RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2649
(1637 letters)
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs to
the AAA class of chaperone-like ATPases. The core of the
380 kDa motor unit contains a concatenated chain of six
AAA modules, of which four correspond to the ATP binding
sites with P-loop signatures described previously, and
two are modules in which the P loop has been lost in
evolution. This C-terminal domain carries the D6 region
of the dynein motor where the P-loop has been lost in
evolution but the general structure of a potential ATP
binding site appears to be retained.
Length = 706
Score = 1064 bits (2754), Expect = 0.0
Identities = 423/713 (59%), Positives = 532/713 (74%), Gaps = 20/713 (2%)
Query: 934 FQPGVSSPV-DFLTNTLWGGVRALSNLEEFKNLDKDIEAAAKRWKKYIEGETPEKDKLPQ 992
+ V +P D+LT WG + LS LEEF+ LD DIE AKRWKK+ + E PE++KLPQ
Sbjct: 1 IESTVPNPKLDWLTVQQWGSICRLSELEEFRGLDDDIEKNAKRWKKWYDSEAPEEEKLPQ 60
Query: 993 EWK-NKSALQRLCIMRCLRPDRMTYAVRSFVEEKMGDRYVNARAIEFEQSYRESSSTTPI 1051
EWK KSA Q+L ++R LRPDRMTYA R+FV EK+G+++V + ++ + Y ESS +TPI
Sbjct: 61 EWKDRKSAFQKLLLLRALRPDRMTYAARNFVSEKLGEKFVEPQPLDLSKIYEESSPSTPI 120
Query: 1052 FFILSPGVDPTRDVEAVGRKMGFTTDLRNLHNVSLGQGQEVIAEETIQIASTKGHWAILQ 1111
FFILSPGVDP++DVE + +KMGF + H+VSLGQGQ IAE+ I+ A+ GHW +LQ
Sbjct: 121 FFILSPGVDPSKDVEKLAKKMGFG---KKFHSVSLGQGQGPIAEKAIETAAKSGHWVMLQ 177
Query: 1112 NVHLVKNWLPTLDKKMEASFEKPHKNYRLFISAEPASDPEYHIIPQGVLDSSIKITNEPP 1171
N+HL +WLPTL+KK+E+ H ++RLF++AEPA IP G+L +SIKITNEPP
Sbjct: 178 NIHLAPSWLPTLEKKLESLTPGSHPDFRLFLTAEPAPS-----IPIGLLQNSIKITNEPP 232
Query: 1172 TGMQANLHKALDNFTQEDLEMCSKEAEYKSILFALCYFHAVVAERRKFGPQGWNRSYPFN 1231
TG++ANL +AL +FTQE LEMC K AE+K ILF LC+FHAVV ERRKFGP GWN+SY FN
Sbjct: 233 TGLKANLLRALSSFTQETLEMCKKPAEFKRILFLLCFFHAVVQERRKFGPLGWNKSYEFN 292
Query: 1232 VGDLTISSLVLYNYLEANN--NVPWEDLRYLFGEIMYGGHITDDWDRRLCRTYLEEYMNP 1289
GDL IS VL NYL+AN VPWEDLRYLFGEIMYGG ITDDWDRRL RTYLEE+ P
Sbjct: 293 EGDLRISLDVLDNYLDANAPDKVPWEDLRYLFGEIMYGGRITDDWDRRLLRTYLEEFFTP 352
Query: 1290 ELLEGETKLAP---GFPAPPNQDYQGYHTYIDESLPPES-PILYGLHPNAEIGFLTTQAE 1345
L + E +LAP GF PP DY+GY YI+E LPPES P YGLHPNAEIGFLT Q E
Sbjct: 353 RLFDPELELAPGDLGFAVPPGTDYEGYLQYIEE-LPPESSPEWYGLHPNAEIGFLTQQTE 411
Query: 1346 NVFKIIFELQPRDTAAAQGSGVTREEKVRQVLDEILDKCPDAFNIKDMMGRV--EDRTPY 1403
+ + + ELQPR+ + GSGV+REE V+QVL +IL+K P F I+++ + E + P
Sbjct: 412 KLIRTLLELQPREAGGSGGSGVSREEVVKQVLRDILEKLPKLFPIEEIKLKRTEEIKDPL 471
Query: 1404 IIVAFQECERMNILMSEIKRSLKELNLGLKGELTITTDMEALEYSIFMDTVPPSWEKRAY 1463
V FQE ERMN L+ EI+RSLKEL+LGLKGELT+T D+E L ++F VP SW K AY
Sbjct: 472 FRVLFQEIERMNKLLKEIRRSLKELDLGLKGELTMTNDLEDLAKALFKGRVPASWAKLAY 531
Query: 1464 PSMLGLGGWFADLMLRLKELENWVGDFQLPSSVWLAGFFNPQSFLTAIMQSTARKNEWPL 1523
PS+ LG W DL+ R+++L++W DF P +VWL+GFFNPQSFLTAIMQS ARKN+WPL
Sbjct: 532 PSLKPLGSWVTDLLRRIRQLQDWTEDFGKPKTVWLSGFFNPQSFLTAIMQSVARKNKWPL 591
Query: 1524 DKMCLQCDVTKKQREDFTQAPRDGAYVNGLYMEGARWDIALGVISDAKLKELFPMMPVIY 1583
DK+CLQ DVTKK++E+F APRDG YV+GL++EGARWD G++ +++ KELF MPVI+
Sbjct: 592 DKLCLQTDVTKKEKEEFDSAPRDGFYVHGLFLEGARWDGQNGLLLESRPKELFSPMPVIW 651
Query: 1584 IKAITQDKQDLRNMYECPVYKTRQRGP-NYVWTFNLKTKEKPAKWTMAGVALL 1635
+KA+ DKQ+ +++YECPVYKT RG YV+TF LKTKE P+KW +AGVALL
Sbjct: 652 VKAVPADKQEEKSVYECPVYKTETRGGTTYVFTFLLKTKEPPSKWILAGVALL 704
>gnl|CDD|193256 pfam12780, AAA_8, P-loop containing dynein motor region D4. The
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D4 ATP-binding region of
the motor.
Length = 268
Score = 295 bits (756), Expect = 8e-91
Identities = 145/281 (51%), Positives = 187/281 (66%), Gaps = 51/281 (18%)
Query: 45 YNEIVASMNLVLFEDAMSHICRINRIMEAPRGNALLVGVGGSGKQSLSRLSAFISTLEPF 104
YNE+ A MNLVLFEDAM+H+CRINRI+E+PRGNALLVGVGGSGKQSLSRL+A+IS+L+ F
Sbjct: 1 YNEVNAVMNLVLFEDAMAHVCRINRILESPRGNALLVGVGGSGKQSLSRLAAYISSLDVF 60
Query: 105 QIQLKKNYGIPDLKIDLASLYLKAGLKNAGIMFLMTDSQVADEKFLVIINDMLASGEVPD 164
QI L+K YGIPDLKIDLA+ +KAG+KN +FLMTD+QVADE+FLV+IND+LASGE+PD
Sbjct: 61 QITLRKGYGIPDLKIDLAAQCIKAGVKNVPTVFLMTDAQVADEQFLVLINDLLASGEIPD 120
Query: 165 LFTDDEIENIVNNIAAEPEIPLTADLDPLTMLTDDATIAFWNNEGLPNDRMSTENATIL- 223
LF DDE+ENI++++ E+ ++ +D W DR+ + IL
Sbjct: 121 LFMDDEVENIISSV--RNEVK--------SLGLNDTRENCWK---FFIDRVRRQLKVILC 167
Query: 224 ---------VNSQRWPLMID----------PQEVL------------------RKPCAVF 246
V S+++P +++ PQ+ L + + F
Sbjct: 168 FSPVGSVLRVRSRKFPAVVNCTAIDWFHEWPQDALVSVSARFLEETEGIPWEVKASISFF 227
Query: 247 MAYVHSSVNQISVSYLLNERRYNYTTPKSFLEQIDLYAKLL 287
MAYVH+SVN++S YL NERRYNYTTPKSFLEQI LY LL
Sbjct: 228 MAYVHTSVNEMSRVYLANERRYNYTTPKSFLEQIKLYQSLL 268
Score = 48.4 bits (115), Expect = 1e-05
Identities = 16/22 (72%), Positives = 19/22 (86%)
Query: 558 SKIDWFHEWPQEALESVSLKFL 579
+ IDWFHEWPQ+AL SVS +FL
Sbjct: 189 TAIDWFHEWPQDALVSVSARFL 210
>gnl|CDD|193253 pfam12777, MT, Microtubule-binding stalk of dynein motor. the 380
kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This family is the region between D4 and D5 and is the
two predicted alpha-helical coiled coil segments that
form the stalk supporting the ATP-sensitive microtubule
binding component.
