RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1308
(607 letters)
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 294 bits (754), Expect = 1e-89
Identities = 132/328 (40%), Positives = 194/328 (59%), Gaps = 30/328 (9%)
Query: 251 EKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIG 309
E E E+ LE+RLK R++GQ+ A+ +S AI+R G D + P+ FLFLG +G+G
Sbjct: 476 EDEKEKLLN--LERRLKKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVG 533
Query: 310 KTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKC 369
KTELAK LA + ++A IR+DMSEY EKH V++LIGAPPGY+G+++GGQLT+ +++
Sbjct: 534 KTELAKALAEALF-GDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRK 592
Query: 370 PNAVVLFDEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHA 429
P +V+L DE++KAHPDV +LLQ+ D+GRLTDG+G+T++ ++ I +MTSN S EI + A
Sbjct: 593 PYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDA 652
Query: 430 LQLRKEGEEFSKRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVY 489
D K+ V LK+HF R EFL RI+EI+
Sbjct: 653 D----------------------GDDFADKEALKEA-VMEELKKHF-RPEFLNRIDEIIP 688
Query: 490 FLPFSKSELHTLVCRELNFWAKKALDKHNINIVWDIDV-ETILADGYDVHYGARSIKHEV 548
F P SK L +V +LN AK+ L + I + + + + GYD YGAR ++ +
Sbjct: 689 FNPLSKEVLERIVDLQLNRLAKR-LAERGITLELSDEAKDFLAEKGYDPEYGARPLRRAI 747
Query: 549 ERQVVSQLAAAHEKSVIGKGSFVRLYVQ 576
++++ LA I G V++ V
Sbjct: 748 QQEIEDPLADEILFGKIEDGGTVKVDVD 775
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 262 bits (673), Expect = 1e-77
Identities = 124/312 (39%), Positives = 187/312 (59%), Gaps = 37/312 (11%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIGKTELAKQLAFY 320
+E+ L +R+VGQ+ A+ +S AI+R G +D + P+ FLFLG +G+GKTELAK LA +
Sbjct: 559 MEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEF 618
Query: 321 IHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVD 380
+ D ++A +R+DMSEY EKH VA+LIGAPPGY+G+++GGQLT+ +++ P +VVLFDEV+
Sbjct: 619 LF-DDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVE 677
Query: 381 KAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHALQLRKEGEEFS 440
KAHPDV VLLQ+ D+GRLTDG+G+T++ ++ + +MTSNL S I + + E
Sbjct: 678 KAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQE---LAGGDDYEEM 734
Query: 441 KRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVYFLPFSKSELHT 500
+ V +L+ HFR EFL RI+EIV F P + ++
Sbjct: 735 RE-----------------------AVMEVLRAHFR-PEFLNRIDEIVVFHPLGREQIAR 770
Query: 501 LVCRELNFWAKKALDKHNINIVWDIDVETILAD-GYDVHYGARSIKHEVERQVVSQLAAA 559
+V +L K+ ++ I + LA+ GYD YGAR +K ++R++ + LA
Sbjct: 771 IVEIQLGRLRKRLAERK-ITLELSDAALDFLAEAGYDPVYGARPLKRAIQREIENPLAKK 829
Query: 560 ------HEKSVI 565
+ I
Sbjct: 830 ILAGEVADGDTI 841
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 239 bits (613), Expect = 2e-69
Identities = 120/298 (40%), Positives = 181/298 (60%), Gaps = 19/298 (6%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLV-FLFLGSSGIGKTELAKQLAFY 320
+E+ L RI+GQ+ A+ +S AI+R G + + P+ FLF G +G+GKTEL K LA Y
Sbjct: 503 MEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASY 562
Query: 321 IHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVD 380
++A IRLDMSEY EKH V+KLIG+PPGY+G+++GGQLT+ ++K P VVLFDE++
Sbjct: 563 FF-GSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIE 621
Query: 381 KAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHALQLRKEGEEFS 440
KAHPD+ +LLQ+ D+GRLTD KG+TI+ K+ + +MTSNL S I + G F
Sbjct: 622 KAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVI-----ETNSGGLGFE 676
Query: 441 KRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVYFLPFSKSELHT 500
+S+ Q L ++V LK+ F R EFL R++EI+ F +K+++
Sbjct: 677 LSENQLSEKQYKRL---------SNLVNEELKQFF-RPEFLNRLDEIIVFRQLTKNDV-W 725
Query: 501 LVCRELNFWAKKALDKHNINIVWDIDVETILAD-GYDVHYGARSIKHEVERQVVSQLA 557
+ + K L++ I + ++T+L + GY+ YGAR ++ + R + LA
Sbjct: 726 EIAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEGYNPLYGARPLRRAIMRLLEDPLA 783
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 224 bits (572), Expect = 4e-64
Identities = 106/301 (35%), Positives = 165/301 (54%), Gaps = 40/301 (13%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIGKTELAKQLAFY 320
LE+ LK +I GQ+ AI+ + +AIKR G D + P+ FLF+G +G+GKTELAKQLA
Sbjct: 447 LEKNLKAKIFGQDEAIDQLVSAIKRSRAGLGDPNKPVGSFLFVGPTGVGKTELAKQLA-- 504
Query: 321 IHRDKKE---AFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFD 377
+E +R DMSEY EKH V++LIG+PPGY+G + GG LT ++K P+ V+L D
Sbjct: 505 -----EELGVHLLRFDMSEYMEKHTVSRLIGSPPGYVGFEQGGLLTDAVRKHPHCVLLLD 559
Query: 378 EVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHALQLRKEGE 437
E++KAHPD+ +LLQ+ D LTD G+ + ++ I +MTSN ++E+++ + E
Sbjct: 560 EIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGGENS 619
Query: 438 EFSKRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVYFLPFSKSE 497
E S I + F P EF R++ I++F S+
Sbjct: 620 E-------------SKSLKAIKKLFS-----P---------EFRNRLDAIIHFNDLSEEM 652
Query: 498 LHTLVCRELNFWAKKALDKHNINIVWDIDVETILAD-GYDVHYGARSIKHEVERQVVSQL 556
+V + L+ + +K NI + D + LA+ GYD +GAR + ++ ++ L
Sbjct: 653 AEKIVKKFLDELQDQLNEK-NIELELTDDAKKYLAEKGYDEEFGARPLARVIQEEIKKPL 711
Query: 557 A 557
+
Sbjct: 712 S 712
Score = 31.9 bits (73), Expect = 1.2
Identities = 38/144 (26%), Positives = 61/144 (42%), Gaps = 34/144 (23%)
Query: 251 EKEAEERRKY--PLEQRLK----DRIVGQESAIN-IISAAIKRKENGWTDDDHPLVFLFL 303
+K + KY L ++ K D ++G+E + I +RK+N +PL +
Sbjct: 158 KKGQDALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKN------NPL---LV 208
Query: 304 GSSGIGKTELAKQLAFYIHRDK-----KEAFI-RLDMSEYQEKHEVAKLIGAPPGYLGHD 357
G G+GKT + + LA I K K A I LDM + A Y G
Sbjct: 209 GEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMG----------TLLAGTKYRGDF 258
Query: 358 DG--GQLTKRLKKCPNAVVLFDEV 379
+ + ++K PNA++ DE+
Sbjct: 259 EERLKAVVSEIEKEPNAILFIDEI 282
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 205 bits (523), Expect = 4e-63
Identities = 78/189 (41%), Positives = 115/189 (60%), Gaps = 25/189 (13%)
Query: 299 VFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDD 358
FLFLG +G+GKTELAK LA + D++ A IR+DMSEY E+H V++LIGAPPGY+G+++
Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFGDER-ALIRIDMSEYMEEHSVSRLIGAPPGYVGYEE 63
Query: 359 GGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTS 418
GGQLT+ +++ P ++VL DE++KAHP V LLQ+ + G LTD +G+ ++ ++ +F+MT
Sbjct: 64 GGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFIMTG 123
Query: 419 NLASNEIAQHALQLRKEGEEFSKRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRD 478
N S +I S S L + +V +LK+ F
Sbjct: 124 NFGSEKI-----------------------SDASRLGDSPDYELLKELVMDLLKKGFIP- 159
Query: 479 EFLGRINEI 487
EFLGR+ I
Sbjct: 160 EFLGRLPII 168
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 220 bits (562), Expect = 4e-62
Identities = 125/368 (33%), Positives = 212/368 (57%), Gaps = 37/368 (10%)
Query: 191 SALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAEDANIKQILQKYAEKYADLQR 250
S L YG ++ EL + A ++ + + + DA I ++L ++ + R
Sbjct: 499 SELQYG------KIPELEKQLAAATQLEGKTMRLLRNKVTDAEIAEVLARWTG--IPVSR 550
Query: 251 EKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIG 309
E+E + +EQ L R++GQ A+ +S AI+R G +D + P+ FLFLG +G+G
Sbjct: 551 MLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVG 610
Query: 310 KTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKC 369
KTEL K LA ++ D +A +R+DMSE+ EKH V++L+GAPPGY+G+++GG LT+ +++
Sbjct: 611 KTELCKALANFMF-DSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRR 669
Query: 370 PNAVVLFDEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHA 429
P +V+L DEV+KAHPDV +LLQ+ D+GRLTDG+G+T++ ++ + +MTSNL S+ I
Sbjct: 670 PYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQ--- 726
Query: 430 LQLRKEGEEFSKRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVY 489
E F + + H K+ +V ++ +F R EF+ RI+E+V
Sbjct: 727 -------ERFGELDYA---------------HMKE-LVLGVVSHNF-RPEFINRIDEVVV 762
Query: 490 FLPFSKSELHTLVCRELNFWAKKALDKHNINIVWDIDVETILADGYDVHYGARSIKHEVE 549
F P + + ++ +L K+ ++ + D ++ + +GYD YGAR +K ++
Sbjct: 763 FHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQ 822
Query: 550 RQVVSQLA 557
+Q+ + LA
Sbjct: 823 QQIENPLA 830
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 201 bits (513), Expect = 2e-55
Identities = 99/300 (33%), Positives = 166/300 (55%), Gaps = 31/300 (10%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIGKTELAKQLAFY 320
L RL +R++GQ+ A+ I+ I+ G D PL VFL +G SG+GKTE A LA
Sbjct: 560 LPDRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL 619
Query: 321 IHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVD 380
++ ++ I ++MSE+QE H V++L G+PPGY+G+ +GG LT+ +++ P +VVL DEV+
Sbjct: 620 LY-GGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVE 678
Query: 381 KAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHALQ--LRKEGEE 438
KAHPDVL + Q+FD+G + DG+G+ I+ K+ + ++TSN S+ I + E
Sbjct: 679 KAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEA 738
Query: 439 FSKRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVYFLPFSKSEL 498
+ ++P L + F + FLGR+ ++ +LP L
Sbjct: 739 LLEA------------------------LRPELLKVF-KPAFLGRMT-VIPYLPLDDDVL 772
Query: 499 HTLVCRELNFWAKKALDKHNINIVWDID-VETILADGYDVHYGARSIKHEVERQVVSQLA 557
+V +L+ A++ + H +V+ VE I+A +V GAR+I + + ++ +L+
Sbjct: 773 AAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILNQTLLPELS 832
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 163 bits (414), Expect = 1e-42
Identities = 100/301 (33%), Positives = 155/301 (51%), Gaps = 40/301 (13%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL-VFLFLGSSGIGKTELAKQLAFY 320
L RLK + GQ+ AI ++ AIK G + P+ FLF G +G+GKTE+ QL+
Sbjct: 452 LGDRLKMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA 511
Query: 321 IHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVD 380
+ + +R DMSEY E+H V++LIGAPPGY+G D GG LT + K P+AV+L DE++
Sbjct: 512 LGIE----LLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIE 567
Query: 381 KAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQHALQLRKEGEEFS 440
KAHPDV +LLQ+ D G LTD G+ + ++ + VMT+N E + ++ L
Sbjct: 568 KAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGL-------- 619
Query: 441 KRTPSISKSQGSNLDVTISRHFKDHVVQPILKRHFRRDEFLGRINEIVYFLPFSKSELHT 500
I + ++ I + F EF R++ I++F S +H
Sbjct: 620 -----IHQDNSTDAMEEIKKIFT--------------PEFRNRLDNIIWFDHLSTDVIHQ 660
Query: 501 LVCR---ELNFWAKKALDKHNINIVWDIDVETILAD-GYDVHYGARSIKHEVERQVVSQL 556
+V + EL + LD+ +++ + LA+ GYD GAR + ++ + L
Sbjct: 661 VVDKFIVEL----QAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNLKKPL 716
Query: 557 A 557
A
Sbjct: 717 A 717
>gnl|CDD|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate
protein-protein interactions in very diverse families of
proteins. The number of ANK repeats in a protein can
range from 2 to over 20 (ankyrins, for example). ANK
repeats may occur in combinations with other types of
domains. The structural repeat unit contains two
antiparallel helices and a beta-hairpin, repeats are
stacked in a superhelical arrangement; this alignment
contains 4 consecutive repeats.
