RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1651
(141 letters)
>gnl|CDD|212012 cd11622, HR1_PKN_1, First 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 first HR1 domain of
PKN. HR1 domains are anti-parallel coiled-coil (ACC)
domains that bind small GTPases from the Rho family.
Length = 66
Score = 92.7 bits (231), Expect = 6e-26
Identities = 45/64 (70%), Positives = 53/64 (82%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQEL 109
KLEELKE IR+EIRKELKIKEGAE LR+ D+KSL+ V +I+KKSN KL +LH ELQEL
Sbjct: 3 KLEELKEQIRREIRKELKIKEGAENLRKATTDKKSLAHVESILKKSNRKLEDLHQELQEL 62
Query: 110 ESQI 113
E+ I
Sbjct: 63 EAHI 66
>gnl|CDD|128981 smart00742, Hr1, Rho effector or protein kinase C-related kinase
homology region 1 homologues. Alpha-helical domain
found in vertebrate PRK1 and yeast PKC1 protein kinases
C. The HR1 in rhophilin bind RhoGTP; those in PRK1 bind
RhoA and RhoB. Also called RBD - Rho-binding domain.
Length = 57
Score = 53.0 bits (128), Expect = 1e-10
Identities = 25/57 (43%), Positives = 40/57 (70%), Gaps = 1/57 (1%)
Query: 53 ELKEHIRKEIRKELKIKEGAEKLREVAR-DRKSLSDVATIVKKSNSKLSELHNELQE 108
E +R++I KELK+KEGAE +R++ DRK LS+ +++++SN KL L EL++
Sbjct: 1 LRLEDLRRKIEKELKVKEGAENMRKLTSNDRKVLSEAQSMLRESNQKLDLLKEELEK 57
>gnl|CDD|216921 pfam02185, HR1, Hr1 repeat.
Length = 60
Score = 47.5 bits (114), Expect = 2e-08
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 2/59 (3%)
Query: 55 KEHIRKEIRKELKIKEGAEKLREVAR--DRKSLSDVATIVKKSNSKLSELHNELQELES 111
E +RK+I KELKIKEGAE + ++K L + + +++SN K+ L +L++L+
Sbjct: 2 LEQLRKKIEKELKIKEGAENMLRALETDNKKVLQEAESELRESNQKIELLKEQLEKLQK 60
>gnl|CDD|212008 cd00089, HR1, Protein kinase C-related kinase homology region 1
(HR1) domain that binds Rho family small GTPases. The
HR1 domain, also called the ACC (anti-parallel
coiled-coil) finger domain or Rho-binding domain binds
small GTPases from the Rho family. It is found in Rho
effector proteins including PKC-related kinases such as
vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases
C, as well as in rhophilins and Rho-associated kinase
(ROCK). Rho family members function as molecular
switches, cycling between inactive and active forms,
controlling a variety of cellular processes. HR1 domains
may occur in repeat arrangements (PKN contains three HR1
domains), separated by a short linker region.
Length = 68
Score = 46.2 bits (110), Expect = 8e-08
Identities = 22/66 (33%), Positives = 42/66 (63%), Gaps = 3/66 (4%)
Query: 49 NKLEELKEHIRKEIRKELKIKEGAEKLREVARD---RKSLSDVATIVKKSNSKLSELHNE 105
+KL++ E +R+++ KELKI+EGAE L ++ + +K L++V +K+S K+ L +
Sbjct: 1 SKLQQRLEELRRKLEKELKIREGAENLLKLYSNPKVKKDLAEVQLNLKESKEKIDLLKRQ 60
Query: 106 LQELES 111
L+ +
Sbjct: 61 LERYNA 66
>gnl|CDD|212023 cd11633, HR1_Rhophilin-1, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Rhophilin-1.
Rhophilin-1 is a scaffolding protein that functions as
an effector of the Rho family of small GTPases. It has
been implicated in sperm motility. Rhophilin-1 contains
an N-terminal HR1, a central Bro1-like, and a C-terminal
PDZ domain; all are protein-interacting domains. HR1
domains are anti-parallel coiled-coil (ACC) domains that
bind small GTPases from the Rho family; Rhophilin-1
binds RhoA was isolated initially as a RhoA-binding
protein.
Length = 85
Score = 37.5 bits (87), Expect = 2e-04
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQEL 109
KL+ + I ++I KE++++ GAE L + ++K VA + NS L L EL EL
Sbjct: 12 KLQSRRARINQQINKEMRMRAGAENLFKATSNKKVRETVALELSFVNSNLQLLKEELAEL 71
Query: 110 ESQIIMTQGQT 120
S + + Q +
Sbjct: 72 NSSVEIYQSDS 82
>gnl|CDD|212017 cd11627, HR1_Ste20-like, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Schizosaccharomyces
pombe Ste20-like proteins. This group is composed of
predominantly uncharacterized fungal proteins, which
contain two known domains: HR1 at the N-terminal region
and REM (Ras exchanger motif) at the C-terminal region.
One member protein from Schizosaccharomyces pombe is
named Ste16 while its gene is called ste20 (a target of
rapamycin complex 2 subunit). It is a subunit in the
protein kinase TOR complexes in fission yeast. The REM
domain is usually found in nucleotide exchange factors
for Ras-like small GTPases. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family.