Length = 344
Score = 277 bits (709), Expect = 2e-83
Identities = 140/285 (49%), Positives = 175/285 (61%), Gaps = 43/285 (15%)
Query: 313 NEEKKVRAIEEDVSYKQKVCAEDLEKAEPALVAAQEALDTLDKNNLTELKALKAPPQGVI 372
EE KV I ++V+ KQK C EDL KAEPAL+AAQEAL+TL+KNNLTELK+ +PP V+
Sbjct: 61 QEEVKVAVINKEVTEKQKDCEEDLAKAEPALLAAQEALNTLNKNNLTELKSFGSPPDAVV 120
Query: 373 AVCDAVAVLMASKKGKVPKDLGWKGSQ-------------------------LKALKAPP 407
V AV VL A GK+PKD WK ++ LKA+K
Sbjct: 121 NVTAAVMVLTAPG-GKIPKDRSWKAAKVMMGKVDTFLDSLINFDKENIHENCLKAIKPYL 179
Query: 408 Q-----------------GLCAWVINIITFYNVWTFVEPKRKALAAANAELAAASQKLAE 450
GLC+WVINI+ FY V+ VEPKR+AL ANAELAAA +KLA
Sbjct: 180 GDPEFDPEFIRSKSTAAAGLCSWVINIVRFYEVYCDVEPKRQALEKANAELAAAQEKLAR 239
Query: 451 LKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLADRLVNGLASENVRWKDS 510
+KAKIA L A L LT F+ A +KL CQ +AE I LA+RLV GLASENVRW ++
Sbjct: 240 IKAKIAELNANLANLTAAFEKATADKLKCQQEAEATNRTILLANRLVGGLASENVRWAEA 299
Query: 511 VLGLQQSALTLPGDILLVTAFVSYVGCFTRSYRLDLLNKFWLPTI 555
V + +TL GD+LL+TAFVSYVG FT+ YR +L+ +FW+P +
Sbjct: 300 VENFKSQEVTLCGDVLLITAFVSYVGYFTKKYRNELMERFWIPYL 344
Score = 41.9 bits (98), Expect = 0.002
Identities = 21/29 (72%), Positives = 25/29 (86%)
Query: 885 QPKRKALAAANAELAAASQKLAELKAKIA 913
+PKR+AL ANAELAAA +KLA +KAKIA
Sbjct: 217 EPKRQALEKANAELAAAQEKLARIKAKIA 245
>gnl|CDD|193257 pfam12781, AAA_9, ATP-binding dynein motor region D5. The 380 kDa
motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D5 ATP-binding region of
the motor, but has lost its P-loop.
Length = 228
Score = 260 bits (666), Expect = 3e-79
Identities = 122/178 (68%), Positives = 145/178 (81%)
Query: 586 HRYGNKLTVIRLGQKRVMDQIEKAVMSGFVLLIENIGESVDPVLDNLIGRNLIRKGKVVK 645
++YG+ L VIR+GQK +D IE+A+ G +LIENI ES+DPVLD L+GRN I+KG+ +K
Sbjct: 51 NKYGSDLRVIRIGQKGYLDVIEQAISEGDTVLIENIEESIDPVLDPLLGRNTIKKGRYIK 110
Query: 646 IGEKEIDYNPNFKLILHTKLANPHYKPEMQAQTTLINFTVTRDGLEDQLLAEVVKFERPD 705
IG+KE++YNP F+LILHTKLANPHYKPEMQAQ TLINFTVTRDGLEDQLLA VV ERPD
Sbjct: 111 IGDKEVEYNPKFRLILHTKLANPHYKPEMQAQCTLINFTVTRDGLEDQLLAAVVAKERPD 170
Query: 706 LELLKANLTKEQNLFKITLKGLEDDLLMRLSSSGGDVLSDKNLVLNLEKSKKTAKEIE 763
LE LK++LTK+QN FKI LK LED LL RLSS+ G+ L D LV NLE +K TA EIE
Sbjct: 171 LEQLKSDLTKQQNEFKIVLKELEDSLLSRLSSASGNFLGDTALVENLETTKHTAAEIE 228
Score = 84.3 bits (208), Expect = 6e-18
Identities = 34/42 (80%), Positives = 38/42 (90%)
Query: 195 MLTDDATIAFWNNEGLPNDRMSTENATILVNSQRWPLMIDPQ 236
MLTDDA +A WNNEGLP+DRMSTENATIL N +RWPLM+DPQ
Sbjct: 1 MLTDDADVATWNNEGLPSDRMSTENATILGNCERWPLMVDPQ 42
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 134 bits (338), Expect = 4e-31
Identities = 148/1019 (14%), Positives = 299/1019 (29%), Gaps = 168/1019 (16%)
Query: 26 MKMPDWATLHKILSETMTSYNEIVASMNLVLFEDAMSHICRINRIMEAPRGNALLVGVGG 85
M L + E + + V ++DA+ HI R R + G+ +L GV
Sbjct: 1787 MACLLKKDLAVFVEEVRKIFGSSHLDVEAVAYKDALLHILRSRRGLLVVGGHGVLKGVLI 1846
Query: 86 SGKQSLSRLSAFISTLEPFQIQLKKNYGIPDLKIDLASLYLKAGLKNAGIMFLMTDSQVA 145
G +++ +I ++ D + L L+ + + +S
Sbjct: 1847 RGACDAREFVCWLNPRNMREIFGHRDELTGDFRDSLKVQDLRRNIHGGRECLFIFESIPV 1906
Query: 146 DEKFLVIINDMLASGEV-----------------------------PDLFTDDEIENIVN 176
+ FL N +L + T + +
Sbjct: 1907 ESSFLEDFNPLLDNNRFLCLFSGNERIRIPENLRFVFESTSLEKDTEATLTRVFLVYMEE 1966
Query: 177 NIAAEPEIPLTADLDPLTMLTDDA-----TIAF---WNNEGLPNDRMSTENATILVNSQR 228
N+ + D L + A I F W+ E + S E + R
Sbjct: 1967 NLPVVFSACCSQDTSVLAGIRSPALKNRCFIDFKKLWDTEEMSQYANSVETLSRDGG--R 2024
Query: 229 WPLMIDPQEVLRKPCAVFMAYVHSSVN-QISVSYLLNERRYNYTTPKSFLEQIDLYAKLL 287
I+ + + K + + +V + + + F+ + +Y
Sbjct: 2025 VF-FINGELGVGKGALISEVFGDDAVVIEGRGFEISMIEGSLGESKIKFIGGLKVYDARC 2083
Query: 288 KIKFDDNKSGITRFQNGLQKL------------------VSLGNEEK------------- 316
I ++ G++K V LG +EK
Sbjct: 2084 VIYIEELDCTNVNLVEGVRKYNEYGRGMGELKEQLSNTVVILGVKEKNADDALSGTPGER 2143
Query: 317 ---KVRAI------------EEDVSYKQKVCAEDLEKAEPALVAAQEALDTLDKNNLTEL 361
+V+++ EE+V ++ + +PA++ A + + K +L E+
Sbjct: 2144 LEREVKSVFVEAPRDMLFLLEEEVRKRKGSVMKFKSSKKPAVLEAVLFVYKIKKASLREI 2203
Query: 362 KALKAPPQGVIAVCDAVAVLMA-------------------SKKGKVPKDLGWK------ 396
++ PP + + V L+ GK P ++ +
Sbjct: 2204 RSFIRPPGDLCIEMEDVCDLLGFEAKIWFGEQQSLRRDDFIRIIGKYPDEIEFDLEARRF 2263
Query: 397 ------------GSQL-KALKAPPQGLCAWVINIITFYNVWTFVEPKRKALAAANAELAA 443
GS L +A KA W++ V P R+ + E
Sbjct: 2264 REARECSDPSFTGSILNRASKACGPLK-RWLVRECNRSKVLEVKIPLREEEKRIDGEAFL 2322
Query: 444 ASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLADRLVNGLASE 503
+L K + L + + + + + + + L +E
Sbjct: 2323 VEDRLTLGKGLSSDLMTFKLRRRSYYSLDILRVHGKIADMDTVHKDVLRSIFVSEILINE 2382
Query: 504 NVRWKDSVLGLQQSALTLPGDILLVTAFVSYVGCFTRSYRLDLLNK-------------- 549
+ W + + + L GD + Y+G R
Sbjct: 2383 DSEWGGVFSEVPKLMVELDGDGHPSSCLHPYIGTLGFLCRAIEFGMSFIRISKEFRDKEI 2442
Query: 550 -------FWLPTIKKSK-----IDWFHEWPQEALESVSLKFLVKSCESH-------RYGN 590
+ I+ K D+ E + + L ++ S Y
Sbjct: 2443 RRRQFITEGVQKIEDFKEEACSTDYGLENSRIRKDLQDLTAVLNDPSSKIVTSQRQMYDE 2502
Query: 591 KLTV-IRLGQKRVMDQIEKAVMSGFVLLIENIGESVDPVLDNLIGRNLIRKGKVVK--IG 647
K + + + +A G +I + E++D + LI VK I
Sbjct: 2503 KKAILGSFREMEFAFGLSQARREGSDKIIGD-AEALDEEIGRLIKEEFKSNLSEVKVMIN 2561
Query: 648 EKEIDYNPNFKLILHTKLANPHYKPEMQAQTTLINFTVTRDGLEDQLLAEVVKFERPDLE 707
EI + + ++ + Q + F G E ++ + K L
Sbjct: 2562 PPEIVRSTVEAVFWLSEGRSGDMGSIEWKQLIQVMFVSKVLGCETEIPDALEKLVSGPLF 2621
Query: 708 LLKANLTKEQNLFKITLKGLEDDLLMRLSSSGGDVLSDKNLVLNLEKSKKTAKEIEIKVK 767
+ + L + + L L LL +L S ++ + + L KK+ KEIE +
Sbjct: 2622 VHEKALNALKACGSLFLWVLARYLLAKLMLSISNMEQTDEIAVLLHNLKKSRKEIEEEES 2681