Length = 126
Score = 80.5 bits (199), Expect = 4e-18
Identities = 45/150 (30%), Positives = 63/150 (42%), Gaps = 37/150 (24%)
Query: 90 LFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLG 149
L AA G + +K +EN DVN + G TPLH+AA NG ++ V++LLE GA+ N
Sbjct: 11 LHLAASNGHLEVVKLLLENGA-DVNAKDNDGRTPLHLAAKNGHLEIVKLLLEKGADVNAR 69
Query: 150 DLFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLL 209
D G + LH GN +VV+LLL
Sbjct: 70 D------------------------------------KDGNTPLHLAARNGNLDVVKLLL 93
Query: 210 KSGADPTVKDNSGHIPSDYAEDANIKQILQ 239
K GAD +D G P A ++++
Sbjct: 94 KHGADVNARDKDGRTPLHLAAKNGHLEVVK 123
Score = 70.5 bits (173), Expect = 1e-14
Identities = 37/135 (27%), Positives = 55/135 (40%), Gaps = 36/135 (26%)
Query: 114 NMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFEVLLKR 173
N R G TPLH+AA NG ++ V++LLE GA+ N D
Sbjct: 1 NARDEDGRTPLHLAASNGHLEVVKLLLENGADVNAKDND--------------------- 39
Query: 174 EDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAEDAN 233
G + LH G+ E+V+LLL+ GAD +D G+ P A
Sbjct: 40 ---------------GRTPLHLAAKNGHLEIVKLLLEKGADVNARDKDGNTPLHLAARNG 84
Query: 234 IKQILQKYAEKYADL 248
+++ + AD+
Sbjct: 85 NLDVVKLLLKHGADV 99
Score = 57.4 bits (139), Expect = 4e-10
Identities = 37/120 (30%), Positives = 50/120 (41%), Gaps = 37/120 (30%)
Query: 90 LFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLG 149
L AA+ G + +K +E DVN R G TPLH+AA NG +D V++LL+ GA+ N
Sbjct: 44 LHLAAKNGHLEIVKLLLEK-GADVNARDKDGNTPLHLAARNGNLDVVKLLLKHGADVNAR 102
Query: 150 DLFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLL 209
D G + LH G+ EVV+LLL
Sbjct: 103 DKD------------------------------------GRTPLHLAAKNGHLEVVKLLL 126
>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies).
Length = 91
Score = 71.5 bits (176), Expect = 2e-15
Identities = 37/96 (38%), Positives = 53/96 (55%), Gaps = 5/96 (5%)
Query: 124 LHVAAINGKVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNP 183
LH+AA NG ++ V++LLE GA+ NLGD +H A + ++LL+ + N
Sbjct: 1 LHLAAKNGNLELVKLLLEKGADVNLGDTDTALHLAARNGNLEIVKLLLEHGADVNAKDKD 60
Query: 184 NMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKD 219
T ALH GN E+V+LLL+ GAD +KD
Sbjct: 61 GNT-----ALHLAARNGNLEIVKLLLEHGADINLKD 91
Score = 61.5 bits (150), Expect = 7e-12
Identities = 33/92 (35%), Positives = 45/92 (48%), Gaps = 12/92 (13%)
Query: 62 CMYNNLLFASACSLALTLLEC-----QSIKDLTLFRAARYGSAKELKTFIENSKLDVNMR 116
NL L LLE D L AAR G+ + +K +E+ DVN +
Sbjct: 5 AKNGNL------ELVKLLLEKGADVNLGDTDTALHLAARNGNLEIVKLLLEHGA-DVNAK 57
Query: 117 HPLGWTPLHVAAINGKVDNVRVLLEAGANPNL 148
G T LH+AA NG ++ V++LLE GA+ NL
Sbjct: 58 DKDGNTALHLAARNGNLEIVKLLLEHGADINL 89
Score = 32.6 bits (75), Expect = 0.096
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 193 LHYGVVAGNTEVVELLLKSGADPTVKDNS 221
LH GN E+V+LLL+ GAD + D
Sbjct: 1 LHLAAKNGNLELVKLLLEKGADVNLGDTD 29
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 69.5 bits (170), Expect = 5e-14
Identities = 37/152 (24%), Positives = 59/152 (38%), Gaps = 21/152 (13%)
Query: 271 VGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFI 330
VGQE AI + A++ P L G G GKT LA+ +A + R F+
Sbjct: 1 VGQEEAIEALREALELP--------PPKNLLLYGPPGTGKTTLARAIANELFRPGAP-FL 51
Query: 331 RLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVL 390
L+ S+ E VA+L GH L + +K V+ DE+D L
Sbjct: 52 YLNASDLLEGLVVAELF-------GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNAL 104
Query: 391 LQLFDEGRLTDGKGKTIECKDAIFVMTSNLAS 422
L++ + I+ ++ + +N
Sbjct: 105 LRVLETLNDL-----RIDRENVRVIGATNRPL 131
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 67.1 bits (164), Expect = 4e-12
Identities = 37/172 (21%), Positives = 62/172 (36%), Gaps = 27/172 (15%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYI 321
+ L+ +VG E I + A+ + L G G+GKT LA+ LA +
Sbjct: 18 IRSELEKVVVGDEEVIELALLALLAGGH----------VLLEGPPGVGKTLLARALARAL 67
Query: 322 HRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCP-----NAVVLF 376
F+R+ + + L+G Y R P ++L
Sbjct: 68 GLP----FVRIQCTPDLLPSD---LLG-TYAYAALLLEPG-EFRFVPGPLFAAVRVILLL 118
Query: 377 DEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDAIFVMTSNLASNEIAQH 428
DE+++A P+V LL+ +E ++T TI V+ N
Sbjct: 119 DEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVI---ATQNPGEYE 167
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 60.5 bits (146), Expect = 6e-11
Identities = 32/142 (22%), Positives = 50/142 (35%), Gaps = 9/142 (6%)
Query: 296 HPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLG 355
V L +G G GKT LA+ LA + I +D + E+ L+ G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGG-GVIYIDGEDILEEVLDQLLLIIVGGKKA 59
Query: 356 HDDGGQ----LTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKD 411
G +K V++ DE+ LL L +E RL K+
Sbjct: 60 SGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRL---LLLLKSEKN 116
Query: 412 AIFVMTSNLASNEIAQHALQLR 433
++T+N + L+ R
Sbjct: 117 LTVILTTNDEKDLGP-ALLRRR 137
>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction
only].
Length = 235
Score = 60.2 bits (145), Expect = 4e-10
Identities = 42/131 (32%), Positives = 60/131 (45%), Gaps = 11/131 (8%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPNLGD-LFNTVHRTAAEKKMNPFEV-----LLKR 173
G PLH AA G V++LL +GA+ N D +T AA P LL
Sbjct: 73 GRLPLHSAASKGDDKIVKLLLASGADVNAKDADGDTPLHLAALNGNPPEGNIEVAKLLLE 132
Query: 174 EDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAED-- 231
DV N G + LH+ + G+ ++VELLL++GADP +++ G D A
Sbjct: 133 AGADLDVNNLRD-EDGNTPLHWAALNGDADIVELLLEAGADPNSRNSYGVTALDPAAKNG 191
Query: 232 --ANIKQILQK 240
+K +L K
Sbjct: 192 RIELVKLLLDK 202
Score = 41.3 bits (96), Expect = 6e-04
Identities = 26/69 (37%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPNLGDLF-NTVHRTAAEKKMNPFEVLLKREDEFN 178
G TPLH AA+NG D V +LLEAGA+PN + + T AA+ LL +
Sbjct: 147 GNTPLHWAALNGDADIVELLLEAGADPNSRNSYGVTALDPAAKNGRIELVKLLLDKGLHL 206
Query: 179 DVLNPNMTF 187
+L N+
Sbjct: 207 SLLKFNLEG 215
Score = 32.1 bits (72), Expect = 0.72
Identities = 19/68 (27%), Positives = 23/68 (33%)
Query: 178 NDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAEDANIKQI 237
D G LH G+ ++V+LLL SGAD KD G P A
Sbjct: 62 VDRHLAARDLDGRLPLHSAASKGDDKIVKLLLASGADVNAKDADGDTPLHLAALNGNPPE 121
Query: 238 LQKYAEKY 245
K
Sbjct: 122 GNIEVAKL 129
>gnl|CDD|200936 pfam00023, Ank, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities. Repeats 13-24 are especially active,
with known sites of interaction for the Na/K ATPase,
Cl/HCO(3) anion exchanger, voltage-gated sodium channel,
clathrin heavy chain and L1 family cell adhesion
molecules. The ANK repeats are found to form a
contiguous spiral stack such that ion transporters like
the anion exchanger associate in a large central cavity
formed by the ANK repeat spiral, while clathrin and cell
adhesion molecules associate with specific regions
outside this cavity.
Length = 33
Score = 49.5 bits (119), Expect = 3e-08
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPNLGD 150
G TPLH+AA NG ++ V++LLEAGA+ N D
Sbjct: 2 GNTPLHLAARNGHLEVVKLLLEAGADVNARD 32
Score = 44.1 bits (105), Expect = 2e-06
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 189 GFSALHYGVVAGNTEVVELLLKSGADPTVKDN 220
G + LH G+ EVV+LLL++GAD +D
Sbjct: 2 GNTPLHLAARNGHLEVVKLLLEAGADVNARDK 33
>gnl|CDD|165206 PHA02875, PHA02875, ankyrin repeat protein; Provisional.
Length = 413
Score = 55.4 bits (133), Expect = 5e-08
Identities = 32/130 (24%), Positives = 62/130 (47%), Gaps = 11/130 (8%)
Query: 90 LFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLG 149
L A G K ++ ++ K ++ + G TPLH+A I K+D +++L+ GA+P++
Sbjct: 72 LHDAVEEGDVKAVEELLDLGKFADDVFYKDGMTPLHLATILKKLDIMKLLIARGADPDIP 131
Query: 150 --DLFNTVHRTAAEKKMNPFEVLLKREDEFN--DVLNPNMTFLGFSALHYGVVAGNTEVV 205
D F+ +H + E+L+ + + D G + L + G+ +
Sbjct: 132 NTDKFSPLHLAVMMGDIKGIELLIDHKACLDIEDC-------CGCTPLIIAMAKGDIAIC 184
Query: 206 ELLLKSGADP 215
++LL SGA+
Sbjct: 185 KMLLDSGANI 194
Score = 45.0 bits (106), Expect = 9e-05
Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 12/121 (9%)
Query: 114 NMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGDLF----NT-VHRTAAEKKMNPFE 168
++++P + LH A G V V LL+ G + D+F T +H KK++ +
Sbjct: 62 DVKYPDIESELHDAVEEGDVKAVEELLDLGKFAD--DVFYKDGMTPLHLATILKKLDIMK 119
Query: 169 VLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDY 228
+L+ R + D+ N + FS LH V+ G+ + +ELL+ A ++D G P
Sbjct: 120 LLIARGAD-PDIPNTDK----FSPLHLAVMMGDIKGIELLIDHKACLDIEDCCGCTPLII 174
Query: 229 A 229
A
Sbjct: 175 A 175
Score = 41.9 bits (98), Expect = 8e-04
Identities = 29/139 (20%), Positives = 61/139 (43%), Gaps = 9/139 (6%)
Query: 108 NSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLG--DLFNTVHRTAAEKKMN 165
+ ++ N G +P+ +A + +++L++ GA P++ D+ + +H E +
Sbjct: 23 DIGINPNFEIYDGISPIKLAMKFRDSEAIKLLMKHGAIPDVKYPDIESELHDAVEEGDVK 82
Query: 166 PFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIP 225
E LL +DV + G + LH + ++++LL+ GADP + + P
Sbjct: 83 AVEELLDLGKFADDVFYKD----GMTPLHLATILKKLDIMKLLIARGADPDIPNTDKFSP 138
Query: 226 SDYA---EDANIKQILQKY 241
A D ++L +
Sbjct: 139 LHLAVMMGDIKGIELLIDH 157
Score = 33.0 bits (75), Expect = 0.40
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 89 TLFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPN 147
L A G K ++ I++ K +++ G TPL +A G + ++LL++GAN +
Sbjct: 138 PLHLAVMMGDIKGIELLIDH-KACLDIEDCCGCTPLIIAMAKGDIAICKMLLDSGANID 195
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 51.5 bits (124), Expect = 6e-08
Identities = 33/126 (26%), Positives = 54/126 (42%), Gaps = 15/126 (11%)
Query: 300 FLFLGSSGIGKTELAKQLAFYIHRDKKEAF-IRLDMSEYQEK--HEVAKLIGAPPGYLGH 356
L +G G GK+ELA++LA + + D +E K + +
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGAS------W 55
Query: 357 DDGGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGRLTDGKGKTIECKDA---I 413
DG L + ++ + + DE+++A+PDVL LL L DE RL +G +
Sbjct: 56 VDGP-LVRAARE--GEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDGFR 112
Query: 414 FVMTSN 419
+ T N
Sbjct: 113 LIATMN 118
>gnl|CDD|222984 PHA03100, PHA03100, ankyrin repeat protein; Provisional.