Length = 71
Score = 32.3 bits (74), Expect = 0.012
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 52 EELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQELES 111
E+ E +R ++ E KIK+GAE L +V D K+ + + S+L+ + ++ +L S
Sbjct: 4 EQRLEELRGKLEIETKIKDGAENLLQVL-DSKNAKEKKDQRARVESELNSSNRKIAQLTS 62
Query: 112 QI 113
Q+
Sbjct: 63 QL 64
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 34.5 bits (80), Expect = 0.012
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 8/75 (10%)
Query: 46 ALPNKLEELKEHIRKEIRKEL-KIKEGAEKLREVARD------RKSLSDVATIVKKSNSK 98
L +L+EL+E + KE+ +EL KIK+ +KL + AR R+ L + +K + +
Sbjct: 331 ELKEELKELEEEL-KELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEE 389
Query: 99 LSELHNELQELESQI 113
L EL EL+EL+ ++
Sbjct: 390 LEELEEELKELKEEL 404
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 34.5 bits (80), Expect = 0.013
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 43 AEEALPNKLEEL--KEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLS 100
EAL +KL K + +E +K++ +K E +++V + L + +K+ ++S
Sbjct: 55 LSEAL-DKLRSYLPKLNPLREEKKKVSVKSLEELIKDVEEE---LEKIEKEIKELEEEIS 110
Query: 101 ELHNELQELESQI 113
EL NE++ELE +I
Sbjct: 111 ELENEIKELEQEI 123
Score = 30.3 bits (69), Expect = 0.34
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 50 KLEELKEHIRK--EIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQ 107
L +L E + K +L +K V + + DV ++K ++ EL E+
Sbjct: 51 LLTKLSEALDKLRSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEIS 110
Query: 108 ELESQI 113
ELE++I
Sbjct: 111 ELENEI 116
Score = 26.4 bits (59), Expect = 5.4
Identities = 10/52 (19%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 69 KEGAEKLREVARD----RKSLSDVAT---IVKKSNSKLSELHNELQELESQI 113
KE ++++ E + R L + T ++++ +L E+ E + L ++
Sbjct: 187 KELSDEVEEELKKLGFERLELEEEGTPSELIREIKEELEEIEKERESLLEEL 238
>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 = 33.5 bits (77), Expect = 0.025
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 49 NKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQE 108
+LEEL E + E+ L + E+ + R L +++ +++ SK SEL EL+E
Sbjct: 862 EELEELIEELESELEALLNERASLEEALALLRSE--LEELSEELRELESKRSELRRELEE 919
Query: 109 LESQI 113
L ++
Sbjct: 920 LREKL 924
Score = 27.3 bits (61), Expect = 3.8
Identities = 18/54 (33%), Positives = 32/54 (59%)
Query: 60 KEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQELESQI 113
KE++ EL+ E A + + R+ L ++ +K++ +L EL ELQELE ++
Sbjct: 216 KELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKL 269
Score = 26.2 bits (58), Expect = 8.0
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 41 NVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLS 100
L +LEEL+ + + K ++ E E+A + L ++ ++ ++L
Sbjct: 308 RERLANLERQLEELEAQLEELESKLDELAE------ELAELEEKLEELKEELESLEAELE 361
Query: 101 ELHNELQELESQI 113
EL EL+ELES++
Sbjct: 362 ELEAELEELESRL 374
>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3. See
PMID:20395274 for descriptions of different groups.
Length = 462
Score = 33.3 bits (77), Expect = 0.028
Identities = 23/67 (34%), Positives = 26/67 (38%), Gaps = 23/67 (34%)
Query: 23 IRHPVLYELSHKYGFITENVAEEALPNKLEELKEHIRKEIRKELKI-------KEGAEKL 75
IRH VL E VA+ A KLEE E I EI K KE
Sbjct: 8 IRHEVLTE-----------VAKLAFEGKLEEEIEDIPYEIIPGEKPRYRCCVYKE----- 51
Query: 76 REVARDR 82
R + R+R
Sbjct: 52 RAIIRER 58
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 32.8 bits (75), Expect = 0.046
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 45 EALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHN 104
E L ++LE + +R ++RK+ +I+ + R + R K L + ++ EL
Sbjct: 453 EKLESELERFRREVRDKVRKDREIR---ARDRRIERLEKELEE-------KKKRVEELER 502
Query: 105 ELQELE 110
+L EL
Sbjct: 503 KLAELR 508
>gnl|CDD|234677 PRK00174, PRK00174, acetyl-CoA synthetase; Provisional.
Length = 637
Score = 32.4 bits (75), Expect = 0.063
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 15/71 (21%)
Query: 35 YGFITENVAEEALPNKLEELKEHIRKEI-----RKELKIKEGAEK----------LREVA 79
Y F+T EE +EL+ +RKEI ++ G K LR++A
Sbjct: 549 YAFVTLKGGEEPSDELRKELRNWVRKEIGPIAKPDVIQFAPGLPKTRSGKIMRRILRKIA 608
Query: 80 RDRKSLSDVAT 90
+ L D +T
Sbjct: 609 EGEEILGDTST 619
>gnl|CDD|212014 cd11624, HR1_Rhophilin, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Rhophilin.
Rhophilins are scaffolding proteins that function as
effectors of the Rho family of small GTPases.
Vertebrates harbor two proteins, Rhophilin-1 and
Rhophilin-2, whose exact functions are yet to be
determined. Rhophilin-1 has been implicated in sperm
motility. Rhophilin-2 regulates the organization of the
actin cytoskeleton. Rhophilins contain N-terminal HR1,
central Bro1-like, and C-terminal PDZ domains; all are
protein-interacting domains. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; both Rhophilin-1 and
Rhophilin-2 bind RhoA, and Rhophilin-2 has also been
shown to bind RhoB.