Query: 768 EGKKTAKKIDEAREQYRPAAERASVIYFIMNELFKINPIYQFSLKAFTVVFHNAM-TKAK 826
E + +ID + +Y + +R I + + +Y S+ + F K+K
Sbjct: 2682 ESMEIEDRIDALKSEYNASVKRLESIRVEIAMFDEKALMYNKSICELSSEFEKWRRMKSK 2741
Query: 827 KSDNLKGRVANLVESITFMTFQYTSRGLFERDKLIFMAQMTIQVKSLCMGDQHYHVLQQ 885
++ ++ S ++ G R + F+ + V +L + VL
Sbjct: 2742 YLCAIR----YMLMSSEWILDHEDRSGFIHRLDVSFLLRTKRFVSTLLEDKNYRQVLSS 2796
Score = 61.9 bits (150), Expect = 3e-09
Identities = 40/230 (17%), Positives = 64/230 (27%), Gaps = 36/230 (15%)
Query: 1091 EVIAEETIQIASTKGHWAILQNVHLVKNWLPT-LDKKMEASF--EKPHKNYRLFISAEPA 1147
EV A + + W + N+ L W ++ + K ++ S A
Sbjct: 2903 EVYAVLNSLFSRKEKSWFEVYNISLSFGWFKRYVEDVVYPIKASRVCGKVKNMWTSMVDA 2962
Query: 1148 ----------SDPEYHIIPQGVLDSSIKITNEPPTGMQANLHKALDNFTQEDLEMCSKEA 1197
D + L A D+
Sbjct: 2963 DMLPIQLLIAIDSFVSSTYPETGCGYADLVEIDRYPFDYTLVIACDDA------------ 3010
Query: 1198 EYKSILFALCYFHAVVAERRKFGPQGWNRSYPFNVGDLTISSLVLYN--YLEANNNVPWE 1255
F L + HA VA GP+ N F D + +L N +L N W
Sbjct: 3011 ------FYLSWEHAAVASVISAGPKENNEEIYFGDKDFEFKTHLLKNILFLNHLNARKWG 3064
Query: 1256 DLRYLFGEIMYGGHITDDWDRRLCRTYLEEYMNPELLEGETKLAPGFPAP 1305
+ R L I+YG + D ++ Y Y E +++ P
Sbjct: 3065 NNRDLIFTIVYGKKHSLMEDSKVVDKYCRGYGAH---ETSSQILASVPGG 3111
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 44.6 bits (106), Expect = 1e-04
Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 4/94 (4%)
Query: 428 EPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECA 487
R+ L ELA ++LAEL+ ++A L+ QEL + E + ++
Sbjct: 62 PSARERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAE----LERLQKEL 117
Query: 488 EKIDLADRLVNGLASENVRWKDSVLGLQQSALTL 521
+I L EN ++ + L+Q L
Sbjct: 118 ARIKQLSANAIELDEENRELREELAELKQENEAL 151
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 38.4 bits (90), Expect = 0.025
Identities = 18/74 (24%), Positives = 29/74 (39%)
Query: 430 KRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEK 489
K AL N+++A + L+ + L+ ++ L AA E+ Q E A
Sbjct: 51 KDSALDRLNSQIAELADLLSLERQGNQDLQDSVANLRASLSAAEAERSRLQALLAELAGA 110
Query: 490 IDLADRLVNGLASE 503
A+ LA E
Sbjct: 111 GAAAEGRAGELAQE 124
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 37.7 bits (88), Expect = 0.043
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
L A EL + S K++E + ++ L+ LQELT +A +K + E AEKI
Sbjct: 209 LEKARQELRSLSVKISEKRKQLEELQQELQELTIAIEALTNKKSELLEEIAE-AEKI 264
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 37.3 bits (87), Expect = 0.094
Identities = 17/87 (19%), Positives = 37/87 (42%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKID 491
+ L EL + +L EL+A++ LE+ L+EL ++ + + + Q +I+
Sbjct: 344 EKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIE 403
Query: 492 LADRLVNGLASENVRWKDSVLGLQQSA 518
+ + L R + + L +
Sbjct: 404 RLEARLERLEDRRERLQQEIEELLKKL 430
Score = 33.5 bits (77), Expect = 1.1
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLA 493
L AEL +KL EL+ +++ LE ++EL + A E + Q + E++
Sbjct: 255 LEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANL 314
Query: 494 DR 495
+R
Sbjct: 315 ER 316
Score = 33.5 bits (77), Expect = 1.1
Identities = 22/81 (27%), Positives = 36/81 (44%)
Query: 437 ANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLADRL 496
ELA +KL ELK ++ SLEA L+EL + + + Q E K+ +
Sbjct: 335 LAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQ 394
Query: 497 VNGLASENVRWKDSVLGLQQS 517
+ L +E R + + L+
Sbjct: 395 IASLNNEIERLEARLERLEDR 415
Score = 33.1 bits (76), Expect = 1.5
Identities = 17/92 (18%), Positives = 36/92 (39%)
Query: 430 KRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEK 489
+R+ + ++ +K+AEL+ +A L L+EL ++ + KE Q +
Sbjct: 675 RRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734
Query: 490 IDLADRLVNGLASENVRWKDSVLGLQQSALTL 521
+ + V L + + L+ L
Sbjct: 735 LARLEAEVEQLEERIAQLSKELTELEAEIEEL 766
Score = 32.3 bits (74), Expect = 2.8
Identities = 19/97 (19%), Positives = 39/97 (40%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLA 493
+ L A ++LAE +A+I LEA +++L ++ A + + + E+
Sbjct: 763 IEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANL 822
Query: 494 DRLVNGLASENVRWKDSVLGLQQSALTLPGDILLVTA 530
+ L + + L++ L DI + A
Sbjct: 823 RERLESLERRIAATERRLEDLEEQIEELSEDIESLAA 859
Score = 32.0 bits (73), Expect = 3.3
Identities = 16/77 (20%), Positives = 32/77 (41%)
Query: 427 VEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEEC 486
+E R ++ E+ ++L L +I+ LE Q L ++ ++ + Q EE
Sbjct: 269 LEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEEL 328
Query: 487 AEKIDLADRLVNGLASE 503
K+D + L +
Sbjct: 329 ESKLDELAEELAELEEK 345
Score = 30.4 bits (69), Expect = 9.9
Identities = 18/70 (25%), Positives = 34/70 (48%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLA 493
L A+L KL EL ++A LE L+EL ++ ++ E + + EE +++
Sbjct: 318 LEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEEL 377
Query: 494 DRLVNGLASE 503
+ + L S+
Sbjct: 378 EEQLETLRSK 387
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 33.3 bits (77), Expect = 0.12
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 415 INIITFYNVWTFVEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDA 471
+ ++ Y + V A N E+AA +LA+LKA+ LEA +++L D
Sbjct: 1 LLLLFQYLLIFGVNGLS-AYYQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDY 56
>gnl|CDD|233230 TIGR01000, bacteriocin_acc, bacteriocin secretion accessory
protein. This family represents an accessory protein
that works with the bacteriocin maturation and ABC
transport secretion protein described by TIGR01193
[Transport and binding proteins, Other].