Length = 422
Score = 53.5 bits (129), Expect = 2e-07
Identities = 35/144 (24%), Positives = 61/144 (42%), Gaps = 23/144 (15%)
Query: 97 GSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDN--VRVLLEAGANPNLGDLFNT 154
S ++ ++N +VN+++ G LH+ + K+D +++L++ G + N
Sbjct: 119 NSYSIVEYLLDNGA-NVNIKNSDGENLLHLYLESNKIDLKILKLLIDKGVDIN------- 170
Query: 155 VHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGAD 214
N LL + ++ GF+ LHY V N E V+ LL GA+
Sbjct: 171 --------AKNRVNYLLSYG---VPINIKDV--YGFTPLHYAVYNNNPEFVKYLLDLGAN 217
Query: 215 PTVKDNSGHIPSDYAEDANIKQIL 238
P + + G P A N K+I
Sbjct: 218 PNLVNKYGDTPLHIAILNNNKEIF 241
Score = 36.6 bits (85), Expect = 0.039
Identities = 35/188 (18%), Positives = 62/188 (32%), Gaps = 35/188 (18%)
Query: 88 LTLFRAARYGSAKELKTFIENS-KLDVNMRHPLGWTPLHVAAINGKVDN---VRVLLEAG 143
L L+ A + +K ++N ++ + ++ D V++LLE G
Sbjct: 37 LPLYLAKEARNIDVVKILLDNGADINSSTKNNSTPLHYLSNIKYNLTDVKEIVKLLLEYG 96
Query: 144 ANPNLGD------LFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGV 197
AN N D L + + + + E LL N G + LH +
Sbjct: 97 ANVNAPDNNGITPLLYAISKKSNSYSI--VEYLLDNGANVNIK-----NSDGENLLHLYL 149
Query: 198 VAGNTEV------------------VELLLKSGADPTVKDNSGHIPSDYAEDANIKQILQ 239
+ ++ V LL G +KD G P YA N + ++
Sbjct: 150 ESNKIDLKILKLLIDKGVDINAKNRVNYLLSYGVPINIKDVYGFTPLHYAVYNNNPEFVK 209
Query: 240 KYAEKYAD 247
+ A+
Sbjct: 210 YLLDLGAN 217
Score = 29.2 bits (66), Expect = 6.1
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 2/100 (2%)
Query: 132 KVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNP--FEVLLKREDEFNDVLNPNMTFLG 189
KV N++ ++ + + A++ N ++LL + N N T L
Sbjct: 14 KVKNIKYIIMEDDLNDYSYKKPVLPLYLAKEARNIDVVKILLDNGADINSSTKNNSTPLH 73
Query: 190 FSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYA 229
+ + + E+V+LLL+ GA+ DN+G P YA
Sbjct: 74 YLSNIKYNLTDVKEIVKLLLEYGANVNAPDNNGITPLLYA 113
>gnl|CDD|222980 PHA03095, PHA03095, ankyrin-like protein; Provisional.
Length = 471
Score = 50.4 bits (121), Expect = 2e-06
Identities = 43/126 (34%), Positives = 59/126 (46%), Gaps = 17/126 (13%)
Query: 112 DVNMRHPLGWTPLHV--AAINGKV-DNVRVLLEAGANPNLGDL--FNTVH---RTAAEKK 163
DVN R G TPLH+ + KV D VR+LLEAGA+ N + F +H A
Sbjct: 39 DVNFRGEYGKTPLHLYLHYSSEKVKDIVRLLLEAGADVNAPERCGFTPLHLYLYNATTLD 98
Query: 164 MNPFEVLLKREDEFNDVLNPNMTFLGFSALH-Y-GVVAGNTEVVELLLKSGADPTVKDNS 221
+ ++L+K DV + +G + LH Y N +V+ LLL+ GAD D
Sbjct: 99 V--IKLLIKAG---ADVNAKD--KVGRTPLHVYLSGFNINPKVIRLLLRKGADVNALDLY 151
Query: 222 GHIPSD 227
G P
Sbjct: 152 GMTPLA 157
Score = 49.6 bits (119), Expect = 3e-06
Identities = 37/125 (29%), Positives = 51/125 (40%), Gaps = 41/125 (32%)
Query: 102 LKTFIENSKLDVNMRHPLGWTPLHV----AAINGKVDNVRVLLEAGANPNLGDLFNTVHR 157
+K I+ DVN + +G TPLHV IN KV +R+LL GA+ N DL+
Sbjct: 100 IKLLIKA-GADVNAKDKVGRTPLHVYLSGFNINPKV--IRLLLRKGADVNALDLYG---- 152
Query: 158 TAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTV 217
M P VLLK + N E++ LL+ +GAD
Sbjct: 153 ------MTPLAVLLK----SRNA--------------------NVELLRLLIDAGADVYA 182
Query: 218 KDNSG 222
D+
Sbjct: 183 VDDRF 187
Score = 39.6 bits (93), Expect = 0.005
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 90 LFRAARYGSAKELKT--FIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPN 147
L A S K + + +N R+ G TPLH AA+ R L+ GA+ N
Sbjct: 226 LHSMATGSSCKRSLVLPLLIAG-ISINARNRYGQTPLHYAAVFNNPRACRRLIALGADIN 284
Query: 148 L 148
Sbjct: 285 A 285
Score = 39.2 bits (92), Expect = 0.005
Identities = 36/170 (21%), Positives = 50/170 (29%), Gaps = 57/170 (33%)
Query: 66 NLLFASACSLA------LTLLE--CQSIKDLTLFRAARYGSAKELKTFIENSKLDVNMRH 117
LL + + +LL QS K A+ ++ I + D
Sbjct: 171 RLLIDAGADVYAVDDRFRSLLHHHLQSFKP----------RARIVRELIR-AGCDPAATD 219
Query: 118 PLGWTPLHVAAING--KVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFEVLLKRED 175
LG TPLH A K V LL AG + N + +
Sbjct: 220 MLGNTPLHSMATGSSCKRSLVLPLLIAGISINARNRY----------------------- 256
Query: 176 EFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIP 225
G + LHY V N L+ GAD + G+ P
Sbjct: 257 -------------GQTPLHYAAVFNNPRACRRLIALGADINAVSSDGNTP 293
Score = 38.9 bits (91), Expect = 0.008
Identities = 33/99 (33%), Positives = 48/99 (48%), Gaps = 11/99 (11%)
Query: 130 NGKVDNVRVLLEAGANPNL-GDLFNTV-H---RTAAEKKMNPFEVLLKREDEFNDVLNPN 184
N V+ VR LL AGA+ N G+ T H ++EK + +LL+ + N
Sbjct: 24 NVTVEEVRRLLAAGADVNFRGEYGKTPLHLYLHYSSEKVKDIVRLLLEAGADVNAP---- 79
Query: 185 MTFLGFSALHYGVVAGNTE-VVELLLKSGADPTVKDNSG 222
GF+ LH + T V++LL+K+GAD KD G
Sbjct: 80 -ERCGFTPLHLYLYNATTLDVIKLLIKAGADVNAKDKVG 117
>gnl|CDD|205784 pfam13606, Ank_3, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities.
Length = 30
Score = 43.0 bits (102), Expect = 5e-06
Identities = 16/28 (57%), Positives = 22/28 (78%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPN 147
G TPLH+AA NG ++ V++LLE GA+ N
Sbjct: 2 GNTPLHLAARNGNLELVKLLLEHGADIN 29
Score = 33.4 bits (77), Expect = 0.014
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 189 GFSALHYGVVAGNTEVVELLLKSGADP 215
G + LH GN E+V+LLL+ GAD
Sbjct: 2 GNTPLHLAARNGNLELVKLLLEHGADI 28
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 45.7 bits (109), Expect = 5e-06
Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 8/109 (7%)
Query: 295 DHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEK----HEVAKLIGAP 350
+ + G SG GKT L ++LA + + ++ ++ + +G P
Sbjct: 2 RGAGIGVLTGESGSGKTTLLRRLA---RQLPNRRVVYVEAPSLGTPKDLLRKILRALGLP 58
Query: 351 PGYLGHDDG-GQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGR 398
+ + LK+ +++ DE + L L L+D
Sbjct: 59 LSGGTTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSE 107
>gnl|CDD|206028 pfam13857, Ank_5, Ankyrin repeats (many copies).
Length = 56
Score = 43.1 bits (102), Expect = 8e-06
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 106 IENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGD 150
+E+ +D+N G TPLH+AA G ++ V+ LL+ G + NL D
Sbjct: 2 LEHGPIDLNATDGNGNTPLHLAAKYGALELVQWLLKPGVDLNLRD 46
Score = 40.0 bits (94), Expect = 9e-05
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 170 LLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYA 229
LL+ + + N G + LH G E+V+ LLK G D ++D+ G D A
Sbjct: 1 LLEHGPIDLNATDGN----GNTPLHLAAKYGALELVQWLLKPGVDLNLRDSDGLTALDLA 56
>gnl|CDD|204486 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA, pfam00004) it lacks the long
coiled-coil insertion, and instead of helix C4 contains
a beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighboring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N, pfam02861, at the N-terminus
as well as AAA, pfam00004 and AAA_2, pfam07724.
Length = 81
Score = 42.4 bits (101), Expect = 3e-05
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 494 SKSELHTLVCRELNFWAKKALDKHNINIVWDIDV-ETILADGYDVHYGARSIKHEVERQV 552
SK EL +V +L K+ L + I + + + GYD YGAR ++ ++R++
Sbjct: 2 SKEELRQIVDLQLKRLQKR-LAERGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREI 60
Query: 553 VSQLA 557
LA
Sbjct: 61 EDPLA 65
>gnl|CDD|222277 pfam13637, Ank_4, Ankyrin repeats (many copies).
Length = 54
Score = 41.5 bits (98), Expect = 3e-05
Identities = 26/90 (28%), Positives = 35/90 (38%), Gaps = 36/90 (40%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFEVLLKREDEFND 179
G T LH AAI+G+++ V+ LLE G + N D
Sbjct: 1 GRTALHKAAISGRLELVKYLLEKGVDINRTDED--------------------------- 33
Query: 180 VLNPNMTFLGFSALHYGVVAGNTEVVELLL 209
G +ALH GN EV++LLL
Sbjct: 34 ---------GNTALHIAAENGNLEVLKLLL 54
Score = 40.7 bits (96), Expect = 5e-05
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 89 TLFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLL 140
L +AA G + +K +E +D+N G T LH+AA NG ++ +++LL
Sbjct: 4 ALHKAAISGRLELVKYLLEK-GVDINRTDEDGNTALHIAAENGNLEVLKLLL 54
Score = 36.8 bits (86), Expect = 0.001
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 189 GFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYA 229
G +ALH ++G E+V+ LL+ G D D G+ A
Sbjct: 1 GRTALHKAAISGRLELVKYLLEKGVDINRTDEDGNTALHIA 41
>gnl|CDD|197603 smart00248, ANK, ankyrin repeats. Ankyrin repeats are about 33
amino acids long and occur in at least four consecutive
copies. They are involved in protein-protein
interactions. The core of the repeat seems to be an
helix-loop-helix structure.