Length = 76
Score = 29.9 bits (67), Expect = 0.12
Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQEL 109
+L+ + + ++I K++K++ GAE L + ++ K V + NS+L L EL+ +
Sbjct: 6 QLQHKRAALNQKIHKQMKLRAGAENLFKATKNTKVKETVRLELSFVNSQLQLLKEELEGI 65
Query: 110 ESQIIMTQ 117
S + + Q
Sbjct: 66 NSSLEVYQ 73
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 31.4 bits (72), Expect = 0.12
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 44 EEALPNKLEELKEHIR----KEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKL 99
E P+ EEL+ +R E+++ + I+E E R A D + + S L
Sbjct: 231 ELEPPSLDEELEAKVRDLAEDELKEAVGIREKQE--RSAALDAIKEKIEEELSGEEESSL 288
Query: 100 SELHNELQELESQII 114
E+ L++LE + +
Sbjct: 289 KEIKAILEKLEKKPV 303
>gnl|CDD|192488 pfam10228, DUF2228, Uncharacterized conserved protein (DUF2228).
This is a family of conserved proteins of approximately
700 residues found from worms to humans.
Length = 253
Score = 30.5 bits (69), Expect = 0.21
Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 2/97 (2%)
Query: 4 PVYLVQND--RYYWISSEGDYIRHPVLYELSHKYGFITENVAEEALPNKLEELKEHIRKE 61
P + ND + + G+ I +L L+ K I + + K++EL KE
Sbjct: 63 PPLIAFNDAKKGCEFTVVGENIFDAILLFLTKKSKEIPFKKKKISALKKIQELLTEWAKE 122
Query: 62 IRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSK 98
+ L+ K K R+ K+ +V N
Sbjct: 123 LGLSLEQKTKVMKQRKKKVVTKTFHKGGLVVPVDNKT 159
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 30.0 bits (68), Expect = 0.35
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 11 DRYYWISSEGDYIRHPVLYELSHKYGFITENVAEEALPNK---LEELKEHIRKEIRKELK 67
D+ Y I +GDY+ PV E I E V E P + E LKE + + +E+
Sbjct: 27 DKDYKIDRDGDYLLIPVKDE----ANAILEVVVLEEEPVRRRSNENLKEILSDRLPEEVL 82
>gnl|CDD|212009 cd11619, HR1_CIP4-like, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Cdc42-Interacting
Protein 4 and similar proteins. This subfamily is
composed of Cdc42-Interacting Protein 4 (CIP4), Formin
Binding Protein 17 (FBP17), FormiN Binding Protein
1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L
are Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. It functions downstream of Cdc42 in
PDGF-dependent actin reorganization and cell migration,
and also regulates the activity of PDGFRbeta. It uses
Src as a substrate in regulating the invasiveness of
breast tumor cells. CIP4 may also play a role in the
pathogenesis of Huntington's disease. Members of this
subfamily typically contain an N-terminal F-BAR
(FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain,
central HR1 domain, and a C-terminal SH3 domain. HR1
domains are anti-parallel coiled-coil (ACC) domains that
bind small GTPases from the Rho family; the HR1 domain
of CIP4 binds Cdc42 and TC10. Translocation of CIP4 is
facilitated by its binding to TC10 at the plasma
membrane.
Length = 77
Score = 28.3 bits (64), Expect = 0.40
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATI---VKKSNSKLSELHNEL 106
K++EL+ KEI KE K ++G K++ V L D A++ + + KL +L EL
Sbjct: 11 KIDELE----KEIEKETKSRDGLMKMKGVYEQNPQLGDPASVEGQLAEYAKKLDKLREEL 66
Query: 107 QELES 111
Q+ +
Sbjct: 67 QKYQG 71
>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase.
Length = 455
Score = 29.8 bits (67), Expect = 0.41
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 38 ITENVAEEA--LPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKS 95
+ + +EA + +LE+ E + KE K E L+E+ +D + + + K+
Sbjct: 373 GEKTIVKEARQIEEELEKEVEKLGKEEESLFKRVALEEGLKELEQD--EENFLKELSKEE 430
Query: 96 NSKLSELHNELQELESQI 113
L +L E E+E
Sbjct: 431 KELLEKLKMEASEVEKLF 448
>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 = 29.6 bits (67), Expect = 0.51
Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 25 HPVLYELSHKY-GFITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRK 83
+ + +L + E + L ++LE+ +++LK + L+E+ K
Sbjct: 171 NSIKPKLRDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLK-----KLLQEIMIKVK 225
Query: 84 SLSDVATIVKKSNSKLSELHNELQELESQI 113
L ++ +++ SK+ +L N+ EL ++I
Sbjct: 226 KLEELEEELQELESKIEDLTNKKSELNTEI 255
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.7 bits (67), Expect = 0.58
Identities = 21/69 (30%), Positives = 40/69 (57%)
Query: 45 EALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHN 104
E L K+EEL+ IR+E+++ ++ EKL E+ + + L + +++ KL E+
Sbjct: 657 EELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQ 716
Query: 105 ELQELESQI 113
++ELES+
Sbjct: 717 LIEELESRK 725
Score = 29.3 bits (66), Expect = 0.80
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSEL 102
+A +LEE E + EIR+EL+ E E+L E + L + +++ +L EL
Sbjct: 651 LLQAALEELEEKVEELEAEIRRELQRIENEEQLEEK---LEELEQLEEELEQLREELEEL 707
Query: 103 HNELQELESQIIMTQGQ 119
+L E+E I + +
Sbjct: 708 LKKLGEIEQLIEELESR 724
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 29.3 bits (66), Expect = 0.60
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 45 EALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDR-KSLSDVATIVKKSNSKLSELH 103
AL +L EL++ I E+R+ L + + +L +K SKL +L
Sbjct: 316 VALEAQLAELRQQIAAELRQILA---SLPNELALLEQQEAALEKELAQLKGRLSKLPKLQ 372
Query: 104 NELQELESQI 113
+L+ELE +
Sbjct: 373 VQLRELEREA 382
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 28.9 bits (65), Expect = 0.73
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 26 PVLYELSHK-YGFITENVAEEALPNKLEELKEHIRKE--IRK-----ELKIKEGAEKLRE 77
PVLY + E V EE ++E L E ++K I + +K+ E L
Sbjct: 238 PVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDG 297
Query: 78 VARD--RKSLSDVATIVKKSNS 97
+ +K L ++A + K
Sbjct: 298 LPDGRAKKPLQEIAKYIGKRKY 319
>gnl|CDD|224583 COG1669, COG1669, Predicted nucleotidyltransferases [General
function prediction only].