Length = 457
Score = 35.8 bits (83), Expect = 0.17
Identities = 50/286 (17%), Positives = 100/286 (34%), Gaps = 46/286 (16%)
Query: 629 LDNLIGRNLIRKGKVVKIGEKEIDYNPNFKLILHTKLANPHYKPEMQAQTTLINFTVTRD 688
+N I N +++ K VK G+ + Y+ + + D
Sbjct: 66 SNNAIKENYLKENKFVKKGDLLVVYDNGNE------------------ENQKQLLEQQLD 107
Query: 689 GLEDQLLAEVVKFERPDLELLKANLTKEQNLFKITLKGLEDDLLMRLSSSGGDVLSDKNL 748
L+DQ + L+ LK ++ +N F +L + + S+
Sbjct: 108 NLKDQKKS---------LDTLKQSIENGRNQFPTDDSFGYRNLFNGYLAQVESLTSETQQ 158
Query: 749 VLNLEKSKKTAKEIEIKVKEG--KKTAKKIDEAREQYRPAAERASVIYFIMNELFKINPI 806
+ +++ A E + KT +K+ + + + V F N +
Sbjct: 159 QNDKSQTQNEAAEKTKAQLDQQISKTDQKLQDYQALKNAISNGTKVANF--NPYQSLYEN 216
Query: 807 YQFSLKAFTVVFHNAMTKAKKSDNLKGRVANLVESITFMTFQYTSRGLFERDKLIFMAQM 866
YQ LK+ + K+ ++ ++ L +SI ++Q GL + + +
Sbjct: 217 YQAQLKSASDKDQKNQVKSTILATIQQQIDQLQKSIA--SYQVQKAGLTKSTASNYASSQ 274
Query: 867 TIQVKSLCMGDQHYHVLQQPKRKALAAANAELAAASQKLAELKAKI 912
++ L K + LA E+ +QKL EL++KI
Sbjct: 275 NSKLAQL-------------KEQQLAKVKQEITDLNQKLLELESKI 307
Score = 32.0 bits (73), Expect = 3.1
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 430 KRKALAAANAELAAASQKLAELKAKIASLEATLQE 464
K + LA E+ +QKL EL++KI SL+ Q+
Sbjct: 282 KEQQLAKVKQEITDLNQKLLELESKIKSLKEDSQK 316
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 36.3 bits (84), Expect = 0.18
Identities = 39/233 (16%), Positives = 86/233 (36%), Gaps = 35/233 (15%)
Query: 277 LEQIDLYAKLLKIKFDDNKSGITRFQNGLQKLVSL---GNEEKKVRAIEEDVSYKQKVCA 333
LE+++ K++ K + + ++ LQ+L L + + E++ + K
Sbjct: 542 LEELE--ELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELK 599
Query: 334 EDLEKAEPALVAAQEALDTLD--------KNNLTELKALKAPPQGVIAVCDAVAVLMASK 385
+ L++ E L +E L +L+ + EL++ + + + +
Sbjct: 600 KKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEEL 659
Query: 386 KGKVPKDLGWKGSQLKALKAPPQGLCAWVINIITFYNVWTFVEPKRKALAAANAELAAAS 445
+ KV + L+A + + N E K + L EL
Sbjct: 660 EEKV-----------EELEAEIRRELQRIENEEQL-------EEKLEELEQLEEELEQLR 701
Query: 446 QKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLADRLVN 498
++L EL K+ +E ++EL E + + E+ + ++L + L
Sbjct: 702 EELEELLKKLGEIEQLIEELES----RKAELEELKKELEKLEKALELLEELRE 750
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 36.2 bits (84), Expect = 0.18
Identities = 37/210 (17%), Positives = 84/210 (40%), Gaps = 22/210 (10%)
Query: 300 RFQNGLQKLVSLGNEEKKVRAIEEDVSYKQKVCAEDLEKAEPALVAAQEALDTLDKNNLT 359
+ +++ L +E +++R E++ + E++E+ E + +E L+ L+
Sbjct: 261 ELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEE 320
Query: 360 ELKALKAPP------QGVIAVCDAVAVLMASKKGKVPKDLGWKGSQLKALKAPPQGLCAW 413
+ L+ + + + + + ++ + +L AL + L
Sbjct: 321 LEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEEL--- 377
Query: 414 VINIITFYNVWTFVEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAV 473
E R+ LA AELA +L ELK +I SLE L+ L+++ +
Sbjct: 378 -------------FEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424
Query: 474 KEKLFCQNQAEECAEKIDLADRLVNGLASE 503
+E + + EE +++ + + L +
Sbjct: 425 EELKELEAELEELQTELEELNEELEELEEQ 454
Score = 33.9 bits (78), Expect = 0.81
Identities = 17/71 (23%), Positives = 29/71 (40%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDLA 493
L AE +L EL+ + LE L+EL + +E + + EE K++
Sbjct: 865 LEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERL 924
Query: 494 DRLVNGLASEN 504
+ + L E
Sbjct: 925 EVELPELEEEL 935
Score = 33.1 bits (76), Expect = 1.4
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKID 491
L EL ++L ELK ++ LEA +EL D+ +EK + + E ++
Sbjct: 844 LDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELA 901
Score = 32.0 bits (73), Expect = 3.4
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
+ L EL ++L EL+A+ LE L+EL ++ + +E +++ E E+I
Sbjct: 848 EEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEI 907
Query: 491 DLADRLVNGLASEN 504
+ + L ++
Sbjct: 908 EKLRERLEELEAKL 921
Score = 30.8 bits (70), Expect = 7.8
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
+ LA A+L ++L LK ++ SLE L+EL + + ++ + + E++
Sbjct: 673 EEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEEL 732
Query: 491 -DLADRL 496
L RL
Sbjct: 733 EQLQSRL 739
Score = 30.5 bits (69), Expect = 9.1
Identities = 20/106 (18%), Positives = 44/106 (41%), Gaps = 7/106 (6%)
Query: 427 VEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKL-------FC 479
E + + E+ +KL EL+ ++ LE L+EL ++ + EK
Sbjct: 823 RERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKEL 882
Query: 480 QNQAEECAEKIDLADRLVNGLASENVRWKDSVLGLQQSALTLPGDI 525
+ + EE E++ + + L E + ++ + L+ L ++
Sbjct: 883 EEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVEL 928
Score = 30.5 bits (69), Expect = 9.3
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 427 VEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEEC 486
+E + E+ +++ EL+ K+ LE L+EL + E+L + + E
Sbjct: 816 LESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKE-----LEELKEELEELE- 869
Query: 487 AEKIDLADRL 496
AEK +L D L
Sbjct: 870 AEKEELEDEL 879
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 35.8 bits (83), Expect = 0.20
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKID 491
+ A A EL +L LK +I L+ Q++ F V E+L +A+ A +
Sbjct: 203 RERAEAQGELGRLEAELEVLKRQIDELQLERQQIEQTFREEVLEEL---TEAQ--ARLAE 257
Query: 492 LADRLV 497
L +RL
Sbjct: 258 LRERLN 263
>gnl|CDD|220211 pfam09375, Peptidase_M75, Imelysin. The imelysin peptidase was
first identified in Pseudomonas aeruginosa. The active
site residues have not been identified. However, His201
and Glu204 are completely conserved in the family and
occur in an HXXE motif that is also found in family M14.
Length = 282
Score = 35.4 bits (82), Expect = 0.20
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 416 NIITFYNVWTFVEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKE 475
N+ NV+ R LAAA+ LA A + A+ A+ A L L D A+ +
Sbjct: 208 NLEGLRNVYLGGPGLRDLLAAADPALA------ARIDAQFAAALAALAALDTPLDQALAD 261
Query: 476 K 476
Sbjct: 262 A 262
>gnl|CDD|234541 TIGR04320, Surf_Exclu_PgrA, SEC10/PgrA surface exclusion domain.
This model describes a conserved domain found in surface
proteins of a number of Firmutes. Many members have
LPXTG C-terminal anchoring motifs and a substantial
number have the KxYKxGKxW putative sorting signal at the
N-terminus. The tetracycline resistance plasmid pCF10 in
Enterococcus faecalis promotes conjugal plasmid transfer
in response to sex pheromones, but PgrA/Sec10 encoded by
that plasmid, a member of this family, specifically
inhibits the ability of cells to receive homologous
plasmids. The phenomenon is called surface exclusion.
Length = 356
Score = 34.7 bits (80), Expect = 0.34
Identities = 29/131 (22%), Positives = 39/131 (29%), Gaps = 27/131 (20%)
Query: 333 AEDLEKAEPALVAAQEALDTLDKNNLTELKALKAPPQGVIAVCDAVAVLMASKKGKVPKD 392
L+ + AL AQ L T AL A A+A
Sbjct: 253 PNSLKALQAALATAQADLAAAQTALNTAQAALTTAQTAYAAAQAALATAQK--------- 303
Query: 393 LGWKGSQLKALKAPPQGLCAWVINIITFYNVWTFVEPKRKALAAANAELAAASQKLAELK 452
+L +A + + ALA A A LA A + LA L
Sbjct: 304 ------ELANAQAQALQTAQ------------NNLATAQAALANAEARLAKAKEALANLN 345
Query: 453 AKIASLEATLQ 463
A +A +A L
Sbjct: 346 ADLAKKQAALD 356
Score = 30.8 bits (70), Expect = 6.7
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEAT-LQELTDKFDAAVK 474
AL A AAA LA + ++A+ +A LQ + A
Sbjct: 282 AALTTAQTAYAAAQAALATAQKELANAQAQALQTAQNNLATAQA 325
>gnl|CDD|234956 PRK01490, tig, trigger factor; Provisional.
Length = 435
Score = 34.4 bits (80), Expect = 0.49
Identities = 11/48 (22%), Positives = 26/48 (54%)
Query: 759 AKEIEIKVKEGKKTAKKIDEAREQYRPAAERASVIYFIMNELFKINPI 806
+ ++++ + + T +E RE++R AER + +++E+ K I
Sbjct: 319 QQGLDLEGQFLEDTGTTEEEPREEFREQAERRVKLGLLLDEIAKAEEI 366
>gnl|CDD|150231 pfam09486, HrpB7, Bacterial type III secretion protein (HrpB7).