Length = 30
Score = 40.6 bits (96), Expect = 3e-05
Identities = 15/29 (51%), Positives = 22/29 (75%)
Query: 120 GWTPLHVAAINGKVDNVRVLLEAGANPNL 148
G TPLH+AA NG ++ V++LL+ GA+ N
Sbjct: 2 GRTPLHLAAENGNLEVVKLLLDKGADINA 30
Score = 35.3 bits (82), Expect = 0.003
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 189 GFSALHYGVVAGNTEVVELLLKSGADPTV 217
G + LH GN EVV+LLL GAD
Sbjct: 2 GRTPLHLAAENGNLEVVKLLLDKGADINA 30
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 43.0 bits (102), Expect = 5e-05
Identities = 32/130 (24%), Positives = 45/130 (34%), Gaps = 33/130 (25%)
Query: 301 LFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGG 360
L G G GKT LAK +A + FI + SE V+K +G L
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAP----FIEISGSE-----LVSKYVGESEKRL-----R 47
Query: 361 QLTKRLKKCPNAVVLFDEVDKAHP-----------DVLTVLLQLFDEGRLTDGKGKTIEC 409
+L + KK V+ DE+D V+ LL D + K
Sbjct: 48 ELFEAAKKLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSK------ 101
Query: 410 KDAIFVMTSN 419
I + +N
Sbjct: 102 --VIVIAATN 109
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 44.5 bits (105), Expect = 2e-04
Identities = 23/39 (58%), Positives = 25/39 (64%)
Query: 112 DVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGD 150
D N R G TPLH+A NG V VRVLLE GA+P L D
Sbjct: 107 DPNCRDYDGRTPLHIACANGHVQVVRVLLEFGADPTLLD 145
Score = 43.7 bits (103), Expect = 2e-04
Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 37/115 (32%)
Query: 125 HVAAINGKVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPN 184
+AA +G R+LL GA+PN D
Sbjct: 88 QLAA-SGDAVGARILLTGGADPNCRD---------------------------------- 112
Query: 185 MTFLGFSALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAEDANIKQILQ 239
+ G + LH G+ +VV +LL+ GADPT+ D G P + AE+ ++++Q
Sbjct: 113 --YDGRTPLHIACANGHVQVVRVLLEFGADPTLLDKDGKTPLELAEENGFREVVQ 165
>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 = 43.8 bits (104), Expect = 3e-04
Identities = 43/170 (25%), Positives = 77/170 (45%), Gaps = 41/170 (24%)
Query: 239 QKYAEKYADLQREKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPL 298
KY+++ DL+R KE + Y L+ ++K+RI+ + A+ + +K
Sbjct: 302 GKYSKENLDLKRAKEILDEDHYGLK-KVKERIL-EYLAVQKLRGKMKGP----------- 348
Query: 299 VFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKL-------IGAPP 351
+ +G G+GKT L K +A ++R F+R + + A++ +GA P
Sbjct: 349 ILCLVGPPGVGKTSLGKSIAKALNRK----FVRFSLGGV---RDEAEIRGHRRTYVGAMP 401
Query: 352 GYLGHDDGGQLTKRLKKCP--NAVVLFDEVDKA----HPDVLTVLLQLFD 395
G++ + LKK N + L DE+DK D + LL++ D
Sbjct: 402 --------GRIIQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLD 443
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 41.0 bits (96), Expect = 3e-04
Identities = 32/152 (21%), Positives = 56/152 (36%), Gaps = 27/152 (17%)
Query: 269 RIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA---------- 318
R+VG+E + + A++R +G P L G SG GKT L ++L
Sbjct: 1 RLVGREEELERLLDALRRARSG-----GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKC 55
Query: 319 FYIHRDKKEAFI--------RLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCP 370
R+ AF +L E + + + A G + L + L++
Sbjct: 56 DQAERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLL 115
Query: 371 NA----VVLFDEVDKAHPDVLTVLLQLFDEGR 398
V++ D++ A + L +L L
Sbjct: 116 ARARPLVLVLDDLQWADEESLDLLAALLRRLE 147
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 42.5 bits (100), Expect = 5e-04
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 10/64 (15%)
Query: 255 EERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELA 314
E + P+ +RL D+++GQE A+ II A K+K N L +G G+GK+ LA
Sbjct: 5 ETTEEIPVPERLIDQVIGQEEAVEIIKKAAKQKRN----------VLLIGEPGVGKSMLA 54
Query: 315 KQLA 318
K +A
Sbjct: 55 KAMA 58
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 42.4 bits (100), Expect = 5e-04
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 1/100 (1%)
Query: 301 LFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGG 360
L +G +G GK A+ + R + FI + + Y E + A+L G G GG
Sbjct: 105 LIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGG 164
Query: 361 QLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGRLT 400
+ ++ + DE+ + P+ LL++ +EG
Sbjct: 165 K-AGLFEQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYR 203
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 42.2 bits (99), Expect = 9e-04
Identities = 38/138 (27%), Positives = 60/138 (43%), Gaps = 10/138 (7%)
Query: 87 DLTLFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANP 146
L A G+A L+ ++ +KLD ++ G TPLH+AA G D V VLL+ N
Sbjct: 526 ASNLLTVASTGNAALLEELLK-AKLDPDIGDSKGRTPLHIAASKGYEDCVLVLLKHACNV 584
Query: 147 NLGDLF-NTVHRTA-AEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEV 204
++ D NT A + K F +L F + +P+ L +
Sbjct: 585 HIRDANGNTALWNAISAKHHKIFRILY----HFASISDPHA---AGDLLCTAAKRNDLTA 637
Query: 205 VELLLKSGADPTVKDNSG 222
++ LLK G + +D+ G
Sbjct: 638 MKELLKQGLNVDSEDHQG 655
Score = 31.0 bits (70), Expect = 2.1
Identities = 35/126 (27%), Positives = 55/126 (43%), Gaps = 14/126 (11%)
Query: 55 IRQSN-NTCMYNNLLFASACSLALTLLECQSIKDL-----TLFRAARYGSAKELKTFIEN 108
IR +N NT ++N + A + L SI D L AA+ +K ++
Sbjct: 586 IRDANGNTALWNAIS-AKHHKIFRILYHFASISDPHAAGDLLCTAAKRNDLTAMKELLKQ 644
Query: 109 SKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGDLFNTVHRTAAEKKMNPFE 168
L+V+ G T L VA VD VR+L+ GA+ + + + + E + E
Sbjct: 645 G-LNVDSEDHQGATALQVAMAEDHVDMVRLLIMNGADVDKANTDDDF--SPTELR----E 697
Query: 169 VLLKRE 174
+L KRE
Sbjct: 698 LLQKRE 703
>gnl|CDD|165205 PHA02874, PHA02874, ankyrin repeat protein; Provisional.
Length = 434
Score = 41.5 bits (97), Expect = 0.001
Identities = 49/202 (24%), Positives = 83/202 (41%), Gaps = 42/202 (20%)
Query: 78 TLLECQ---SIKDLT----LFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAIN 130
T+L+C +IKD L A + G + +K E DVN+ G P+H+A +
Sbjct: 109 TILDCGIDVNIKDAELKTFLHYAIKKGDLESIKMLFE-YGADVNIEDDNGCYPIHIAIKH 167
Query: 131 GKVDNVRVLLEAGANPNLGDLF--NTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFL 188
D +++LLE GA N+ D + +H A ++L+ + + T L
Sbjct: 168 NFFDIIKLLLEKGAYANVKDNNGESPLHNAAEYGDYACIKLLIDHGNHIMNKCKNGFTPL 227
Query: 189 --------------------------GFSALHYGV-VAGNTEVVELLLKSGADPTVKDNS 221
G + LH+ + + +++++LL AD ++KDN
Sbjct: 228 HNAIIHNRSAIELLINNASINDQDIDGSTPLHHAINPPCDIDIIDILLYHKADISIKDNK 287
Query: 222 GHIPSDYA-----EDANIKQIL 238
G P D A +D IK I+
Sbjct: 288 GENPIDTAFKYINKDPVIKDII 309
Score = 41.1 bits (96), Expect = 0.001
Identities = 41/162 (25%), Positives = 71/162 (43%), Gaps = 24/162 (14%)
Query: 90 LFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNL- 148
L A R G AK ++ FI D+N + PL A G D +++L++ G + ++
Sbjct: 39 LIDAIRSGDAKIVELFI-KHGADINHINTKIPHPLLTAIKIGAHDIIKLLIDNGVDTSIL 97
Query: 149 --GDLFNTVHRTAAEK--KMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEV 204
+ + +T + +N + LK TFL HY + G+ E
Sbjct: 98 PIPCIEKDMIKTILDCGIDVNIKDAELK-------------TFL-----HYAIKKGDLES 139
Query: 205 VELLLKSGADPTVKDNSGHIPSDYAEDANIKQILQKYAEKYA 246
+++L + GAD ++D++G P A N I++ EK A
Sbjct: 140 IKMLFEYGADVNIEDDNGCYPIHIAIKHNFFDIIKLLLEKGA 181
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 41.2 bits (97), Expect = 0.002
Identities = 35/138 (25%), Positives = 52/138 (37%), Gaps = 12/138 (8%)
Query: 87 DLTLFRAARYGSAKELKTFIENSK-LDVNMRHPLGWTPLHVAAINGKVDNVRVLLEA-GA 144
+ AA G + +E K L++N LG + L VAAI + + LL
Sbjct: 18 EKAFLPAAERGDLASVYRDLEEPKKLNINCPDRLGRSALFVAAIENENLELTELLLNLSC 77
Query: 145 NPNLGDLFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMT--------FLGFSALHYG 196
+GD +H + E +LL F + G +ALH
Sbjct: 78 RGAVGD--TLLHAISLEYVDAVEAILLHLLAAFRKSGPLELANDQYTSEFTPGITALHLA 135
Query: 197 VVAGNTEVVELLLKSGAD 214
N E+V+LLL+ GA
Sbjct: 136 AHRQNYEIVKLLLERGAS 153
>gnl|CDD|198154 smart01086, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA) it lacks the long coiled-coil
insertion, and instead of helix C4 contains a
beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N at the N-terminus as well as
AAA and AAA_2.
Length = 90
Score = 37.0 bits (87), Expect = 0.003
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 2/84 (2%)
Query: 494 SKSELHTLVCRELNFWAKKALDKHNINIVWDIDVETILAD-GYDVHYGARSIKHEVERQV 552
K +L +V LN K+ L + I + + + LA+ GYD YGAR ++ ++R++
Sbjct: 2 DKEDLVRIVDLPLNALQKR-LAEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQREL 60
Query: 553 VSQLAAAHEKSVIGKGSFVRLYVQ 576
LA + G V + V
Sbjct: 61 EDPLAELILSGELKDGDTVVVDVD 84
>gnl|CDD|165207 PHA02876, PHA02876, ankyrin repeat protein; Provisional.
Length = 682
Score = 40.4 bits (94), Expect = 0.003
Identities = 39/134 (29%), Positives = 60/134 (44%), Gaps = 11/134 (8%)
Query: 86 KDLTLFRAARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAING-KVDNVRVLLEAGA 144
K+ L A++ S L + DVN ++ G TPL++ A NG +N+R L+ GA
Sbjct: 273 KNTPLHHASQAPSLSRLVPKLLERGADVNAKNIKGETPLYLMAKNGYDTENIRTLIMLGA 332
Query: 145 NPNLGD-LFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGF---SALHYGVVAG 200
+ N D L+ T A+ N V+ E L N+ + + +HY V
Sbjct: 333 DVNAADRLYITPLHQASTLDRNKDIVITLLE------LGANVNARDYCDKTPIHYAAVRN 386
Query: 201 NTEVVELLLKSGAD 214
N ++ LL GAD
Sbjct: 387 NVVIINTLLDYGAD 400
Score = 30.0 bits (67), Expect = 4.9
Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 13/136 (9%)
Query: 93 AARYGSAKELKTFIENSKLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGD-- 150
AA G+AK + + DVN+ + L A + +D ++ +++ +N N D
Sbjct: 185 AAERGNAKMVNLLLSYGA-DVNIIALDDLSVLECAVDSKNIDTIKAIIDNRSNINKNDLS 243
Query: 151 LFNTVHRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGN-TEVVELLL 209
L + E + ++ + +D N + LH+ A + + +V LL
Sbjct: 244 LLKAIRNEDLETSLLLYDAGFS-VNSIDDCKN--------TPLHHASQAPSLSRLVPKLL 294
Query: 210 KSGADPTVKDNSGHIP 225
+ GAD K+ G P
Sbjct: 295 ERGADVNAKNIKGETP 310
Score = 29.6 bits (66), Expect = 5.6
Identities = 31/105 (29%), Positives = 46/105 (43%), Gaps = 5/105 (4%)
Query: 112 DVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGAN-PNLGDLFNTVHRTAAEKKMNPFEVL 170
+VN R TP+H AA+ V + LL+ GA+ L T A NP+ +
Sbjct: 367 NVNARDYCDKTPIHYAAVRNNVVIINTLLDYGADIEALSQKIGTALHFAL-CGTNPYMSV 425
Query: 171 LKREDEFNDVLNPNMTFLGFSALHYGVVAG-NTEVVELLLKSGAD 214
D +V + N + LHY +V+E+LL +GAD
Sbjct: 426 KTLIDRGANVNSKNKDL--STPLHYACKKNCKLDVIEMLLDNGAD 468
Score = 29.3 bits (65), Expect = 7.8
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 191 SALHYGVVAGNTEVVELLLKSGADPTVKDNSGHIPSDYAEDAN 233
+ +HY GN ++V LLL GAD + + A D+
Sbjct: 180 TPIHYAAERGNAKMVNLLLSYGADVNIIALDDLSVLECAVDSK 222
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 39.4 bits (92), Expect = 0.005
Identities = 37/166 (22%), Positives = 63/166 (37%), Gaps = 36/166 (21%)
Query: 237 ILQKYAEKYADLQREKEAEERRKYP----LEQRLKDRIVGQESAINIISAAI----KRKE 288
IL++ + + +E E P ++ L + ++GQE A ++S A+ KR
Sbjct: 42 ILEEELGTRKESKEYEEEFELSYLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLN 101
Query: 289 NGWTDDDHPLV------FLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHE 342
V L +G +G GKT LA+ LA + + +++ E
Sbjct: 102 FEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLA-------RILNVPFAIADATTLTE 154
Query: 343 VAKLIGAPPGYLGHDDGGQLTKRLKKC-------PNAVVLFDEVDK 381
GY+G D L K L+ ++ DE+DK
Sbjct: 155 A--------GYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDK 192
>gnl|CDD|222939 PHA02878, PHA02878, ankyrin repeat protein; Provisional.