Length = 97
Score = 28.0 bits (63), Expect = 0.79
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLR---EVARDR-KSLSDVATIV----KKSNSKLSE 101
K + I ++I+ ELK K G +++ AR K SD+ +V K+ L
Sbjct: 2 KTVSELKKILRKIKPELKEKYGVKRVAVFGSYARGEQKPDSDIDILVEFEPGKTLLDLVR 61
Query: 102 LHNELQEL 109
L +EL +L
Sbjct: 62 LEDELSDL 69
>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 = 28.8 bits (65), Expect = 0.80
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 40 ENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKL 99
+ P +LE+ ++ +R +KI +EK +++ ++ L ++ ++ +K
Sbjct: 198 ADELNLCDPLELEKARQELRS---LSVKI---SEKRKQLEELQQELQELTIAIEALTNKK 251
Query: 100 SELHNELQELESQI 113
SEL E+ E E
Sbjct: 252 SELLEEIAEAEKIR 265
>gnl|CDD|212018 cd11628, HR1_CIP4_FNBP1L, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of vertebrate
Cdc42-Interacting Protein 4 and FormiN Binding Protein
1-Like. CIP4 and FNBP1L are Cdc42 effectors that bind
Wiskott-Aldrich syndrome protein (WASP) and function in
endocytosis. FNBP1L, also called Toca-1 (Transducer of
Cdc42-dependent actin assembly 1), forms a complex with
neural WASP; the complex induces the formation of
filopodia and endocytic vesicles. FNBP1L is required for
Cdc42-induced actin assembly and is essential for
autophagy of intracellular pathogens. CIP4 may also play
a role in phagocytosis. It functions downstream of Cdc42
in PDGF-dependent actin reorganization and cell
migration, and also regulates the activity of PDGFRbeta.
It uses Src as a substrate in regulating the
invasiveness of breast tumor cells. CIP4 may also play a
role in the pathogenesis of Huntington's disease. CIP4
and FNBP1L contain an N-terminal F-BAR domain, a central
HR1 domain, and a C-terminal SH3 domain. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; the HR1 domain of CIP4
binds Cdc42 and TC10. Translocation of CIP4 is
facilitated by its binding to TC10 at the plasma
membrane.
Length = 81
Score = 27.6 bits (61), Expect = 0.90
Identities = 15/74 (20%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATI---VKKSNSKLSELHNEL 106
+L++ + + +E++KE+ E K+++V + D A++ + ++ S + L EL
Sbjct: 8 RLQQKIDELSRELQKEMDQSEALMKMKDVYEKNPQMGDPASLQPQIAETASNIDRLRGEL 67
Query: 107 QELESQIIMTQGQT 120
+ E+ + +G+
Sbjct: 68 HKYEAWLAEAEGRV 81
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.9 bits (65), Expect = 0.96
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 37 FITENVAEEALPNKLEELKEHI--------RKEIRKELKIKEGAEKLREVARDRKSLSDV 88
+ N+LEELK I R R E +E E E+ + L ++
Sbjct: 385 LAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEEL 444
Query: 89 ATIVKKSNSKLSELHNELQELESQI 113
+++ +L EL + L+ELE ++
Sbjct: 445 NEELEELEEQLEELRDRLKELEREL 469
Score = 27.4 bits (61), Expect = 3.0
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 49 NKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSD--VATIVKKSNSKLSELHNEL 106
+LE+L E + K++ K + E AE+ +E+ + + L + +K+ +L EL EL
Sbjct: 189 ERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEEL 248
Query: 107 QELESQIIMTQGQ 119
LE ++ Q +
Sbjct: 249 SRLEEELEELQEE 261
Score = 25.8 bits (57), Expect = 9.6
Identities = 19/85 (22%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLRE--------VARDRKSLSDVATIVKK 94
E L ++LEEL+E + + + +++E E+L E +A+ ++ + ++ +
Sbjct: 731 ELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQA 790
Query: 95 SNSKLSELHNELQELESQIIMTQGQ 119
+L EL EL+E E ++ + +
Sbjct: 791 LQEELEELEEELEEAERRLDALERE 815
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 28.6 bits (64), Expect = 0.97
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 47 LPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKS-LSDVATIVKKSNSKLSELHNE 105
L +LE+L+E I + + +KE + LRE+ + + L + +K+ +L EL +
Sbjct: 91 LQEELEDLEERIAELESELEDLKEDLQLLRELLKSLEERLESLEESIKELAKELRELRQD 150
Query: 106 L----QELESQIIMTQ 117
L +EL ++ Q
Sbjct: 151 LREEVEELREELERLQ 166
>gnl|CDD|234956 PRK01490, tig, trigger factor; Provisional.
Length = 435
Score = 28.6 bits (65), Expect = 1.0
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREV 78
LEELK IRK + +E K + A+ V
Sbjct: 262 LEELKADIRKNLEREKKEAQRAKVKEAV 289
>gnl|CDD|237381 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
Length = 342
Score = 28.6 bits (64), Expect = 1.0
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 34 KYGFITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEK 74
KY +T++ A + L N +E L E IR ++ K I G EK
Sbjct: 130 KYKKMTKSQAPKGLANAMEALVEFIRLDVAKS-NIGHGYEK 169
>gnl|CDD|212024 cd11634, HR1_Rhophilin-2, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Rhophilin-2.