This entry represents proteins encoded by genes which
are found in type III secretion operons in a narrow
range of species including Xanthomonas, Burkholderia and
Ralstonia.
Length = 158
Score = 33.3 bits (76), Expect = 0.50
Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 14/63 (22%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKIDL 492
AA +AAA Q L A + ++ + Q + E+ D
Sbjct: 87 GHRAAEQAVAAARQALQAKVAALGAVRRKIARN--------------DAQIDVYRERADR 132
Query: 493 ADR 495
R
Sbjct: 133 LRR 135
Score = 32.5 bits (74), Expect = 0.87
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVK-EKLFCQNQAEECAEKID 491
A+AAA L A L ++ KIA +A + ++ D + E+ ++ +E AE+
Sbjct: 94 AVAAARQALQAKVAALGAVRRKIARNDAQIDVYRERADRLRRAEEAAREDAEDEEAEEAL 153
Query: 492 LADRL 496
LA R
Sbjct: 154 LARRR 158
>gnl|CDD|226424 COG3909, COG3909, Cytochrome c556 [Energy production and
conversion].
Length = 147
Score = 32.9 bits (75), Expect = 0.50
Identities = 24/104 (23%), Positives = 30/104 (28%), Gaps = 22/104 (21%)
Query: 376 DAVAVLMASKK----GKVPKDLGWKGSQLKALKAPPQGLCAWVINIITFYNVWT----FV 427
DA V A K P L GS+ +A P +W F
Sbjct: 56 DAEKVKAALATLSENAKKPPTLFPAGSETGETRALPA--------------IWEDMADFK 101
Query: 428 EPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDA 471
K A LAAA +KA +L A + A
Sbjct: 102 AKAAKFGADVEKLLAAAPTDQDGVKAAYGTLGADCGSCHQTYRA 145
>gnl|CDD|131610 TIGR02559, HrpB7, type III secretion protein HrpB7. This family of
genes is found in type III secretion operons in a narrow
range of species including Xanthomonas, Burkholderia and
Ralstonia.
Length = 158
Score = 33.0 bits (75), Expect = 0.57
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLF-CQNQAEECAEK 489
R A L AA Q A +A + +L A L A K ++ Q + C E+
Sbjct: 78 RAYRDVLEAHLGAAEQAEAAARAALQALAAALA--------AKKREIARLDAQIDVCRER 129
Query: 490 IDLADR 495
+ R
Sbjct: 130 AERLRR 135
Score = 31.5 bits (71), Expect = 2.0
Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
R AL A A LAA +++A L A+I + L +AA +E L EE AE+
Sbjct: 99 RAALQALAAALAAKKREIARLDAQIDVCRERAERLRRAGEAAREEAL------EEEAEEA 152
Query: 491 DLADRL 496
L RL
Sbjct: 153 ALGRRL 158
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 34.3 bits (79), Expect = 0.69
Identities = 16/45 (35%), Positives = 21/45 (46%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEK 476
KA A AE+ AA +KL LK + ++LE LQ K
Sbjct: 27 KASKADKAEIDAAIEKLKALKLEKSALEKELQAAVGAGGDGAASK 71
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 33.2 bits (76), Expect = 1.1
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 427 VEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEE 485
+E ++K LA N+EL+A +KL EL+A + L+ + + A +E A
Sbjct: 205 LEERKKTLAQLNSELSADQKKLEELRANESRLKNEIASA-EAAAAKAREAAAAAEAAAA 262
Score = 33.2 bits (76), Expect = 1.3
Identities = 19/44 (43%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 883 LQQPKRKALAAANAELAAASQKLAELKAKIAISMMKKEIAREEL 926
L + ++K LA N+EL+A +KL EL+A S +K EIA E
Sbjct: 204 LLEERKKTLAQLNSELSADQKKLEELRAN--ESRLKNEIASAEA 245
Score = 30.5 bits (69), Expect = 9.6
Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 9/100 (9%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKF-DAAVKEKLFCQNQAEECAEK 489
+K +AA ++ + A+L+ ++ SLE + L + + A K + A+ A
Sbjct: 44 QKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARL 103
Query: 490 IDLADRLVN--GLASENVRWKDSVLGLQQSALTLPGDILL 527
L + +E + LQ+S P +L+
Sbjct: 104 NALEVQEREQRRRLAEQLAA------LQRSGRNPPPALLV 137
>gnl|CDD|222709 pfam14362, DUF4407, Domain of unknown function (DUF4407). This
family of proteins is found in bacteria. Proteins in
this family are typically between 366 and 597 amino
acids in length. There is a single completely conserved
residue R that may be functionally important.
Length = 297
Score = 33.0 bits (76), Expect = 1.2
Identities = 21/65 (32%), Positives = 23/65 (35%), Gaps = 10/65 (15%)
Query: 436 AANAELAAASQKLAELK----AKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKID 491
+L AA +L LK A IA LEA L AAV EK
Sbjct: 186 EKREKLDAAQARLETLKARLDAAIAQLEAQKAALERNRQAAVAEK------QARIEANDG 239
Query: 492 LADRL 496
L RL
Sbjct: 240 LLARL 244
>gnl|CDD|234283 TIGR03623, TIGR03623, probable DNA repair protein. Members of this
protein family are bacterial proteins of about 900 amino
acids in length. Members show extended homology to
proteins in TIGR02786, the AddB protein of double-strand
break repair via homologous recombination. Members of
this family, therefore, may be DNA repair proteins.
Length = 874
Score = 33.5 bits (77), Expect = 1.3
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 13/86 (15%)
Query: 1446 EYSIFMDTVPPSWEKRAYPSMLGLGGWF--ADLMLRLKELENWVGDFQLPSSVWLAGF-- 1501
E +F+ W + + + GW A L +L +L G +LP + LAGF
Sbjct: 120 ETRLFLQ-----W-RTRFEARCRREGWIDAAQLPEQLLDLLE-QGGLRLPKQIILAGFDE 172
Query: 1502 FNP--QSFLTAIMQSTARKNEWPLDK 1525
P Q+ L A+ +W +
Sbjct: 173 LTPQQQALLAALEARGVDVQQWLPES 198
>gnl|CDD|181574 PRK08881, rpsN, 30S ribosomal protein S14; Reviewed.
Length = 101
Score = 30.9 bits (71), Expect = 1.4
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 430 KRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVK 474
KRK L A A K AELKA I+ + +E +++A +K
Sbjct: 12 KRKKLVAKYAA------KRAELKAIISDPNLSDEE---RYEARLK 47
>gnl|CDD|224482 COG1566, EmrA, Multidrug resistance efflux pump [Defense
mechanisms].
Length = 352
Score = 32.7 bits (75), Expect = 1.6
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQ 463
R AL A A LAAA +L L+A++AS +A +
Sbjct: 90 RAALEQAEAALAAAEAQLRNLRAQLASAQALIA 122
>gnl|CDD|197275 cd09178, PLDc_N_Snf2_like, N-terminal putative catalytic domain of
uncharacterized HKD family nucleases fused to putative
helicases from the Snf2-like family. N-terminal
putative catalytic domain of uncharacterized archaeal
and prokaryotic HKD family nucleases fused to putative
helicases from the Snf2-like family, which belong to the
DNA/RNA helicase superfamily II (SF2). Although
Snf2-like family enzymes do not possess helicase
activity, they contain a helicase-like region, where
seven helicase-related sequence motifs are found,
similar to those in DEAD/DEAH box helicases, which
represent the biggest family within the SF2 superfamily.
In addition to the helicase-like region, members of this
family also contain an N-terminal putative catalytic
domain with one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified as members of the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 134
Score = 31.4 bits (72), Expect = 1.7
Identities = 27/88 (30%), Positives = 34/88 (38%), Gaps = 18/88 (20%)
Query: 612 SGFVLLIENIGESVDPVLDNLIGRNLIRKGKV-VKIGEKEIDYNPNFKLILHTKLANPHY 670
SGF LL E + L LIG LI++GKV +++ K LH K
Sbjct: 34 SGFRLLKEELEN--FEKLRILIGIELIKEGKVEIRVYTKG---------FLHAKAYLFDG 82
Query: 671 KPEMQAQTTLI----NFTVTRDGLEDQL 694
T I NF T+ GL L
Sbjct: 83 PDNDNGPGTAIVGSSNF--TKAGLTGNL 108
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 30.7 bits (70), Expect = 1.8
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAA 472
A A LAAA A +A+ A LEA L E + +A
Sbjct: 78 AQEEAEERLAAA---RAAAEAERAELEAELAEAAAEAEAL 114
Score = 29.2 bits (66), Expect = 6.2
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEATLQE 464
A AAA AE A +LAE A+ +LE L+
Sbjct: 88 AARAAAEAERAELEAELAEAAAEAEALEEELEA 120
>gnl|CDD|204187 pfam09278, MerR-DNA-bind, MerR, DNA binding. Members of this
family of DNA-binding domains are predominantly found in
the prokaryotic transcriptional regulator MerR. They
adopt a structure consisting of a core of three alpha
helices, with an architecture that is similar to that of
the 'winged helix' fold.