Length = 477
Score = 39.1 bits (91), Expect = 0.006
Identities = 32/112 (28%), Positives = 45/112 (40%), Gaps = 11/112 (9%)
Query: 112 DVNM--RHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGDLFNT--VHRTAAEKKMNPF 167
D+NM RH T LH A N +LL GAN N+ D N +H
Sbjct: 159 DINMKDRHKGN-TALHYATENKDQRLTELLLSYGANVNIPDKTNNSPLHHAVKHYNKPIV 217
Query: 168 EVLLKREDEFNDVLNPNMTFLGFSALHYGV-VAGNTEVVELLLKSGADPTVK 218
+LL+ N G + LH V + ++++LLL+ G D K
Sbjct: 218 HILLE-----NGASTDARDKCGNTPLHISVGYCKDYDILKLLLEHGVDVNAK 264
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 38.7 bits (91), Expect = 0.007
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 258 RKY-PLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQ 316
RKY P Q +D ++GQE + + AIK H +LF G G GKT +A+
Sbjct: 6 RKYRP--QTFED-VIGQEHIVQTLKNAIKNGRIA-----H--AYLFSGPRGTGKTSIARI 55
Query: 317 LA 318
A
Sbjct: 56 FA 57
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 37.5 bits (87), Expect = 0.020
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 10/81 (12%)
Query: 265 RLKDRIVGQESAINIISAAIKRK------ENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
L I+GQ+ A ++ A++ + D+ P L +G +G+GKTE+A++LA
Sbjct: 9 ELDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKNILMIGPTGVGKTEIARRLA 68
Query: 319 FYIHRDKKEAFIRLDMSEYQE 339
FI+++ +++ E
Sbjct: 69 KLA----NAPFIKVEATKFTE 85
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 37.6 bits (87), Expect = 0.021
Identities = 47/190 (24%), Positives = 82/190 (43%), Gaps = 45/190 (23%)
Query: 247 DLQREKEAEERRKYPLEQRLKDRIV---GQESAINIISAAIKRKENGWTDDDHPLVFLFL 303
DL++ +E + Y LE R+KDRI+ +S +N I I +
Sbjct: 312 DLRQAQEILDTDHYGLE-RVKDRILEYLAVQSRVNKIKGPI---------------LCLV 355
Query: 304 GSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEV----AKLIGAPPGYLGHDDG 359
G G+GKT L + +A + ++R+ + +++ E+ IG+ P
Sbjct: 356 GPPGVGKTSLGQSIA----KATGRKYVRMALGGVRDEAEIRGHRRTYIGSMP-------- 403
Query: 360 GQLTKRLKK--CPNAVVLFDEVDKAHPDV----LTVLLQLFDEGRLTDGKGKTIEC---- 409
G+L +++ K N + L DE+DK D+ + LL++ D + +E
Sbjct: 404 GKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDL 463
Query: 410 KDAIFVMTSN 419
D +FV TSN
Sbjct: 464 SDVMFVATSN 473
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 37.0 bits (87), Expect = 0.023
Identities = 28/77 (36%), Positives = 36/77 (46%), Gaps = 14/77 (18%)
Query: 246 ADLQREKEAEERRKYPLEQRLKDRIVGQESAIN----IISAAIKRKENGWTDDDHPLVFL 301
L+ E++ ER P + L + I GQE I AA KR E DH V L
Sbjct: 6 ETLEEEEDEIERSLRP--KSLDEFI-GQEKVKENLKIFIEAAKKRGEA----LDH--VLL 56
Query: 302 FLGSSGIGKTELAKQLA 318
+ G G+GKT LA +A
Sbjct: 57 Y-GPPGLGKTTLANIIA 72
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 37.3 bits (87), Expect = 0.027
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 10/54 (18%)
Query: 265 RLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
RL D+++GQE A+ +I A K++ + + +GS G GK+ LAK +A
Sbjct: 28 RLIDQVIGQEHAVEVIKKAAKQRRH----------VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It has
been suggested that torsins play a role in effectively
managing protein folding and that possible breakdown in
a neuroprotective mechanism that is, in part, mediated
by torsins may be responsible for the neuronal
dysfunction associated with dystonia.
Length = 127
Score = 35.0 bits (81), Expect = 0.028
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 262 LEQRLKDRIVGQESAINIISAAIKRKENGWTDDDH---PLVFLFLGSSGIGKTELAKQLA 318
LE+ L R+ GQ ++ ++K G ++ PLV F G +G GK +A+ +A
Sbjct: 19 LERDLARRLFGQHLVKQLVVRSVK----GHWENPKPRKPLVLSFHGWTGTGKNFVAEIIA 74
Query: 319 FYIHRD 324
++RD
Sbjct: 75 DNLYRD 80
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 36.8 bits (86), Expect = 0.035
Identities = 39/157 (24%), Positives = 69/157 (43%), Gaps = 49/157 (31%)
Query: 240 KYAEKYADLQREKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLV 299
K ++ DL++ ++ ++ Y LE ++K+RI+ + A+ ++ +K +
Sbjct: 306 KRSKDKLDLKKAEKILDKDHYGLE-KVKERIL-EYLAVQKLTKKLKGP-----------I 352
Query: 300 FLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRL------DMSE-------YQEKHEVAKL 346
+G G+GKT L K +A + R F+R+ D +E Y
Sbjct: 353 LCLVGPPGVGKTSLGKSIAKALGRK----FVRISLGGVRDEAEIRGHRRTY--------- 399
Query: 347 IGAPPGYLGHDDGGQLTKRLKKC--PNAVVLFDEVDK 381
IGA P G++ + +KK N V L DE+DK
Sbjct: 400 IGAMP--------GKIIQGMKKAGVKNPVFLLDEIDK 428
>gnl|CDD|165154 PHA02791, PHA02791, ankyrin-like protein; Provisional.
Length = 284
Score = 35.8 bits (82), Expect = 0.045
Identities = 34/115 (29%), Positives = 58/115 (50%), Gaps = 13/115 (11%)
Query: 99 AKELKTFIENS---KLDVNMRHPLGWTPLHVAAINGKVDNVRVLLEAGANPNLGDLFNTV 155
+K+LK+F+ + K DV+ G + L+ A + V V LL AGA NL + +
Sbjct: 11 SKQLKSFLSSKDAFKADVH-----GHSALYYAIADNNVRLVCTLLNAGALKNLLENEFPL 65
Query: 156 HRTAAEKKMNPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGNTEVVELLLK 210
H+ A + ++LL F+ + + G +AL+Y V +GN + V+L +K
Sbjct: 66 HQAATLEDTKIVKILL-----FSGMDDSQFDDKGNTALYYAVDSGNMQTVKLFVK 115
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 35.7 bits (83), Expect = 0.067
Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 243 EKYADLQREKEAEERRKYPLEQR--LKDRIVGQESAINIISAAI----KRKENGWTDDDH 296
E+ + EKE E P E + L + ++GQE A ++S A+ KR N +DD
Sbjct: 35 EELKEALDEKELSELPT-PKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDV 93
Query: 297 PLV---FLFLGSSGIGKTELAKQLA 318
L L +G +G GKT LA+ LA
Sbjct: 94 ELSKSNILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 35.6 bits (82), Expect = 0.070
Identities = 34/121 (28%), Positives = 41/121 (33%), Gaps = 23/121 (19%)
Query: 268 DRIVGQESAIN----IISAAIKRKEN-GWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIH 322
D I G E A I +KR E P L G G GKT LAK +A
Sbjct: 242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESR 301
Query: 323 RDKKEAFIRLDMSEYQEKH--EVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVD 380
FI + SE K E K I K K P +++ DE+D
Sbjct: 302 SR----FISVKGSELLSKWVGESEKNIREL-----------FEKARKLAP-SIIFIDEID 345
Query: 381 K 381
Sbjct: 346 S 346
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 35.3 bits (82), Expect = 0.079
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 266 LKDRIVGQESAINIISAAIKRKE--NGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
L ++GQ AI +++AAIK+ +LF G G+G+ A
Sbjct: 2 LFANLIGQPLAIELLTAAIKQNRIAPA---------YLFAGPEGVGRKLAALCFI 47
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 35.3 bits (82), Expect = 0.090
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 264 QRLKDRIVGQESAINIISAAI------KRKENGWTDDDHPLVFLFLGSSGIGKTELAKQL 317
L I+GQ+ A ++ A+ + E D+ P L +G +G+GKTE+A++L
Sbjct: 11 SELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRL 70
Query: 318 A 318
A
Sbjct: 71 A 71
>gnl|CDD|149048 pfam07768, PVL_ORF50, PVL ORF-50-like family. This is a family of
sequences found in both bacteria and bacteriophages.
This region is approximately 130 residues long and in
some cases is found as part of the PVL (Panton-Valentine
leukocidin) group of genes, which encode a member of the
leukocidin group of bacterial toxins that kill
leukocytes by creation of pores in the cell membrane.
PVL appears to be a virulence factor associated with a
number of human diseases.