Rhophilin-2 is a scaffolding protein that functions as
an effector of the Rho family of small GTPases. It plays
a role in regulating the organization of the actin
cytoskeleton. Rhophilin-2 contains an N-terminal HR1, a
central Bro1-like, and a C-terminal PDZ domain; all are
protein-interacting domains. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; Rhophilin-2 has been shown
to bind both RhoA and RhoB.
Length = 82
Score = 27.3 bits (60), Expect = 1.1
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 49 NKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQE 108
+KL+ + + ++I K ++++ GAE L + + K V + NS L L EL+
Sbjct: 8 SKLQNQRAVLNQQILKAMRMRAGAENLLKATTNNKVREQVLLELSFVNSDLQLLKEELEG 67
Query: 109 LESQIIMTQ 117
L + + Q
Sbjct: 68 LNISVEVYQ 76
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 1.1
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 51 LEELKEHIR--KEIRKELK-IKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQ 107
+EELK+ I +E KELK +KE AE+ +++ + D ++K S+L E N ++
Sbjct: 268 IEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIE 327
Query: 108 EL 109
E
Sbjct: 328 ER 329
Score = 26.6 bits (59), Expect = 6.6
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 39 TENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSK 98
TEN+ EE + K +EL+E +R+ ++ E E+L ++ ++ K L ++ +++ +
Sbjct: 188 TENI-EELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKE 246
Query: 99 LSELHNELQELESQI 113
L L ++LE +I
Sbjct: 247 LESLEGSKRKLEEKI 261
Score = 26.2 bits (58), Expect = 8.3
Identities = 19/67 (28%), Positives = 37/67 (55%)
Query: 47 LPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNEL 106
+ ++E L++ I++ E IKE ++L EV R+ +S +++ KL + EL
Sbjct: 174 IKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKEL 233
Query: 107 QELESQI 113
+EL+ +I
Sbjct: 234 EELKEEI 240
>gnl|CDD|218311 pfam04888, SseC, Secretion system effector C (SseC) like family.
SseC is a secreted protein that forms a complex together
with SecB and SecD on the surface of Salmonella. All
these proteins are secreted by the type III secretion
system. Many mucosal pathogens use type III secretion
systems for the injection of effector proteins into
target cells. SecB, SseC and SecD are inserted into the
target cell membrane. where they form a small pore or
translocon. In addition to SseC, this family includes
the bacterial secreted proteins PopB, PepB, YopB and
EspD which are thought to be directly involved in pore
formation, and type III secretion system translocon.
Length = 303
Score = 28.6 bits (64), Expect = 1.1
Identities = 12/54 (22%), Positives = 21/54 (38%)
Query: 67 KIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQELESQIIMTQGQT 120
+ + L + + + L V +K+ KL E + + SQ I G T
Sbjct: 242 EAGKLEADLALLRAEMEQLQAVIKQLKEEFKKLQEQFQQAMKSISQAIQQSGDT 295
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 28.2 bits (64), Expect = 1.2
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 50 KLEELKEHIRKEI---RKELKIKEGAEKLREVARDRKSLSDVATI 91
+LE + IR+ I RKEL E +K RE+ R R+ S V T+
Sbjct: 3 QLETDRRLIRERIAKLRKEL---EKVKKQRELQRARRKRSGVPTV 44
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 28.7 bits (64), Expect = 1.3
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 27 VLYELSHKYGFITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEK 74
+L E+ + E + E + + E E +R ++ E IK+ AE+
Sbjct: 430 LLSEILKIEEELKEGIPIEGVLDVFPEDVEFLRSILKDEEVIKKVAER 477
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 28.4 bits (64), Expect = 1.3
Identities = 11/56 (19%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 42 VAEEALPNKLEELKEHI-RKEIRKELKIKEGAEKLREVARD-RKSLSDVATIVKKS 95
+ E + +LE + I + +KE +E E L+E+ + ++ ++ + S
Sbjct: 536 IVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIGDHLAGS 591
>gnl|CDD|213313 cd05966, ACS, Acetyl-CoA synthetase (also known as acetate-CoA
ligase and acetyl-activating enzyme). Acetyl-CoA
synthetase (ACS) catalyzes the formation of acetyl-CoA
from acetate, CoA, and ATP. Synthesis of acetyl-CoA is
carried out in a two-step reaction. In the first step,
the enzyme catalyzes the synthesis of acetyl-AMP
intermediate from acetate and ATP. In the second step,
acetyl-AMP reacts with CoA to produce acetyl-CoA. This
enzyme is widely present in all living organisms. The
activity of this enzyme is crucial for maintaining the
required levels of acetyl-CoA, a key intermediate in
many important biosynthetic and catabolic processes.
Acetyl-CoA is used in the biosynthesis of glucose, fatty
acids, and cholesterol. It can also be used in the
production of energy in the citric acid cycle.
Eukaryotes typically have two isoforms of acetyl-CoA
synthetase, a cytosolic form involved in biosynthetic
processes and a mitochondrial form primarily involved in
energy generation.
Length = 602
Score = 28.3 bits (64), Expect = 1.3
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 15/71 (21%)
Query: 35 YGFITENVAEEALPNKLEELKEHIRKEI-----RKELKIKEGAEK----------LREVA 79
Y F+T E +ELK+H+RKEI E+ G K LR++A
Sbjct: 529 YAFVTLKDGVEPSDELRKELKKHVRKEIGPIATPDEIIFVPGLPKTRSGKIMRRILRKIA 588
Query: 80 RDRKSLSDVAT 90
+ L D +T
Sbjct: 589 AGEEELGDTST 599
>gnl|CDD|223526 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains
amidotransferase and phosphosugar isomerase domains
[Cell envelope biogenesis, outer membrane].