Length = 65
Score = 29.4 bits (67), Expect = 1.8
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 442 AAASQKLAELKAKIASLEATLQELTD 467
A +KLAEL+A+IA L+A EL
Sbjct: 39 ALLREKLAELEARIAELQALRAELDA 64
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 32.3 bits (74), Expect = 1.8
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 9/86 (10%)
Query: 434 LAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQ---NQAEECAEKI 490
L A +L Q++ K+ LE LQEL K + +K +AE+ E+
Sbjct: 206 LDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEKKLEQC 265
Query: 491 DLADRLVNGLASENVRWKDSVLGLQQ 516
E + K+ + LQ
Sbjct: 266 RGFTF------KEIEKLKEQLKLLQS 285
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 33.0 bits (76), Expect = 2.0
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
R+ L + +LAA +L E+ ++A L +L + AA + L A EKI
Sbjct: 292 RRELYTSRRQLAAEQYRLVEMARELAELNEAESDLEQDYQAA-SDHLNLVQTALRQQEKI 350
Query: 491 D 491
+
Sbjct: 351 E 351
Score = 32.6 bits (75), Expect = 2.6
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 17/72 (23%)
Query: 438 NAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQ--------------- 482
AEL +++ EL+ +A E+ Q+ + + A KE L N+
Sbjct: 836 EAELRQLNRRRVELERALADHESQEQQQRSQLEQA-KEGLSALNRLLPRLNLLADETLAD 894
Query: 483 -AEECAEKIDLA 493
EE E++D A
Sbjct: 895 RVEEIREQLDEA 906
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 32.6 bits (75), Expect = 2.0
Identities = 10/58 (17%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 749 VLNLEKSKKTAKEIEIKVKEGKKTAKKIDEAREQYRPAAERASVIYFIMNELFKINPI 806
+ NL K + + + + + + +E RE+++ AE+ + ++ E+ K +
Sbjct: 310 IDNLLKQALQQLQ-QQGIDSLEASGESEEELREEFKEEAEKRVKLGLLLEEIAKEEKL 366
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 31.9 bits (72), Expect = 2.9
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 4/91 (4%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEE---CA 487
R+ LAAA LA A Q+LA L + L+ L+ L ++ + Q ++ A
Sbjct: 122 RQELAAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASA 181
Query: 488 EKIDLADRLVNGLASENVRWKDSVLGLQQSA 518
++ + L S + + L + +A
Sbjct: 182 TQLKSQVLDLK-LRSAQIEQEAQNLATRANA 211
>gnl|CDD|133410 cd04783, HTH_MerR1, Helix-Turn-Helix DNA binding domain of the
MerR1 transcription regulator. Helix-turn-helix (HTH)
transcription regulator MerR1. MerR1 transcription
regulators, such as Tn21 MerR and Tn501 MerR, mediate
response to mercury exposure in eubacteria. These
proteins are comprised of distinct domains that harbor
the regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain winged HTH motifs that mediate DNA binding,
while the C-terminal domains have three conserved
cysteines that define a mercury binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 126
Score = 30.3 bits (69), Expect = 3.4
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 444 ASQKLAELKAKIASL---EATLQELTDK 468
A QKLAE+ KIA L A+LQEL +
Sbjct: 82 AEQKLAEVDEKIADLQRMRASLQELVSQ 109
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 31.9 bits (73), Expect = 3.5
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQEL 465
LA A AE+A+ ++AEL A+I LE+ L+ +
Sbjct: 318 ELAEAEAEIASLEARVAELTARIERLESLLRTI 350
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 31.6 bits (72), Expect = 3.5
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 878 QHYHVLQQPKRKALAAANAELAAASQKLAELKAKIA-IS 915
Q + + + KAL AN + AA +++L EL+ K+A IS
Sbjct: 88 QELEGILKQQAKALDQANRQQAALAKQLDELQQKVATIS 126
Score = 31.2 bits (71), Expect = 5.0
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEAT 461
KAL AN + AA +++L EL+ K+A++ +
Sbjct: 99 KALDQANRQQAALAKQLDELQQKVATISGS 128
>gnl|CDD|226676 COG4223, COG4223, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 422
Score = 31.9 bits (72), Expect = 3.6
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 432 KALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAA 472
+A AE + A +AEL +IA+LE +L E D +AA
Sbjct: 220 PLESALPAERSTALAAVAELNGRIAALEQSLNEPADDIEAA 260
>gnl|CDD|178769 PLN03230, PLN03230, acetyl-coenzyme A carboxylase carboxyl
transferase; Provisional.
Length = 431
Score = 31.5 bits (71), Expect = 3.9
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 969 IEAAAKRWKKYIEGETPEKDKLPQEWKNKSALQRLC 1004
A + KK +E E P +KLPQ AL+ L
Sbjct: 27 RPAKIVKGKKRLEHEYPWPEKLPQGELTTGALKILN 62
>gnl|CDD|185541 PTZ00292, PTZ00292, ribokinase; Provisional.
Length = 326
Score = 31.2 bits (71), Expect = 4.1
Identities = 37/188 (19%), Positives = 74/188 (39%), Gaps = 21/188 (11%)
Query: 48 IVASMNLVLFEDAMSHICRINRIMEAPRGNALLVGVGGSG-KQSL--SRLSA---FISTL 101
+V S N D + ++ R+ ++ E G + G GG G Q++ S+L A + +
Sbjct: 20 VVGSSNT----DLIGYVDRMPQVGETLHGTSFHKGFGGKGANQAVMASKLGAKVAMVGMV 75
Query: 102 --EPFQIQLKKNYGIPDLKIDLASLYLKAGLKNAGIMFLMTDSQVADEKFLVIINDMLAS 159
+ F KN+ ++ + + + + G+ + D++ + + ++I A+
Sbjct: 76 GTDGFGSDTIKNF--KRNGVNTSFVS-RTENSSTGLAMIFVDTKTGNNEIVIIPG---AN 129
Query: 160 GEV-PDLFTD--DEIENIVNNIAAEPEIPLTADLDPLTMLTDDATIAFWNNEGLPNDRMS 216
+ P + D I+NI + + EIPL LD L + +N P
Sbjct: 130 NALTPQMVDAQTDNIQNICKYLICQNEIPLETTLDALKEAKERGCYTVFNPAPAPKLAEV 189
Query: 217 TENATILV 224
L
Sbjct: 190 EIIKPFLK 197
>gnl|CDD|222255 pfam13600, DUF4140, N-terminal domain of unknown function
(DUF4140). This family is often found at the N-terminus
of its member proteins, with DUF4139, pfam13598, at the
C-terminus.
Length = 101
Score = 29.6 bits (67), Expect = 4.2
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 443 AASQKLAELKAKIASLEATLQELTDKFDAAVKEKLF 478
A S LAEL+ ++ +LE L L + +A + F
Sbjct: 64 ATSPALAELEEELRALEDELAALEAEKEALEAQIKF 99
>gnl|CDD|182114 PRK09854, cmtB, putative PTS system mannitol-specific transporter
subunit IIA; Provisional.