Length = 118
Score = 33.3 bits (76), Expect = 0.11
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 226 SDYAEDANIKQILQKYAEKYADLQREKEAEERRKYP 261
+Y E + I Q+ E+ + +R KEAE RRK P
Sbjct: 52 KEYREIKKSENIEQERKERELERKRRKEAELRRKKP 87
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 35.4 bits (81), Expect = 0.11
Identities = 31/127 (24%), Positives = 49/127 (38%), Gaps = 19/127 (14%)
Query: 301 LFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGG 360
G G GK+ L +L + + + + E + AK++ G G
Sbjct: 153 YLEGGRGSGKSFLISELCDEG----GQRIVEIHLREITD----AKVLI---GTYTSPKPG 201
Query: 361 QLTKRLKKCPNAV-----VLFDEVDKAHPDVLTVLLQLFDEGRLT-DGKGKTIECKDA-- 412
AV +LF +DKA VL+ LL L ++ RL +G+T+ D
Sbjct: 202 DFEWMKGVLIEAVVSGDWILFKRIDKAPHGVLSYLLTLLEKRRLLIPSRGETVLAHDNFQ 261
Query: 413 IFVMTSN 419
IF +S
Sbjct: 262 IFFTSSM 268
Score = 31.1 bits (70), Expect = 2.5
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 28/132 (21%)
Query: 273 QESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRL 332
Q++ +N + AA PL L G + GKT + Y+ R+ F+R+
Sbjct: 874 QKNYLNTMRAASLSN--------FPL--LIQGPTSSGKTSMIL----YLARETGHKFVRI 919
Query: 333 DMSEYQEKHEVAKLIGAPPGYLGHDDG------GQLTKRLKKCPNAVVLFDEVDKAHPDV 386
+ E+ + + + IG Y+ DDG G L + L++ ++ DE++ A DV
Sbjct: 920 NNHEHTD---LQEYIGT---YVTDDDGSLSFKEGVLVEALRR--GYWIVLDELNLAPTDV 971
Query: 387 LTVLLQLFDEGR 398
L L +L D+ R
Sbjct: 972 LEALNRLLDDNR 983
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 34.7 bits (80), Expect = 0.13
Identities = 47/186 (25%), Positives = 80/186 (43%), Gaps = 37/186 (19%)
Query: 239 QKYAEKYADLQREKEAEERRKY-------PLEQRLK----DRIVGQESAINIISAAIKRK 287
Q+ + D + +KE E+ K PL ++ + D I+GQE I + AA+
Sbjct: 25 QQTNKITIDKESKKELEKLNKMRAIRLTEPLSEKTRPKSFDEIIGQEEGIKALKAAL--- 81
Query: 288 ENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDK------KEAFIRLDMS--EYQE 339
+ H +++ G G+GKT A+ + ++ AF+ +D + + E
Sbjct: 82 --CGPNPQHVIIY---GPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDE 136
Query: 340 KHEVAKLIGA--PPGYLGHDDGGQLTKRLKKCPNAV------VLF-DEVDKAHPDVLTVL 390
+ LIG+ P Y G G K P AV VLF DE+ + HP + L
Sbjct: 137 RGIADPLIGSVHDPIYQGAGPLGIAGIPQPK-PGAVTRAHGGVLFIDEIGELHPVQMNKL 195
Query: 391 LQLFDE 396
L++ ++
Sbjct: 196 LKVLED 201
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 34.8 bits (80), Expect = 0.14
Identities = 38/140 (27%), Positives = 57/140 (40%), Gaps = 36/140 (25%)
Query: 250 REKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKEN-----GWTDDDHPLVFLFLG 304
RE++ E L D ++GQE A ++ EN W P LF G
Sbjct: 108 REEDREIISDITL-----DDVIGQEEAKRKCRLIMEYLENPERFGDWA----PKNVLFYG 158
Query: 305 SSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGG---- 360
G GKT +AK LA + K + + + +LIG ++G DG
Sbjct: 159 PPGTGKTMMAKALA----NEAKVPLLLV---------KATELIGE---HVG--DGARRIH 200
Query: 361 QLTKRLKKCPNAVVLFDEVD 380
+L +R +K +V DE+D
Sbjct: 201 ELYERARKAAPCIVFIDELD 220
>gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system,
component A2. The enzyme that catalyzes the final step
in methanogenesis, methyl coenzyme M reductase, contains
alpha, beta, and gamma chains. In older literature, the
complex of alpha, beta, and gamma chains was termed
component C, while this single chain protein was termed
methyl coenzyme M reductase system component A2 [Energy
metabolism, Methanogenesis].
Length = 520
Score = 34.4 bits (79), Expect = 0.19
Identities = 44/190 (23%), Positives = 77/190 (40%), Gaps = 39/190 (20%)
Query: 165 NPFEVLLKREDEFNDVLNPNMTFLGFSALHYGVVAGN---------TEVVELLLKSGADP 215
PF L DE L+P L +AL V A EV+E L +D
Sbjct: 186 EPFLFL---ADEPTGTLDPQTAKLVHNALEEAVKASGISMVLTSHWPEVIEDL----SDK 238
Query: 216 TVKDNSGHIPSDYAEDANIKQILQKYAEKYADLQREKEAEERRKYPLEQRLKDRIV---- 271
+ +G I E+ +++ + E +++++E E E + + R +
Sbjct: 239 AIWLENGEI----KEEGTPDEVVAVFMEGVSEVEKECEVEVGEPIIKVRNVSKRYISVDR 294
Query: 272 GQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIR 331
G A++ +S +K E +F +G+SG GKT L+K +A + E +R
Sbjct: 295 GVVKAVDNVSLEVKEGE----------IFGIVGTSGAGKTTLSKIIAGVLEPTSGEVNVR 344
Query: 332 L-----DMSE 336
+ DM++
Sbjct: 345 VGDEWVDMTK 354
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 34.1 bits (78), Expect = 0.22
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 14/102 (13%)
Query: 243 EKYADLQREKEAEE----------RRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWT 292
K D+ RE + E ++++ L L D ++S I I+ IK
Sbjct: 112 LKIEDILRENDFSESYIKDINEFIKKEFSLSD-LDDYDKVRDSVIIYIAKTIK-CSGSII 169
Query: 293 DDDHPLVFLFLGSSGIGK-TELAKQLAFY-IHRDKKEAFIRL 332
D+ VF+ +G +G+GK T +AK A Y I+ D K I++
Sbjct: 170 DNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKI 211
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 33.0 bits (76), Expect = 0.26
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 7/79 (8%)
Query: 292 TDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKH-EVAKLIGAP 350
+ P+ L G G GKTELA+ L + +R+D E + H + +L A
Sbjct: 7 PPQERPVAVLLGGQPGAGKTELARALLEELGGGN---VVRIDPDELRTYHPDYDELQKAD 63
Query: 351 P---GYLGHDDGGQLTKRL 366
P L D + ++L
Sbjct: 64 PKDASELTQPDASRWVEKL 82
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 33.3 bits (76), Expect = 0.46
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 270 IVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
I+GQE I+ AI + ++F G GIGKT +AK A
Sbjct: 18 IIGQELIKKILVNAILN-------NKLTHAYIFSGPRGIGKTSIAKIFA 59
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 33.1 bits (76), Expect = 0.48
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 258 RKY-PLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQ 316
RKY P + D +VGQE + +S A++ +LF G G+GKT +A+
Sbjct: 8 RKYRP--KTFDD-VVGQEHVVKTLSNALENGRI-------AHAYLFSGPRGVGKTTIARI 57
Query: 317 LA 318
LA
Sbjct: 58 LA 59
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.1 bits (70), Expect = 0.48
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 304 GSSGIGKTELAKQLA-----FYIHRD---KKEAFIRLDMSEYQEKHEVAKLI 347
G G GK+ LAK+LA I D ++E LD E + +L+
Sbjct: 6 GPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELL 57
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 32.6 bits (75), Expect = 0.57
Identities = 33/127 (25%), Positives = 47/127 (37%), Gaps = 22/127 (17%)
Query: 259 KY-PLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQL 317
KY P + L D +VG E A + I+ W L G G+GKT LA L
Sbjct: 7 KYRP--KTLSD-VVGNEKAKEQLREWIES----WLKGKPKKALLLYGPPGVGKTSLAHAL 59
Query: 318 AFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFD 377
A D I L+ S+ + + ++ G + L ++L D
Sbjct: 60 A----NDYGWEVIELNASDQRTADVIERVAGE----------AATSGSLFGARRKLILLD 105
Query: 378 EVDKAHP 384
EVD H
Sbjct: 106 EVDGIHG 112
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 32.3 bits (74), Expect = 0.68
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 7/55 (12%)
Query: 286 RKENGWTDDDHPL----VFLFLGSSGIGK-TELAKQLAFYIHRDKKE--AFIRLD 333
RK ++ + V +G +G+GK T LAK A Y+ KK+ A I D
Sbjct: 188 RKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTD 242
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 32.3 bits (74), Expect = 0.70
Identities = 34/128 (26%), Positives = 47/128 (36%), Gaps = 24/128 (18%)
Query: 249 QREKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGI 308
RE + E RR + L +VG+ A+ + I + D + L G SG
Sbjct: 122 LRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAKV----APSDASV--LITGESGT 175
Query: 309 GKTELAKQLAFYIH---RDKKEAFIRLDMSEYQE--------KHEVAKLIGAP---PGYL 354
GK EL +A IH K FI ++ + E HE GA G
Sbjct: 176 GK-EL---VARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAITRRIGRF 231
Query: 355 GHDDGGQL 362
+GG L
Sbjct: 232 EQANGGTL 239
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 32.4 bits (74), Expect = 0.72
Identities = 41/143 (28%), Positives = 61/143 (42%), Gaps = 41/143 (28%)
Query: 295 DHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYL 354
D P L G G GKT LAK +A FIR+ SE+ +K YL
Sbjct: 177 DPPRGVLLYGPPGTGKTMLAKAVA----HHTTATFIRVVGSEFVQK------------YL 220
Query: 355 GHDDGGQLTK---RLKK--CPNAVVLFDEVDK-----------AHPDVLTVLLQLFDEGR 398
G +G ++ + RL + P +++ DEVD A +V +LL+L ++
Sbjct: 221 G--EGPRMVRDVFRLARENAP-SIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQ-- 275
Query: 399 LTDGKGKTIECKDAIFVMTSNLA 421
DG +T K +M +N A
Sbjct: 276 -MDGFDQTTNVK---VIMATNRA 294
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 32.1 bits (74), Expect = 0.75
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 12/59 (20%)
Query: 264 QRLKDRIVGQESAIN----IISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
+ L + +GQE I AA KR E DH L G G+GKT LA +A
Sbjct: 23 KTLDE-FIGQEKVKEQLQIFIKAAKKRGEA----LDH---VLLFGPPGLGKTTLAHIIA 73
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 32.6 bits (74), Expect = 0.79
Identities = 29/103 (28%), Positives = 46/103 (44%), Gaps = 12/103 (11%)
Query: 302 FLGSSGIGKTELA-KQLAFYIHRDKKEAFIRLDMS------EYQEKHEVAKLIGAPPGYL 354
L +G+ ELA +QL ++E I ++ + EY+ + LI P
Sbjct: 39 LLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSMVHEYEGNEYLINLIDTP---- 94
Query: 355 GHDD-GGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDE 396
GH D GG +T+ ++ A+V+ V+ P TVL Q E
Sbjct: 95 GHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKE 137
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 31.9 bits (73), Expect = 0.94
Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 16/101 (15%)
Query: 293 DDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKK-----EAFIRLDMS-EYQEKH---EV 343
D+ V +G G+GKT LAKQ I+ D ++ + +S Y E ++
Sbjct: 15 MSDNLGVVGIVGMGGVGKTTLAKQ----IYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDI 70
Query: 344 AKLIGAPPGYLGHDDGGQLTKRLKKC---PNAVVLFDEVDK 381
+ +G + +L ++K+ +++ D+V +
Sbjct: 71 LQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWE 111
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 32.1 bits (74), Expect = 0.94
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 12/103 (11%)
Query: 303 LGSSGIGKTELA-KQLAFYIHRDKKEAFIRLDMS------EYQEKHEVAKLIGAPPGYLG 355
L +G+ ELA +QLA +++ I + + EY+ K + LI P G
Sbjct: 41 LAGAGMISEELAGEQLALDFDEEEQARGITIKAANVSMVHEYEGKEYLINLIDTP----G 96
Query: 356 HDD-GGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEG 397
H D GG +T+ ++ A+V+ D V+ P TVL Q E
Sbjct: 97 HVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRER 139
