITKWCEQVTLPDEVPELMRRAFTRLRNGRPGPVVLELPVDVLAEELDELPLDHR 190
Query: 211 RSLRKRNGVKPA 222
S R R G P
Sbjct: 191 PSRRSRPGADPV 202
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 28.4 bits (64), Expect = 6.5
Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 22/101 (21%)
Query: 340 LLKKELELNKLQQKIGR------EVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE 393
LL KEL+L + +QK EVE+ +K+ + L +L+ ++ EL K D+ +E
Sbjct: 141 LLGKELDLRESRQKALSRPLELAEVEKALKEAIKN--LAARLQQLQAELDNLKSDEANLE 198
Query: 394 EKFR------ERIKD-----KKVPPPVM---EVLNEELAKL 420
K ER + + V P M E L EEL KL
Sbjct: 199 AKIERKKQELERTQKRLQALQSVRPAFMEEYEKLEEELQKL 239
>gnl|CDD|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201). This is
a family of coiled-coil proteins from eukaryotes. The
function is not known.
Length = 177
Score = 27.9 bits (63), Expect = 6.8
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 332 KRLMLS--LSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGL 384
K ML L LKKEL+ + + R+ KVK + K L++Q K ++++ GL
Sbjct: 85 KLHMLEEELERLKKELKEKEERLAKLRKELYKVKLERDK--LRKQNKKLRQQGGL 137
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 28.9 bits (66), Expect = 7.0
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 17/66 (25%)
Query: 356 REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNE 415
+E+ +KV ++ I + +K +K+ L+ +DK+AI+ K E L +
Sbjct: 544 KELGDKVPADEKEKI-EAAIKELKE--ALKGEDKEAIKAK--------------TEELTQ 586
Query: 416 ELAKLG 421
KLG
Sbjct: 587 ASQKLG 592
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 27.6 bits (62), Expect = 7.1
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 321 QQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKK 380
Q+ +E+ P + LK E E NK ++K R E+K +++ RK +Q K K
Sbjct: 71 QRQAAKEVKKPGISTKAQQALKLEHERNKQEKKK-RSKEKKEEEKERKR-QLKQQKKKAK 128
>gnl|CDD|223010 PHA03215, PHA03215, nuclear protein UL24; Provisional.
Length = 262
Score = 28.3 bits (63), Expect = 7.4
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 205 GGARKKRSLR--KRNGVKPAVPTESEEAPPVPGPGPDEPKP 243
GAR+ RS R + P VP E A P P P
Sbjct: 202 RGARRPRSRRRPRGGAAGPPVPAEP--AAPERPPADPTPTS 240
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.6 bits (65), Expect = 7.7
Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 342 KKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEK-----DDKDAIEEKF 396
+ LE + K+ E E++++++ + E+ + ++KE L++ + ++ EK
Sbjct: 57 EALLEAKEEIHKLRNEFEKELRERRNELQKLEK-RLLQKEENLDRKLELLEKREEELEKK 115
Query: 397 RERIKDKKVPPPVMEVLNEELAKL 420
+ ++ K+ +E EEL +L
Sbjct: 116 EKELEQKQQ---ELEKKEEELEEL 136
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 28.4 bits (64), Expect = 8.5
Identities = 12/61 (19%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 357 EVEEKVKQQHRKYILQEQLKAIKKELGLEKDD--KDAIEEKFRERIKDKKVPPPVMEVLN 414
E + ++Q+ R+ L EQ + + E G + + + ++++ +R+ + +P V+ +L
Sbjct: 453 EFQAFLEQERRRSELVEQ-RTREAEEGRARLELARQQVQQELEQRLAGRSLPEVVVTLLR 511
Query: 415 E 415
+
Sbjct: 512 Q 512
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 28.3 bits (63), Expect = 8.8
Identities = 28/118 (23%), Positives = 48/118 (40%), Gaps = 24/118 (20%)
Query: 286 EQLMILLQQENSPVVDNPIYLADLGAALTG--AEGTEQQAILEEMDIPKRL--------- 334
+ L +L + + + G L G E Q+ +LE + ++
Sbjct: 130 QGLAVLERSRGGQLYGKLLRFDSNGQELDGDPLERELQKRLLEVETLRDQVDKMVEQQVR 189
Query: 335 MLS-----LSLLKKELELN-----KLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 382
+++ L L K+ L+LN + QQ V EK + Q R LQ +L A++ EL
Sbjct: 190 VINSQLERLRLEKRRLQLNGQLDDEFQQHY---VAEKSELQKRLAQLQTELDALRAEL 244