Length = 147
Score = 30.3 bits (68), Expect = 4.2
Identities = 22/90 (24%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 601 RVMDQIEKAVMSGFVLLIENIGESVDPVLDNLIGRNLIRKGKVVKIGEKEIDYNPNFKLI 660
R+ D ++ +S + ++ E++D + +L+ +N I + + I + I+ P + I
Sbjct: 2 RLSDYFPESSIS-VIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYY--I 58
Query: 661 LHTKLANPHYKPEMQAQTTLINFTVTRDGL 690
L +A PH +PE A T ++ T+ G+
Sbjct: 59 LAPGVAMPHARPECGALKTGMSLTLLEQGV 88
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 31.8 bits (72), Expect = 4.3
Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 20/150 (13%)
Query: 321 IEEDVSYKQKVCAE--DLEKAEPA------LVAAQEALDTLDKNNLTELKALKAPPQGVI 372
++E + + K+ E DL+K P L A ++ LD LDK + +A + +
Sbjct: 1128 VQELCADRDKLNIEVEDLKKTTPKSLWLKDLDALEKELDKLDKEDAKAEEAREKLQRAAA 1187
Query: 373 --AVCDAVAVLMASKKGKVPKDLGWKGSQLKALKAPPQGLCAWVINIITFYNVWTFVEPK 430
A V + K PK + KA ++ + T NV V+PK
Sbjct: 1188 RGESGAAKKVSRQAPKKPAPKK-----TTKKASESETTEETYGSSAMETE-NVAEVVKPK 1241
Query: 431 RKALAAANAELAAASQ----KLAELKAKIA 456
+A A A AA + ++ +LK ++A
Sbjct: 1242 GRAGAKKKAPAAAKEKEEEDEILDLKDRLA 1271
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 31.1 bits (71), Expect = 4.3
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 831 LKGRVANLVESITFMTFQYTSRGLFERDKLIFMAQMTIQVKSLCMGDQHYHVLQQ--PKR 888
LKG S++ T+++ + DK ++ + Q+K L Y L+ +R
Sbjct: 1 LKGLFGKFTSSVSKSTYKFNEPDPWFEDKRQYIDSLESQLKKL------YKALELLVNQR 54
Query: 889 KALAAANAELAAASQKLAELKAKIAIS 915
K LA+A E A + LA L+ +S
Sbjct: 55 KELASATGEFAKSLAMLASLELSTGLS 81
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 31.6 bits (73), Expect = 4.3
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAA 472
+ A ++ ELK +I +LEA L EL + +
Sbjct: 60 QAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEEL 99
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 31.4 bits (71), Expect = 4.6
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 268 YNYTTPKSFLEQIDLYAKLLKIKFDD---NKSGITRFQNGLQKLVSLGNEEKKV 318
+N K L++ K LK+ F D NK+ + ++NGL V NE K+
Sbjct: 181 FNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTVFFYENGLVDFVDYINETKET 234
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 31.1 bits (70), Expect = 4.7
Identities = 40/209 (19%), Positives = 65/209 (31%), Gaps = 25/209 (11%)
Query: 302 QNGLQKLVSLGNEEKKVRAIEEDVSYKQKV-CAEDLEKAEPALVAAQEALDTLDKNNLTE 360
Q +K + E K +A E++ + + + E+ + A A ++A L++ E
Sbjct: 79 QQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQA--QLEQKQQEE 136
Query: 361 LKALKAPPQGVIAVCDAVAVLMASKKGKVPKDLGWKGSQLKALKAPPQGLCAWVINIITF 420
A Q A + K K + K + +
Sbjct: 137 QARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAE-------- 188
Query: 421 YNVWTFVEPKRKALAAANAELAAASQK-------LAELKAKIASLEATLQELTDKFDAAV 473
K A A A+ AA K AE KA+ A+ E E A
Sbjct: 189 -------AAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAK 241
Query: 474 KEKLFCQNQAEECAEKIDLADRLVNGLAS 502
+K +A E D + GL+S
Sbjct: 242 ADKAAAAAKAAERKAAAAALDDIFGGLSS 270
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 31.6 bits (72), Expect = 5.3
Identities = 15/71 (21%), Positives = 32/71 (45%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQNQAEECAEKI 490
K + N + ++L EL+A + LE+ L +L + D + + + EE +I
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQI 912
Query: 491 DLADRLVNGLA 501
+ + ++ L
Sbjct: 913 EKKRKRLSELK 923
>gnl|CDD|217565 pfam03449, GreA_GreB_N, Transcription elongation factor,
N-terminal. This domain adopts a long alpha-hairpin
structure.
Length = 71
Score = 28.2 bits (64), Expect = 6.3
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 432 KALAAA--------NAELAAASQKLAELKAKIASLEATLQ 463
KA+A A NAE AA ++ E++A+I LE L
Sbjct: 28 KAIAEAREHGDLSENAEYHAAKEEQREIEARIRELEDRLA 67
>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 = 29.6 bits (67), Expect = 6.4
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 79 LLVGVGGSGKQSLS-RLSAFISTLEPFQIQLKKNYGIPDLK 118
LLVG G+GK L+ RL+A +S F +QL ++ DLK
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLK 43
>gnl|CDD|226369 COG3851, UhpB, Signal transduction histidine kinase,
glucose-6-phosphate specific [Signal transduction
mechanisms].
Length = 497
Score = 30.9 bits (70), Expect = 6.5
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 9/92 (9%)
Query: 833 GRVANLVESITFMTFQYTSRGLFERDKLIFMAQMTIQVKSLCMGDQHYHVLQQPKRKALA 892
+A+L+ SI + T R D L+ + + L + Q L Q +K L
Sbjct: 227 ALLASLLNSIALTIARQTWRFSHLVDLLLSLLAQALTGLGLGIAIQRLRELNQRLQKEL- 285
Query: 893 AANAELAAASQKLAELKAKIAISMMKKEIARE 924
A N LA ++L + I +K++ARE
Sbjct: 286 ARNRALA---EQLISTEESI-----RKDVARE 309
>gnl|CDD|237621 PRK14139, PRK14139, heat shock protein GrpE; Provisional.
Length = 185
Score = 29.9 bits (68), Expect = 6.5
Identities = 19/49 (38%), Positives = 22/49 (44%)
Query: 427 VEPKRKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKE 475
E A AA A AAA L+A++A EA EL D F A E
Sbjct: 13 AEEAGAAAQAAAAAAAAAEDAAPALEAELAEAEAKAAELQDSFLRAKAE 61
>gnl|CDD|201519 pfam00943, Alpha_E2_glycop, Alphavirus E2 glycoprotein. E2 forms a
heterodimer with E1. The virus spikes are made up of 80
trimers of these heterodimers (sindbis virus).
Length = 403
Score = 30.7 bits (70), Expect = 6.9
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 666 ANPHYKPEMQAQTTLINFTVTRDGLE 691
A P+ E T NFTVT +GLE
Sbjct: 288 AEPNPTHEWITGPTTRNFTVTEEGLE 313
>gnl|CDD|221268 pfam11853, DUF3373, Protein of unknown function (DUF3373). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 472 to 574 amino acids in
length.
Length = 485
Score = 31.0 bits (70), Expect = 7.0
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 433 ALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVK 474
AAA A++ QK+ LK ++A L+A L++L + D K
Sbjct: 19 PAAAAAADIDLL-QKIEALKKELAELKAQLKDLQKRVDKTEK 59
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily. The
DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain consisting
of a core beta(8)-alpha(8) motif with the eight parallel
beta strands forming an enclosed barrel surrounded by
eight alpha helices. The domain has a catalytic center
containing a divalent cation-binding site formed by a
cluster of invariant residues that cap the core of the
barrel. In addition, the catalytic site includes three
invariant residues - an aspartate (D), an arginine (R),
and a glutamate (E) - which is the basis for the domain
name "DRE-TIM".
Length = 265
Score = 30.5 bits (70), Expect = 7.1
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 1364 GSGVTREEKVRQVLDEILDKCPDAFNIKDMMGRVEDRTPYIIVAFQECERMNILMSEIKR 1423
T E V +V + + D ++KD +G TP + L+ ++
Sbjct: 139 FGCKTDPEYVLEVAKALEEAGADEISLKDTVGLA---TPEEVAE---------LVKALRE 186
Query: 1424 SLKELNLGL 1432
+L ++ LGL
Sbjct: 187 ALPDVPLGL 195
>gnl|CDD|149649 pfam08663, HalX, HalX domain. HalX is a domain of unknown
function, previously (mis)annotated as HoxA-like
transcriptional regulator.
Length = 71
Score = 28.1 bits (63), Expect = 7.1
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 430 KRKAL-AAANAELAAASQKLAELKAKIASLEATLQELTDKFDAAVKEKLFCQN 481
KR AL A S + EL+ +I L L D+ DA E LF Q
Sbjct: 19 KRAALEAEKPDAELEDSDEYQELQERIEELRDDLDATLDELDADDFEALFRQL 71
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 29.9 bits (68), Expect = 7.1
Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 8/116 (6%)
Query: 637 LIRKGKVVKIGEKEIDYNPNFKLILHTKLANPHYKPEMQAQTTLINFTVTRDGLED-QLL 695
L R G V++ + ++T N Y P ++ L T + ++ ++
Sbjct: 18 LARNGHEVRL----WGRDEELIEEINTTRENVKYLPGIKLPDNLRATTDLEEAIKGADII 73
Query: 696 AEVV--KFERPDLELLKANLTKEQNLFKITLKGLEDDLLMRLSSSGGDVLSDKNLV 749
V + R L+ LK L+ L +T KG+E L LS + L +
Sbjct: 74 VLAVPSQALREVLKQLKGLLSPGAILVSLT-KGIEPGTLKLLSEIIEEELPINPIA 128
>gnl|CDD|218051 pfam04380, BMFP, Membrane fusogenic activity. BMFP consists of two
structural domains, a coiled-coil C-terminal domain via
which the protein self-associates as a trimer, and an
N-terminal domain disordered at neutral pH but adopting
an amphipathic alpha-helical structure in the presence
of phospholipid vesicles, high ionic strength, acidic pH
or SDS. BMFP interacts with phospholipid vesicles though
the predicted amphipathic alpha-helix induced in the
N-terminal half of the protein and promotes aggregation
and fusion of vesicles in vitro.
Length = 79
Score = 28.2 bits (64), Expect = 7.3
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 439 AELAAASQKLAELKAKIASLEA 460
A LA +KL L+A++A+LEA
Sbjct: 57 AVLARTREKLEALEARVAALEA 78
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 30.9 bits (70), Expect = 7.4
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 323 EDVSYKQKVCAEDLEKAEPALVAAQEALDTLDKNNLTELKALKAPPQGVIAVCDAVAVLM 382
+D K K+ D E A+ EAL+ L+KN L E + + + V +VC+ + M
Sbjct: 556 QDEKVKGKLSDSDKATIEKAI---DEALEWLEKNQLAEKEEFEHKQKEVESVCNPIMTKM 612
Query: 383 ASKKG 387
G
Sbjct: 613 YQAAG 617
>gnl|CDD|212015 cd11625, HR1_PKN_3, Third Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Protein Kinase N.