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 31.7 bits (72), Expect = 1.4
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 228 YAEDANIKQILQKYAEKYAD-LQREKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKR 286
+ +KQ Y ++ + E EAEE + L ++ G E+ I+A +
Sbjct: 375 QSSQRELKQTEAAYCKRLDEKRLFEDEAEEEARQRLADDEEEVRAGDEAREEKIAANSQV 434
Query: 287 KE 288
+
Sbjct: 435 ID 436
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 30.3 bits (69), Expect = 1.4
Identities = 33/138 (23%), Positives = 56/138 (40%), Gaps = 25/138 (18%)
Query: 271 VGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFI 330
G +A++ +S +K E + +G +G GK+ L + +A + E I
Sbjct: 9 YGGRTALDNVSLTLKAGE----------IVALVGPNGSGKSTLLRAIAGLLKPTSGEILI 58
Query: 331 RLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQ-----LTKRLKKCPNAVVLFDEVDKA-HP 384
E+ + I GY+ GGQ L + L P+ ++L DE P
Sbjct: 59 DGKDIAKLPLEELRRRI----GYVPQLSGGQRQRVALARALLLNPD-LLLLDEPTSGLDP 113
Query: 385 D----VLTVLLQLFDEGR 398
+L +L +L +EGR
Sbjct: 114 ASRERLLELLRELAEEGR 131
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 31.5 bits (72), Expect = 1.5
Identities = 33/142 (23%), Positives = 62/142 (43%), Gaps = 20/142 (14%)
Query: 268 DRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKE 327
DRIV ++ I ++ A++ G + VF++ G +G GKT + K + + ++
Sbjct: 15 DRIVHRDEQIEELAKALRPILRGSRPSN---VFIY-GKTGTGKTAVTKYVMKELEEAAED 70
Query: 328 AFIRL---------DMSEYQEKHEVA-KLIGAPPG--YLGHDDG---GQLTKRLKKC-PN 371
+R+ + YQ E+A +L G+ G +L K L + +
Sbjct: 71 RDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDS 130
Query: 372 AVVLFDEVDKAHPDVLTVLLQL 393
+++ DE+D D +L QL
Sbjct: 131 LIIVLDEIDYLVGDDDDLLYQL 152
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 31.4 bits (71), Expect = 1.6
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 25/94 (26%)
Query: 250 REKEAEERRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDD-----------HP- 297
RE+ A +R+Y + K +I +++ A K E+GWT D HP
Sbjct: 463 RERRAM-KREY---EEFKVKINA------LVATAQKVPEDGWTMQDGTPWPGNNVRDHPG 512
Query: 298 LVFLFLGSSGIGKTELAKQLA--FYIHRDKKEAF 329
++ +FLG SG+ E +L Y+ R+K+ F
Sbjct: 513 MIQVFLGHSGVRDVE-GNELPRLVYVSREKRPGF 545
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 31.6 bits (72), Expect = 1.6
Identities = 23/103 (22%), Positives = 47/103 (45%), Gaps = 11/103 (10%)
Query: 301 LFLGSSGIGKTELAKQLAFYIHRDKKEA---FIRLDMSEYQEKHEVAKLIGAPPGYLGHD 357
L G G+GK LA IH + + A +I ++ Y ++ + +G+
Sbjct: 352 LLCGEEGVGK----ALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRT---DS 404
Query: 358 DGGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEGRLT 400
+ G+L+K + + ++V+ P++ + LLQ+ G +T
Sbjct: 405 ENGRLSK-FELAHGGTLFLEKVEYLSPELQSALLQVLKTGVIT 446
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 30.8 bits (70), Expect = 1.6
Identities = 30/99 (30%), Positives = 42/99 (42%), Gaps = 20/99 (20%)
Query: 285 KRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKH--- 341
KRKE G L +F G+ G GKT +A+ L +M+ + H
Sbjct: 30 KRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFK----------EMNVLSKGHLIE 79
Query: 342 -EVAKLIGAPPGYLGHDDGGQLTKR-LKKCPNAVVLFDE 378
E A L+G Y+GH Q T+ +KK V+ DE
Sbjct: 80 VERADLVGE---YIGHT--AQKTREVIKKALGGVLFIDE 113
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance to
organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 30.6 bits (70), Expect = 1.7
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 299 VFLFLGSSGIGKTELAKQLAFYIHRDKKEAFI----RLDMSEYQEKHEVAKLIG 348
+ LG SG GK+ L + + + DK E I +SE +E +E+ K +G
Sbjct: 36 ILAILGGSGSGKSTLLRLILGLLRPDKGEILIDGEDIPQLSE-EELYEIRKRMG 88
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 30.5 bits (70), Expect = 1.8
Identities = 28/77 (36%), Positives = 35/77 (45%), Gaps = 14/77 (18%)
Query: 246 ADLQREKEAEERRKYPLEQRLKDRIVGQESAIN----IISAAIKRKENGWTDDDHPLVFL 301
+ Q E++ ER P +RL + I GQE I AA KR E DH L
Sbjct: 5 PEAQEEEDDVERSLRP--RRLDEYI-GQEKVKENLKIFIEAAKKRGEA----LDH---VL 54
Query: 302 FLGSSGIGKTELAKQLA 318
G G+GKT LA +A
Sbjct: 55 LYGPPGLGKTTLANIIA 71
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 31.0 bits (71), Expect = 1.9
Identities = 28/85 (32%), Positives = 38/85 (44%), Gaps = 24/85 (28%)
Query: 301 LFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGG 360
L G G GKT LAK +A H FIR+ SE V K IG +G
Sbjct: 169 LLYGPPGTGKTLLAKAVA---HE-TNATFIRVVGSEL-----VQKFIG---------EGA 210
Query: 361 QLTKRL-----KKCPNAVVLFDEVD 380
+L + L +K P +++ DE+D
Sbjct: 211 RLVRELFELAREKAP-SIIFIDEID 234
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.1 bits (71), Expect = 2.0
Identities = 21/69 (30%), Positives = 26/69 (37%), Gaps = 16/69 (23%)
Query: 252 KEAEERRKYPLEQR-LKDRIVGQESAIN--IISAAIKRKENGWTDDDHPLVFLFLGSSGI 308
E + KD + GQE A I+AA H L L +G G
Sbjct: 163 PIPSEVIESFSLAPDFKD-VKGQEQAKRALEIAAAG----------GHNL--LLVGPPGT 209
Query: 309 GKTELAKQL 317
GKT LA +L
Sbjct: 210 GKTMLASRL 218
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 31.0 bits (70), Expect = 2.0
Identities = 26/103 (25%), Positives = 42/103 (40%), Gaps = 13/103 (12%)
Query: 288 ENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAK-L 346
+NGW L L +G +GKT L + +A + + F+ + E+ E+A L
Sbjct: 134 QNGW------LNTLIIGPPQVGKTTLLRDIARLLSDGINQ-FLPKKVGIIDERSEIAGCL 186
Query: 347 IGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVDKAHPDVLTV 389
G P G+ L CP A + + P+V+ V
Sbjct: 187 NGVP-----QHGRGRRMDVLDPCPKAEGMMMAIRSMSPEVIIV 224
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 31.0 bits (70), Expect = 2.2
Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 246 ADLQREKEAEERRKYPLE-QRLKDRIVGQESAINIISA-------AIKRKENGWTDDDHP 297
A+ AE + K E + +G E ++A A+ R E G
Sbjct: 253 AEFVDPAAAERKAKLLAEAEAELAEQIGLERVKRQVAALKSSTAMALARAERGLPVAQTS 312
Query: 298 LVFLFLGSSGIGKTELAKQLA 318
LF G G GKT +A+ +A
Sbjct: 313 NHMLFAGPPGTGKTTIARVVA 333
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 30.5 bits (69), Expect = 2.6
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 224 IPSDYAEDANIKQILQKYAEKYADLQREKEAEERRKYPLEQRLKDRIVGQESAINIISAA 283
S A+D +KQI ++ A ++ ++ ++R K LE++LK E+ I + A
Sbjct: 30 AFSAAADDKQLKQIQKEIAALEKKIREQQ--DQRAK--LEKQLKS----LETEIASLEAQ 81
Query: 284 IKRKENG 290
+ +
Sbjct: 82 LIETADD 88
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 30.2 bits (69), Expect = 2.7
Identities = 28/82 (34%), Positives = 34/82 (41%), Gaps = 26/82 (31%)
Query: 266 LKDRIVGQESAINI--ISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHR 323
L D + GQE A I+AA G H L L +G G GKT LAK+L
Sbjct: 2 LAD-VKGQEQAKRALEIAAA------G----GHNL--LMIGPPGSGKTMLAKRL------ 42
Query: 324 DKKEAFIRLDMSEYQEKHEVAK 345
I ++E QE EV
Sbjct: 43 ----PGILPPLTE-QEALEVTA 59
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 30.4 bits (69), Expect = 3.0
Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 11/83 (13%)
Query: 276 AINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMS 335
A++ +S ++ E +F LG +G GKT L K LA + E + L
Sbjct: 20 ALDGVSFEVEPGE----------IFGLLGPNGAGKTTLLKILAGLLKPTSGEILV-LGYD 68
Query: 336 EYQEKHEVAKLIGAPPGYLGHDD 358
+E +V + IG P
Sbjct: 69 VVKEPAKVRRRIGYVPQEPSLYP 91
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 30.1 bits (67), Expect = 3.5
Identities = 34/131 (25%), Positives = 61/131 (46%), Gaps = 20/131 (15%)
Query: 260 YPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAF 319
Y LE L D + E+ I I + K+N + G G+GKT +A++LA+
Sbjct: 168 YCLEDALNDLFI-PETTIETILKRLTIKKN----------IILQGPPGVGKTFVARRLAY 216
Query: 320 YIHRDKKEAFIRLDMSEYQEKHEVAKLI-GAPPGYLG--HDDG--GQLTKRLKKCPNAVV 374
+ +K A R++M ++ + + I G P +G DG ++ K+ P
Sbjct: 217 LLTGEK--APQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKY 274
Query: 375 LF--DEVDKAH 383
+F DE+++A+
Sbjct: 275 VFIIDEINRAN 285
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 30.1 bits (68), Expect = 3.5
Identities = 23/62 (37%), Positives = 28/62 (45%), Gaps = 11/62 (17%)
Query: 258 RKY-PLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQ 316
RKY P Q D + GQE + AI H FLF G+ G+GKT A+
Sbjct: 8 RKYRP--QTFSD-LTGQEHVSRTLQNAIDTGRVA-----H--AFLFTGARGVGKTSTARI 57
Query: 317 LA 318
LA
Sbjct: 58 LA 59
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 30.1 bits (69), Expect = 3.5
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 12/82 (14%)
Query: 249 QREKEAEERRKYP----LEQRLKDRIVGQESAINIISAAI----KRKENGWTDDDHPLV- 299
+ ++EA E ++ P ++ L ++GQE A ++S A+ KR +G DD +
Sbjct: 48 ELKEEAVELKELPTPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQ 107
Query: 300 ---FLFLGSSGIGKTELAKQLA 318
L +G +G GKT LA+ LA
Sbjct: 108 KSNILLIGPTGSGKTLLAQTLA 129
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 30.0 bits (68), Expect = 3.9
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 257 RRKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQ 316
+ LE + + + +E IN +++ + G P + G +G GKT K
Sbjct: 6 NKDVLLEDYIPEELPHREEEINQLASFLAPALRGER----PSNIIIYGPTGTGKTATVKF 61
Query: 317 LA 318
+
Sbjct: 62 VM 63
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 4.5
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 300 FLFLGSSGIGKTELAKQLA 318
L LG G GK+ LAK+LA
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>gnl|CDD|233305 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This
model describes the cyt c biogenesis protein encoded by
ccmA in bacteria. An exception is, an arabidopsis
protein. Quite likely this is encoded by an organelle.
Bacterial c-type cytocromes are located on the
periplasmic side of the cytoplasmic membrane. Several
gene products encoded in a locus designated as 'ccm' are
implicated in the transport and assembly of the
functional cytochrome C. This cluster includes genes:
ccmA;B;C;D;E;F;G and H. The posttranslational pathway
includes the transport of heme moiety, the secretion of
the apoprotein and the covalent attachment of the heme
with the apoprotein. The proteins ccmA and B represent
an ABC transporter; ccmC and D participate in heme
transfer to ccmE, which function as a periplasmic heme
chaperone. The presence of ccmF, G and H is suggested to
be obligatory for the final functional assembly of
cytochrome c [Protein fate, Protein and peptide
secretion and trafficking, Transport and binding
proteins, Other].