Length = 597
Score = 28.3 bits (64), Expect = 1.4
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 44 EEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVAR 80
E +L +L++L HI K + E KIKE A++L +
Sbjct: 421 ERSLIKELQKLPNHIPKVLAAEEKIKELAKRLADAKD 457
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 28.5 bits (64), Expect = 1.4
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 56 EHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQELESQIIM 115
E ++E + E + R R+ + A ++++ +L +L L ELE Q+
Sbjct: 479 EKAQEEQEQAEANVEQLQSELRQLRKRRDEALEA--LQRAERRLLQLRQALDELELQLSP 536
Query: 116 TQG 118
G
Sbjct: 537 QAG 539
Score = 27.0 bits (60), Expect = 4.9
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 2/77 (2%)
Query: 37 FITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSN 96
F E L + EL + ++ + +E +LR+ R + + + N
Sbjct: 255 FEQLLSLELRLQHLHGELVADEERLAEEQEERQEAKNRLRQQLRTLE--DQLKEARDELN 312
Query: 97 SKLSELHNELQELESQI 113
+LS + +L S++
Sbjct: 313 QELSAANAKLAADRSEL 329
>gnl|CDD|149342 pfam08227, DASH_Hsk3, DASH complex subunit Hsk3 like. The DASH
complex is a ~10 subunit microtubule-binding complex
that is transferred to the kinetochore prior to mitosis.
In Saccharomyces cerevisiae DASH forms both rings and
spiral structures on microtubules in vitro. This family
also includes several higher eukaryotic proteins.
However, other DASH subunits do not appear to be
conserved in higher eukaryotes.
Length = 45
Score = 26.1 bits (58), Expect = 1.5
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 96 NSKLSELHNELQELESQIIMTQGQ 119
S+L++L L + E + MT Q
Sbjct: 8 ASQLAQLQANLADTEELLEMTSIQ 31
>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 = 28.1 bits (63), Expect = 1.7
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 44 EEALPNKLEELKEHIRKEI-----RKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSK 98
+ L+E + I KEI +KE +E E + L D+ + ++
Sbjct: 838 LQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQ 897
Query: 99 LSELHNELQELESQI 113
L EL +++ELE+QI
Sbjct: 898 LRELERKIEELEAQI 912
Score = 28.1 bits (63), Expect = 2.1
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARD----RKSLSDVATIVKKSNSK 98
A+ ++ E ++ K L+IK+ KL ++A D + L D+ + +
Sbjct: 425 LNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKE 484
Query: 99 LSELHNELQELESQ 112
LS+L EL E E+Q
Sbjct: 485 LSKLQRELAEAEAQ 498
Score = 27.7 bits (62), Expect = 2.6
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 43 AEEALPNKLEELKEHIRKEI----RKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSK 98
+ +LE+ +E + K + +I+E ++ E + R L++ + +
Sbjct: 309 SIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTE---EYAELKEE 365
Query: 99 LSELHNELQELE 110
L +L EL+E++
Sbjct: 366 LEDLRAELEEVD 377
Score = 25.8 bits (57), Expect = 9.6
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREVARDR-KSLSDVATIVKKSNSKLSELHNELQEL 109
LEEL+E R +L I E ++L + R+R K+ A + +K + EL E + L
Sbjct: 176 LEELEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYELLKEKEAL 235
Query: 110 ESQIIMTQGQ 119
E Q + Q
Sbjct: 236 ERQKEAIERQ 245
>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like. The
sequences found in this family are similar to a region
found in the beta-subunit of glucosidase II, which is
also known as protein kinase C substrate 80K-H (PRKCSH).
The enzyme catalyzes the sequential removal of two
alpha-1,3-linked glucose residues in the second step of
N-linked oligosaccharide processing. The beta subunit is
required for the solubility and stability of the
heterodimeric enzyme, and is involved in retaining the
enzyme within the endoplasmic reticulum.
Length = 176
Score = 27.8 bits (62), Expect = 1.8
Identities = 20/82 (24%), Positives = 28/82 (34%), Gaps = 20/82 (24%)
Query: 38 ITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNS 97
N E E L EH ++ LKIKEG ++ +
Sbjct: 114 KCPNKCGEIARQFEEYLTEH-NNSVKNGLKIKEG-------------------LLLAAQK 153
Query: 98 KLSELHNELQELESQIIMTQGQ 119
K EL L+ELE + Q +
Sbjct: 154 KRDELKKRLKELEDSLPAKQQR 175
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.9 bits (63), Expect = 1.8
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 9/87 (10%)
Query: 30 ELSHKYGFITENVAEEA------LPNKLEELKEH-IRKEIRKELKIKEGAEKLREVARDR 82
E++ + G + EN+ EEA KL EL E E K +E L+E + +
Sbjct: 492 EIAKRLG-LPENIIEEAKKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLK 550
Query: 83 KSLSDVATIVKKS-NSKLSELHNELQE 108
+ L + +++ + L E E Q+
Sbjct: 551 EELEEKKEKLQEEEDKLLEEAEKEAQQ 577
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 27.7 bits (62), Expect = 1.9
Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 18/105 (17%)
Query: 30 ELSHKYGFITENVAEEALPNKLEELK-EHIRKEIRKELKIKEGAEKLR-EVARDRKSL-- 85
EL K E E + LK E RK+ R +I+ +L+ E+ + R+ +
Sbjct: 38 ELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLN-QIRARISQLKEEIEQKRERIEE 96
Query: 86 -------------SDVATIVKKSNSKLSELHNELQELESQIIMTQ 117
S + K+ S+L +L +E++ S++
Sbjct: 97 LKRALAQRRSDLSSASYQLEKRRASQLEKLQDEIKRTRSKLNALH 141
>gnl|CDD|212022 cd11632, HR1_PKN3_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N3. PKN3, also called PKNbeta, is a
serine/threonine protein kinase that is activated by the
Rho family of small GTPases, preferentially by RhoC.