PKN, also called Protein-kinase C-related kinase (PRK),
is a serine/threonine protein kinase that can be
activated by the small GTPase Rho, and by fatty acids
such as arachidonic and linoleic acids. It is involved
in many biological processes including cytoskeletal
regulation, cell adhesion, vesicle transport, glucose
transport, regulation of meiotic maturation and
embryonic cell cycles, signaling to the nucleus, and
tumorigenesis. In some vertebrates, there are three PKN
isoforms from different genes (designated PKN1, PKN2,
and PKN3), which show different enzymatic properties,
tissue distribution, and varied functions. PKN proteins
contain three HR1 domains, a C2 domain, and a kinase
domain. This model characterizes the third HR1 domain of
PKN. HR1 domains are anti-parallel coiled-coil (ACC)
domains that bind small GTPases from the Rho family.
Length = 74
Score = 28.0 bits (63), Expect = 7.6
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 429 PKRKALAAANAELAAASQKLAELKAKIASLEATLQEL 465
+KAL A L+ +SQKL L+ SLE L EL
Sbjct: 41 DDKKALQEAQKSLSESSQKLDLLR---LSLERRLAEL 74
>gnl|CDD|218701 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
C-terminus. In the E. coli cytosol, a fraction of the
newly synthesised proteins requires the activity of
molecular chaperones for folding to the native state.
The major chaperones implicated in this folding process
are the ribosome-associated Trigger Factor (TF), and the
DnaK and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the C-terminal region of
the protein.
Length = 162
Score = 29.5 bits (67), Expect = 7.6
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 772 TAKKIDEAREQYRPAAERASVIYFIMNELFKINPI 806
+ +E RE+++ AE+ + I+ E+ K I
Sbjct: 75 SGSSEEELREEFKEEAEKRVKLGLILEEIAKEEKI 109
>gnl|CDD|179314 PRK01641, leuD, isopropylmalate isomerase small subunit;
Provisional.
Length = 200
Score = 30.1 bits (69), Expect = 7.7
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 167 TDDEIENIVNNIAAEPEIPLTADLDPLTMLTDDATIAF 204
+++++ + + A P LT DL+ T+ D T F
Sbjct: 122 PEEDVDELFKLVEANPGAELTVDLEAQTVTAPDKTFPF 159
>gnl|CDD|163507 TIGR03795, RNP_Burkhold, ribosomal natural product, two-chain TOMM
family. Members of this protein family are found
sparsely, mostly in members of the genus Burkholderia.
Members often occur as tandem homologous genes, such as
BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344,
or else have a duplication. The genes regularly are
encoded near a cyclodehydrogenase/docking protein fusion
protein of TOMM (thiazole/oxazole-modified microcins)
biosynthetic clusters, suggesting a role in bacteriocin
biosynthesis. The role of the putative natural product is
unknown, but function as a two-chain bacteriocin is
suggested [Cellular processes, Biosynthesis of natural
products].
Length = 114
Score = 29.0 bits (65), Expect = 7.8
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 4/56 (7%)
Query: 1580 PVIYIKAIT---QDKQDLRNMYECPVYKTRQR-GPNYVWTFNLKTKEKPAKWTMAG 1631
+Y++AI + + PV + W +LK E + WT G
Sbjct: 14 RAVYLRAIALAWHSPEFKDELLADPVDALEKYFDYRCPWILDLKVTENSSDWTPYG 69
>gnl|CDD|168377 PRK06072, PRK06072, enoyl-CoA hydratase; Provisional.
Length = 248
Score = 30.1 bits (68), Expect = 8.0
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 1394 MGRVEDRTPYIIVAFQECERMNILMSEIKR----SLKELNLGLKGELTITT 1440
M +VE R Y IV +++N L E++ LK++N K + I T
Sbjct: 1 MIKVESREGYAIVTMSRPDKLNALNLEMRNEFISKLKQINADPKIRVVIVT 51
>gnl|CDD|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA
binding. This is the middle region of a family of TATA
element modulatory factor 1 proteins conserved in
eukaryotes that contains at its N-terminal section a
number of leucine zippers that could potentially form
coiled coil structures. The whole proteins bind to the
TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding of
TATA binding protein. TMFs are evolutionarily conserved
golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells.
Length = 74
Score = 28.0 bits (63), Expect = 8.2
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 431 RKALAAANAELAAASQKLAELKAKIASLEATLQELTDKFDAA 472
+ A+ +++AELK K+ LE L+ L ++ A
Sbjct: 32 NNTIKKLRAKNKELEKEIAELKKKLEKLEKELENLEERLKRA 73
>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 = 30.7 bits (70), Expect = 8.4
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 17/88 (19%)
Query: 427 VEPKRKALAAANAELAAASQ----------KLAELKAKIASLEATLQELTDKFDA----- 471
+E R+ +AA EL A + +LAEL+A++A+LEA L L ++
Sbjct: 421 LEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQEKELV 480
Query: 472 -AVKEKLFCQNQAEECAEKIDLADRLVN 498
A+ L + +A+ A D A
Sbjct: 481 EAILA-LRAELEADADAPADDDAALRAQ 507
>gnl|CDD|201967 pfam01778, Ribosomal_L28e, Ribosomal L28e protein family.
Length = 114
Score = 28.7 bits (65), Expect = 8.5
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 744 SDKNLVL---NLEKSKKTAKEIE-IKVKEG-KKTAKKIDEAREQYRP-----AAERASVI 793
+ +VL +++ K AK E + + + +K K+I +A YRP A RAS +
Sbjct: 51 AKGGVVLVTKKPKRAHKPAKLWEKVTLSKNYRKALKQIKKALAYYRPDLIKKAKRRASKL 110
Query: 794 Y 794
Sbjct: 111 L 111
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 30.5 bits (70), Expect = 8.8
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 435 AAANAELAAASQKLAELK----AKIASLEATLQELTDKFDAAVKEKL 477
A ANAE ++L E + + I E TL+EL DK A KEK+
Sbjct: 512 AEANAEEDKKRKELVEARNQADSLIYQTEKTLKELGDKVPADEKEKI 558
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.7 bits (69), Expect = 8.8
Identities = 31/125 (24%), Positives = 46/125 (36%), Gaps = 33/125 (26%)
Query: 1050 PIFFILSPGVDPTRDVEAVGRKMGF---------TTDLRNLHNVSL---GQGQEVIAEET 1097
PI SPGV T + A+ RK G TDL +L L G+ +
Sbjct: 1545 PILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAP 1604
Query: 1098 IQIASTKGHWAILQNVHLV----------------KNWLPTLDKKMEASFEKPHKNYRLF 1141
A G W +L ++L + ++P LDK + H N+R+F
Sbjct: 1605 FLHAMRDGGWVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDV-----HPNFRVF 1659
Query: 1142 ISAEP 1146
+ P
Sbjct: 1660 AAQNP 1664
>gnl|CDD|213279 cd05911, Firefly_Luc_like, Firefly luciferase of light emitting
insects and 4-Coumarate-CoA Ligase (4CL). This family
contains two functionally unique groups of proteins; one
group is insect firefly luciferases and the other is
plant 4-coumarate:coenzyme A ligases. However, they
share significant sequence similarity in spite of their
functional diversity. Luciferase catalyzes the
production of light in the presence of MgATP, molecular
oxygen, and luciferin. In the first step, luciferin is
activated by acylation of its carboxylate group with
ATP, resulting in an enzyme-bound luciferyl adenylate.
In the second step, luciferyl adenylate reacts with
molecular oxygen, producing an enzyme-bound excited
state product (Luc=O*) and releasing AMP. This
excited-state product then decays to the ground state
(Luc=O), emitting a quantum of visible light.
4-coumarate:coenzyme A ligase is a key enzyme in the
phenylpropanoid metabolic pathway for monolignol and
flavonoid biosynthesis. It catalyzes the synthesis of
hydroxycinnamate-CoA thioesters in a two-step reaction,
involving the formation of hydroxycinnamate-AMP
anhydride and then the nucleophilic substitution of AMP
by CoA. The phenylpropanoid pathway is one of the most
important secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 487
Score = 30.3 bits (69), Expect = 9.7
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 708 LLKANLTKEQNLFKITLKGLEDDLLMRLSSSG------GDVLSDKNLVLNLEKSKKTAKE 761
LL+ L E L +DD L SSG G +LS KN++ NL + + T K
Sbjct: 125 LLEPRLGAEDEFRPTPLIDGKDDTAALLYSSGTTGLPKGVMLSHKNIIANLSQVQDTLKG 184
Query: 762 IEIKVKE 768
+
Sbjct: 185 NPDSSND 191
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.134 0.395
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 84,184,814
Number of extensions: 8538400
Number of successful extensions: 10387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10276
Number of HSP's successfully gapped: 175
Length of query: 1637
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1527
Effective length of database: 6,058,662
Effective search space: 9251576874
Effective search space used: 9251576874
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 (21.7 bits)
S2: 66 (29.2 bits)