>gnl|CDD|197232 cd09134, PLDc_PSS_G_neg_1, Catalytic domain, repeat 1, of
phosphatidylserine synthases from gram-negative
bacteria. Catalytic domain, repeat 1, of
phosphatidylserine synthases (PSSs) from gram-negative
bacteria. There are two subclasses of PSS enzymes in
bacteria: subclass I of gram-negative bacteria and
subclass II of gram-positive bacteria. It is common that
PSSs in gram-positive bacteria and yeast are tight
membrane-associated enzymes. By contrast, the
gram-negative bacterial PSSs, such as Escherichia coli
PSS, are commonly bound to the ribosomes. They are
peripheral membrane proteins that can interact with the
surface of the inner membrane by binding to the lipid
substrate (CDP-diacylglycerol) and the lipid product
(phosphatidylserine). The prototypical member of this
subfamily is Escherichia coli PSS (also called
CDP-diacylglycerol-L-serine O-phosphatidyltransferase,
EC 2.7.8.8), which catalyzes the exchange reactions
between CMP and CDP-diacylglycerol, and between serine
and phosphatidylserine. The phosphatidylserine is then
decarboxylated by phosphatidylserine decarboxylase to
yield phosphatidylethanolamine, the major phospholipid
in Escherichia coli. It also catalyzes the hydrolysis of
CDP-diacylglycerol to form phosphatidic acid with the
release of CMP. PSS may utilize a ping-pong mechanism
involving a phosphatidyl-enzyme intermediate, which is
distinct from those of gram-positive bacterial
phosphatidylserine synthases. Moreover, all members in
this subfamily have two HKD motifs (H-x-K-x(4)-D, where
x represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
constitute an active site for the formation of a
covalent substrate-enzyme intermediate.
Length = 173
Score = 27.6 bits (62), Expect = 9.0
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 150 EVLTLPDRLRLVLL-----AHRRIKIVAPY-EDVDEGPKVMN 185
+VL P R LL A +RI IVA Y ED + G ++++
Sbjct: 12 DVLYSPKDFRARLLELISNAKKRIYIVALYLEDDEAGREILD 53
>gnl|CDD|185644 PTZ00465, PTZ00465, rhoptry-associated protein 1 (RAP-1);
Provisional.
Length = 565
Score = 28.2 bits (62), Expect = 9.7
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 350 LQQKIGREVEEKVKQ--QHRKYILQEQLKAIKKEL--GLEKDDKDAIEEKFRERIKD--K 403
L + IG+ +E ++ Q K+ L E + KE + + K I E + K+ K
Sbjct: 402 LDENIGQPTKEFFREAPQVTKHFLDENIAQPTKEFFRDVPQVTKKVITENIAQPTKEFLK 461
Query: 404 KVPPPVMEVLNEELAK 419
+VP M+VLNE +A+
Sbjct: 462 EVPHTTMKVLNENIAQ 477
>gnl|CDD|235205 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E;
Validated.
Length = 630
Score = 28.2 bits (64), Expect = 9.9
Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 343 KELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKD 402
+EL L L ++ ++ +++ +++ ++ ++ + A +G + + R +
Sbjct: 561 EELGLKGLSEEEVEKIIDEIVEENIDFVKEKGMGAFGPLMGE-------VMAELRGKADG 613
Query: 403 KKVPPPVMEVLNEELAK 419
K V + E L E L K
Sbjct: 614 KLVSEILREKLKEILNK 630
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
0.315 0.136 0.384
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,465,194
Number of extensions: 2420265
Number of successful extensions: 2930
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2855
Number of HSP's successfully gapped: 227
Length of query: 442
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 342
Effective length of database: 6,502,202
Effective search space: 2223753084
Effective search space used: 2223753084
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: 42 (22.0 bits)
S2: 61 (27.4 bits)