Both PKN1 and RhoC show limited and barely detectable
expression in normal tissues, but are both upregulated
in cancer cells, particularly in late-stage
malignancies. PKN3 has been implicated to play a role in
the metastatic growth and invasiveness of cancer cells,
downstream of the oncogenic phosphoinositide 3-kinase
signaling network. PKN3 shares a common domain
architecture with other PKNs, containing three HR1
domains, a C2 domain, and a kinase domain. In addition,
PKN3 contains two proline-rich regions between its C2
and kinase domains, and has been shown to associate with
SH3 domain containing proteins like GRAFs, GAP for RhoA,
and Cdc42Hs. This model characterizes the second HR1
domain of PKN3. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family; PKN3 binds Rho family GTPases,
preferentially RhoC.
Length = 74
Score = 26.4 bits (58), Expect = 2.0
Identities = 16/60 (26%), Positives = 37/60 (61%), Gaps = 5/60 (8%)
Query: 56 EHIRKEIRKELKIKEGAEKLREV-----ARDRKSLSDVATIVKKSNSKLSELHNELQELE 110
E +++++ ELK+K+GAE + + +++RK L+ +++ S +K+ L ++ +LE
Sbjct: 12 EALKRQLHVELKVKQGAENMIQTYSSGTSKERKLLATAQQMLQDSRTKIELLRMQIVKLE 71
>gnl|CDD|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain.
The small mechanosensitive channel, MscS, is a part of
the turgor-driven solute efflux system that protects
bacteria from lysis in the event of osmotic shock. The
MscS protein alone is sufficient to form a functional
mechanosensitive channel gated directly by tension in
the lipid bilayer. The MscS proteins are heptamers of
three transmembrane subunits with seven converging M3
domains, and this MscS_porin is towards the N-terminal
of the molecules. The high concentration of negative
charges at the extracellular entrance of the pore helps
select the cations for efflux.
Length = 239
Score = 27.6 bits (62), Expect = 2.3
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 48 PNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQ 107
P +L EL++ + + + + L SLS + + ++ S+L EL +LQ
Sbjct: 51 PKELRELRQELEALKKTDAPVFPELANL--------SLSQLEQRLAQTLSQLQELQEQLQ 102
Query: 108 ELESQIIMTQGQTVTSPTA 126
+ SQ+I Q + +
Sbjct: 103 QENSQLIELQTRPERAQQQ 121
>gnl|CDD|212019 cd11629, HR1_FBP17, Protein kinase C-related kinase homology region
1 (HR1) Rho-binding domain of Formin Binding Protein 17.
FBP17, also called FormiN Binding Protein 1 (FNBP1), is
involved in dynamin-mediated endocytosis. It is
recruited to clathrin-coated pits late in the
endocytosis process and may play a role in the
invagination and scission steps. FBP17 binds in vivo to
tankyrase, a protein involved in telomere maintenance
and mitogen activated protein kinase (MAPK) signaling.
It also binds to the Fas ligand and may be implicated in
the inflammatory response. FBP17 contains an N-terminal
F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs)
domain, central HR1 domain, and a C-terminal SH3 domain.
HR1 domains are anti-parallel coiled-coil (ACC) domains
that bind small GTPases from the Rho family; the HR1
domain of the related protein, CIP4, binds Cdc42 and
TC10. Translocation of CIP4 is facilitated by its
binding to TC10 at the plasma membrane.
Length = 77
Score = 26.5 bits (58), Expect = 2.3
Identities = 13/64 (20%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQEL 109
KL++ + + K+I+KE+ ++ K+++V + D A++ + +L E+ +++L
Sbjct: 7 KLQQKVDELNKDIQKEMDQRDALTKMKDVYIKNPQMGDPASV----DHRLEEITQNIEKL 62
Query: 110 ESQI 113
++
Sbjct: 63 RVEV 66
>gnl|CDD|112836 pfam04037, DUF382, Domain of unknown function (DUF382). This
domain is specific to the human splicing factor 3b
subunit 2 and it's orthologues. Splicing factor 3b
subunit 2 or SAP145 is a suppressor of U2 snRNA
mutations. Pre-mRNA splicing is catalyzed by a large
ribonucleoprotein complex called the spliceosome.
Spliceosomes are multi-component enzymes that catalyze
pre-mRNA splicing and form step-wise by the ordered
interaction of UsnRNPs and non-snRNP proteins with
short conserved regions of the pre-mRNA at the 5' and
3' splice sites and branch site.
Length = 129
Score = 26.8 bits (60), Expect = 2.4
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 53 ELKEHIRK----EIRKELKIKEGAEKLREVARDR 82
EL + I E+R L KE + L++ R+R
Sbjct: 55 ELPDFIEATGIAEMRDALLEKEAEKTLKQKQRER 88
>gnl|CDD|113013 pfam04223, CitF, Citrate lyase, alpha subunit (CitF). In
citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6
cleaves intracellular citrate into acetate and
oxaloacetate, and is organised as a functional complex
consisting of alpha, beta, and gamma subunits. The
gamma subunit serves as an acyl carrier protein (ACP),
and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA
prosthetic group. The citrate lyase is active only if
this prosthetic group is acetylated; this acetylation
is catalyzed by an acetate:SH-citrate lyase ligase. The
alpha subunit substitutes citryl for the acetyl group
to form citryl-S-ACP. The beta subunit completes the
reaction by cleaving the citryl to yield oxaloacetate
and (regenerated) acetyl-S-ACP. This family represents
the alpha subunit EC:2.8.3.10.