Length = 198
Score = 29.3 bits (66), Expect = 4.7
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 304 GSSGIGKTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDG 359
G +GIGKT L + LA + D E +R + E YLGH G
Sbjct: 33 GPNGIGKTTLLRILAGLLRPDSGE--VRWNG---TALAEQRDEPHRNILYLGHLPG 83
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of a
conjugation cascade to attach Ub or Ubls, covalently to
substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 29.6 bits (67), Expect = 5.3
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 16/89 (17%)
Query: 218 KDNSGHIPSDYAEDANIKQILQKYAEKYADLQREKEAEE-------RRKYP--LEQRLKD 268
++G +PS Y E + +++ D + +EA + R K P +E+ D
Sbjct: 217 SAHNGQLPSTYKEKKEFRDLVRSLMRSNEDEENFEEAIKAVNKALNRTKIPSSVEEIFND 276
Query: 269 ----RIVGQESAINIISAAIKR---KENG 290
+ Q S+ I++ A+K +ENG
Sbjct: 277 DRCENLTSQSSSFWIMARALKEFVAEENG 305
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 29.5 bits (67), Expect = 5.4
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 296 HPLVFLFLGSSGIGKTELAKQLAF 319
P++ L G+SG+G + +A +LA
Sbjct: 91 EPIIILIGGASGVGTSTIAFELAS 114
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 29.6 bits (67), Expect = 5.4
Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 258 RKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHP------LVFLFLGSSGIGKT 311
R +E K + + +K+ + + V LG +GIGKT
Sbjct: 322 RPEEIEFEEKPPRDDKARDTLVEYPDLKKTYGDFKLEVEEGEIYDGEVIGILGPNGIGKT 381
Query: 312 ELAKQLAFYIHRDKKE 327
K LA I D+
Sbjct: 382 TFVKLLAGVIKPDEGS 397
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 29.5 bits (67), Expect = 5.6
Identities = 11/82 (13%), Positives = 32/82 (39%), Gaps = 6/82 (7%)
Query: 310 KTELAKQLAFYIHRDKKEAFIRLDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKC 369
+ + A+ ++ ++ E + + + + K +G + G ++ ++
Sbjct: 257 IAAMQRNGAYVLNDEQAEQLLEVVLLTNKGATPNKKWVGKDASKILKAAGIEVPADIR-- 314
Query: 370 PNAVVLFDEVDKAHPDVLTVLL 391
++ E DK HP V+ +
Sbjct: 315 ----LIIVETDKDHPFVVEEQM 332
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of
the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 29.1 bits (66), Expect = 5.6
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 12/78 (15%)
Query: 272 GQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIR 331
G++ ++ IS +K+ E ++ FLG +G GKT K + I D E I
Sbjct: 11 GKKRVLDDISLHVKKGE----------IYGFLGPNGAGKTTTMKIILGLIKPDSGE--IT 58
Query: 332 LDMSEYQEKHEVAKLIGA 349
D YQ+ E + IGA
Sbjct: 59 FDGKSYQKNIEALRRIGA 76
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 29.0 bits (66), Expect = 5.7
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 12/78 (15%)
Query: 272 GQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFI- 330
G A++ IS IK+ E L +G +G GK+ L + L + E +
Sbjct: 12 GARPALDDISLTIKKGE----------FVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVD 61
Query: 331 RLDMSEYQEKHEVAKLIG 348
D+++ E+ + +G
Sbjct: 62 GKDLTKLS-LKELRRKVG 78
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 29.1 bits (66), Expect = 5.8
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 266 LKDRIVGQESAIN-----IISAAIKRKENGWTD-----DDHPLVFLFLGSSGIGKT---- 311
LK + G++ I+ +K ++ P V LF+G +G+GKT
Sbjct: 31 LKKELKGKKVKDAELLKEILKEYLKEILKETDLELIVEENKPNVILFVGVNGVGKTTTIA 90
Query: 312 ELAKQL 317
+LA +L
Sbjct: 91 KLANKL 96
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 29.1 bits (66), Expect = 5.8
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 297 PLVFLFLGSSGIGKT-ELAKQLAFYIHRDKKEAFIRLD 333
P V L +G G GKT +AK A+ + KK + D
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAAD 38
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 29.4 bits (66), Expect = 6.0
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 270 IVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
I+GQ++ + ++ A++ H +LF G G GKT LA+ A
Sbjct: 19 ILGQDAVVAVLKNALRFNRAA-----H--AYLFSGIRGTGKTTLARIFA 60
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 29.4 bits (66), Expect = 6.2
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 268 DRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLA 318
D +VGQE ++ AA+++ G +LF G G+GKT A+ +A
Sbjct: 14 DEVVGQEHVKEVLLAALRQGRLGHA-------YLFSGPRGVGKTTTARLIA 57
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 29.5 bits (67), Expect = 6.3
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 306 SGIGKTELAKQLAFYI--HRDKKEAFIRLDMSEYQ 338
G+GKT LA +A K A L+MSE Q
Sbjct: 205 PGMGKTALALNIALNAAADGRKPVAIFSLEMSEEQ 239
>gnl|CDD|238501 cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been
shown to function as initial receptors in the ABC uptake
of Zn2+. They belong to the TroA superfamily of
periplasmic metal binding proteins that share a distinct
fold and ligand binding mechanism. They are comprised
of two globular subdomains connected by a single helix
and bind their specific ligands in the cleft between
these domains. A typical TroA protein is comprised of
two globular subdomains connected by a single helix and
can bind the metal ion in the cleft between these
domains. In addition, these proteins sometimes have a
low complexity region containing a metal-binding
histidine-rich motif (repetitive HDH sequence).
Length = 286
Score = 29.3 bits (66), Expect = 6.3
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 123 PLH--VAAINGKVDNVRVLLEAGANP 146
PL AAI G V V VL+ GA+P
Sbjct: 12 PLGFIAAAIMGGVGEVEVLVPPGASP 37
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 29.1 bits (66), Expect = 6.5
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 294 DDHPLVFLFLGSSGIGK-TELAKQLAFY 320
+ P V LF+G +G+GK T +AK LA Y
Sbjct: 136 EKKPFVILFVGVNGVGKTTTIAK-LAKY 162
>gnl|CDD|221059 pfam11285, DUF3086, Protein of unknown function (DUF3086). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 283
Score = 29.2 bits (66), Expect = 6.6
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 234 IKQILQKYAEKYADLQREKEAEERRKYPLEQRLKDRIVGQESAINI 279
+++ L+ ++ L+ E E ERRK +EQ L+ GQ AI
Sbjct: 2 VEEALKDLEQRRQALEIEIEKLERRKEQIEQELRTSFAGQSDAIAR 47
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 28.7 bits (65), Expect = 6.9
Identities = 28/104 (26%), Positives = 43/104 (41%), Gaps = 9/104 (8%)
Query: 303 LGSSGIGKTELAKQLAFYIHR-DKKEAFIRLDMSEYQEKHEVAKLIGAPPGYL------- 354
L S+GI +LA + + R D++E I + S E + YL
Sbjct: 21 LASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYFEYEEEKMDGNDYLINLIDSP 80
Query: 355 GHDD-GGQLTKRLKKCPNAVVLFDEVDKAHPDVLTVLLQLFDEG 397
GH D ++T L+ A+V+ D V+ TVL Q +E
Sbjct: 81 GHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVLRQALEER 124
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 29.2 bits (66), Expect = 6.9
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 264 QRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAF 319
+ L + +GQE + I+ + DH L++ G G+GKT LA +A
Sbjct: 1 KLLAE-FIGQEKVKEQLQLFIEAAKMRQEALDHLLLY---GPPGLGKTTLAHIIAN 52
>gnl|CDD|219342 pfam07227, DUF1423, Protein of unknown function (DUF1423). This
family represents a conserved region approximately 500
residues long within a number of Arabidopsis thaliana
proteins of unknown function.
Length = 446
Score = 29.3 bits (66), Expect = 7.2
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 236 QILQKYAEKYADLQREKEAEERRKYPLEQ 264
+ ++YA KY R EAEE R+Y E+
Sbjct: 393 KSEEEYASKYLK-LRLSEAEEERQYLFEE 420
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 29.1 bits (65), Expect = 7.4
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 9/61 (14%)
Query: 258 RKYPLEQRLKDRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQL 317
RKY Q +D ++ Q+ AI + A+K + G H ++F G G+GKT +A+ L
Sbjct: 10 RKYR-PQFFRD-VIHQDLAIGALQNALKSGKIG-----H--AYIFFGPRGVGKTTIARIL 60
Query: 318 A 318
A
Sbjct: 61 A 61
>gnl|CDD|238461 cd00919, Heme_Cu_Oxidase_I, Heme-copper oxidase subunit I.
Heme-copper oxidases are transmembrane protein complexes
in the respiratory chains of prokaryotes and
mitochondria which catalyze the reduction of O2 and
simultaneously pump protons across the membrane. The
superfamily is diverse in terms of electron donors,
subunit composition, and heme types. The number of
subunits varies from three to five in bacteria and up to
13 in mammalian mitochondria. It has been proposed that
Archaea acquired heme-copper oxidases through gene
transfer from Gram-positive bacteria. Membership in the
superfamily is defined by subunit I, which contains a
heme-copper binuclear center (the active site where O2
is reduced to water) formed by a high-spin heme and a
copper ion. It also contains a low-spin heme, believed
to participate in the transfer of electrons to the
binuclear center. Only subunit I is common to the
entire superfamily. For every reduction of an O2
molecule, eight protons are taken from the inside
aqueous compartment and four electrons are taken from
the electron donor on the opposite side of the membrane.
The four electrons and four of the protons are used in
the reduction of O2; the four remaining protons are
pumped across the membrane. This charge separation of
four charges contributes to the electrochemical gradient
used for ATP synthesis. Two proton channels, the
D-pathway and K-pathway, leading to the binuclear center
have been identified in subunit I of cytochrome c
oxidase (CcO) and ubiquinol oxidase. A well-defined
pathway for the transfer of pumped protons beyond the
binuclear center has not been identified. Electron
transfer occurs in two segments: from the electron
donor to the low-spin heme, and from the low-spin heme
to the binuclear center. The first segment can be a
multi-step process and varies among the different
families, while the second segment, a direct transfer,
is consistent throughout the superfamily.
Length = 463
Score = 29.0 bits (66), Expect = 8.1
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 275 SAINIISAAIKRKENGWTDDDHPLV 299
AIN I+ + + G T D PL
Sbjct: 148 GAINFITTILNMRAPGMTLDKMPLF 172
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 29.3 bits (66), Expect = 8.3
Identities = 25/133 (18%), Positives = 48/133 (36%), Gaps = 18/133 (13%)
Query: 270 IVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAF 329
+ G+E+ + + AA R G + V L G SGIGK+ L ++ I + + F
Sbjct: 2 LYGRETELAQLLAAFDRVSKGRGE-----VVLVAGESGIGKSALVNEVHKPITQQRGY-F 55
Query: 330 IR------LDMSEYQEKHEVAKLIGAPPGYLGHDDGGQLTKRLKKCPNAVVLFDEVDKAH 383
I+ + + G L + ++ + A+ +V
Sbjct: 56 IKGKFDQFERNIPL---SPLVQAFRDLMGQLLSESDTRILSWRARLLAALGENGQVII-- 110
Query: 384 PDVLTVLLQLFDE 396
DV+ L + +
Sbjct: 111 -DVIPELELIIGK 122
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 28.9 bits (66), Expect = 8.4
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 19/79 (24%)
Query: 261 PLEQRLK----DRIVGQESAIN---IISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTEL 313
PL +R++ D +VGQE + + I+ + G G GKT L
Sbjct: 1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEA--------GRLSSMILWGPPGTGKTTL 52
Query: 314 AKQLAFYIHRDKKEAFIRL 332
A+ +A F L
Sbjct: 53 ARIIAGATDAP----FEAL 67
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 29.0 bits (65), Expect = 8.8
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 13/63 (20%)
Query: 258 RKYPLEQRLK--DRIVGQESAINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAK 315
RKY R K ++GQE + I+ A+K ++F G G GKT +A+
Sbjct: 8 RKY----RPKFFKEVIGQEIVVRILKNAVKL-------QRVSHAYIFAGPRGTGKTTIAR 56
Query: 316 QLA 318
LA
Sbjct: 57 ILA 59
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.5 bits (64), Expect = 8.9
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 282 AAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAF 319
+ I+R EN + LG SG+GKT LA L +
Sbjct: 97 SFIERNEN----------IVLLGPSGVGKTHLAIALGY 124
>gnl|CDD|233714 TIGR02082, metH, 5-methyltetrahydrofolate--homocysteine
methyltransferase. This family represents
5-methyltetrahydrofolate--homocysteine methyltransferase
(EC 2.1.1.13), one of at least three different enzymes
able to convert homocysteine to methionine by
transferring a methyl group on to the sulfur atom. It is
also called the vitamin B12(or cobalamine)-dependent
methionine synthase. Other methionine synthases include
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase (MetE, EC 2.1.1.14, the
cobalamin-independent methionine synthase) and
betaine-homocysteine methyltransferase [Amino acid
biosynthesis, Aspartate family].
Length = 1178
Score = 29.0 bits (65), Expect = 9.7
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 228 YAEDANIKQILQKYAEKYADLQREKEAEER----RKYPLEQRLKDRIV 271
+ L + A+ Y + E + R P+E+RL+ +V
Sbjct: 608 LNRRREATEPLLELAQLYEGTTTKSSKEAQQAEWRNLPVEERLEYALV 655
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 28.1 bits (64), Expect = 9.7
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 11/77 (14%)
Query: 276 AINIISAAIKRKENGWTDDDHPLVFLFLGSSGIGKTELAKQLAFYIHRDKKEAFIRLDMS 335
A++ IS +++ E ++ LG +G GKT L K + + D E + L
Sbjct: 15 ALDDISLTVEKGE----------IYGLLGPNGAGKTTLIKIILGLLKPDSGEIKV-LGKD 63
Query: 336 EYQEKHEVAKLIGAPPG 352
+E EV + IG P
Sbjct: 64 IKKEPEEVKRRIGYLPE 80
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
0.319 0.136 0.392
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: 31,054,641
Number of extensions: 3104559
Number of successful extensions: 4001
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3904
Number of HSP's successfully gapped: 225
Length of query: 607
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 504
Effective length of database: 6,369,140
Effective search space: 3210046560
Effective search space used: 3210046560
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: 62 (27.4 bits)