Length = 466
Score = 27.5 bits (61), Expect = 2.4
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 19 EGDYIRHPVLYELSHKYGFITENVAEEALPNKLEELKEHIRK 60
EGDY+ + V+ ++ K GF +A +L N E L EHI+
Sbjct: 31 EGDYVVNMVMEVIA-KMGFKNLTIAPSSLTNVHEPLVEHIKN 71
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 27.6 bits (62), Expect = 2.5
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATI--VKKSNSKLSELHNEL 106
+LE + IR+ I K + E EK RE R ++S S + + V +N+ S L N L
Sbjct: 154 QLETDRRRIRRRIAKLKRELENVEKAREPRRKKRSRSGIPLVALVGYTNAGKSTLFNAL 212
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication,
recombination, and repair].
Length = 444
Score = 27.3 bits (61), Expect = 2.6
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 58 IRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSN 96
I + + + EGA L +V +LS VA +
Sbjct: 13 IFEGYIPQGDLGEGAVLLWDVEGVYLTLSKVAERTGQER 51
>gnl|CDD|220682 pfam10303, DUF2408, Protein of unknown function (DUF2408). This is
a family of proteins conserved in fungi. The function is
unknown.
Length = 125
Score = 26.8 bits (60), Expect = 3.0
Identities = 15/32 (46%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 82 RKSLSDVATIVKKSN-SKLSELHNELQELESQ 112
R+SL +AT K S S+LS+L +L+E+ES
Sbjct: 20 RRSLLSLATRSKFSLASELSQLKEQLKEIESM 51
>gnl|CDD|179599 PRK03580, PRK03580, carnitinyl-CoA dehydratase; Provisional.
Length = 261
Score = 27.4 bits (61), Expect = 3.1
Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 13/58 (22%)
Query: 32 SHKYGFITENVAEEALPNKLEELKEHIR----------KEIRKE---LKIKEGAEKLR 76
+ ++G + V + L ++ EL + + KEI +E + ++E +R
Sbjct: 170 ALRWGIVNRVVPQAELMDRARELAQQLVNSAPLAIAALKEIYRETSEMPVEEAYRYIR 227
>gnl|CDD|216201 pfam00930, DPPIV_N, Dipeptidyl peptidase IV (DPP IV) N-terminal
region. This family is an alignment of the region to
the N-terminal side of the active site. The Prosite
motif does not correspond to this Pfam entry.
Length = 348
Score = 27.3 bits (61), Expect = 3.1
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 1 MNNPVYLVQNDRYYWISSEGDYIRHPVLYELS 32
+PV+L + WIS Y +H LY+L
Sbjct: 234 HQDPVFLRDGSGFLWISERDGY-KHLYLYDLD 264
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 27.6 bits (61), Expect = 3.1
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 39 TENVAEE--ALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSN 96
TE+ AE+ +LE K+ K KELK + A+K + + SD + KKS
Sbjct: 4 TESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSE 63
Query: 97 SK 98
K
Sbjct: 64 KK 65
>gnl|CDD|212020 cd11630, HR1_PKN1_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N1. PKN1, also called PKNalpha or
Protein-kinase C-related kinase 1 (PRK1), is a
serine/threonine protein kinase that is activated by
the Rho family of small GTPases, and by fatty acids
such as arachidonic and linoleic acids. It is expressed
ubiquitously and is the most abundant PKN isoform in
neurons. PKN1 is implicated in a variety of functions
including cytoskeletal reorganization, cardiac cell
survival, cell adhesion, and glucose transport, among
others. PKN1 contains three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the
second HR1 domain of PKN1. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; PKN1 binds the GTPases
RhoA, RhoB, and RhoC, and can also interact weakly with
Rac.
Length = 78
Score = 26.1 bits (57), Expect = 3.2
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 58 IRKEIRKELKIKEGAEKLRE-----VARDRKSLSDVATIVKKSNSKL 99
+ K++ ELK+K+GAE + + +DRK L +++ S +K+
Sbjct: 13 LEKQLNIELKVKQGAENMIQTYANGSTKDRKLLQTAQQMLQDSKTKI 59
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 27.1 bits (60), Expect = 3.5
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 47 LPNKLEELKEHIRKEIRKELKIKEGAEKLREVAR--DRKSLSDVATIVKK 94
LP+ LEE E + +R + L E+A + S +D+A +V++
Sbjct: 409 LPD-LEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVRE 457
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 27.4 bits (61), Expect = 3.6
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 44 EEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSEL 102
EEA+ LEE K+ I KE + + + L + + ++ +V V K K+ E+
Sbjct: 445 EEAILKSLEEFKQSIVKEAALSILEEIREKVLEQAEQGCENQEEVKKEVPKKVKKIPEV 503
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 27.0 bits (61), Expect = 3.6
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 71 GAEKLREVARDRKSLSDVATIVKKSNS-----------KLSELHNELQELESQIIMTQG 118
G L + L ++A ++K S +L EL EL++L++++
Sbjct: 689 GEAALEYLNEQEALLKELAALLKAKPSELPERVEALLEELKELEKELEQLKAKLAAAAA 747
>gnl|CDD|236510 PRK09428, pssA, phosphatidylserine synthase; Provisional.
Length = 451
Score = 27.1 bits (61), Expect = 3.7
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 21/77 (27%)
Query: 3 NPVYLVQNDRY----YWISSEGDYIRHPVLYELSHKYGFITEN-VAEEALPN-------K 50
N VYL Q+D+Y Y + IR+ L + FI +N + A+ K
Sbjct: 156 NNVYLHQHDKYRYDRYHL------IRNAELADSMV--NFIQQNLLNSPAVNRLDQPNRPK 207
Query: 51 LEELKEHIRKEIRKELK 67
+E+K IR + R+ L+
Sbjct: 208 TKEIKNDIR-QFRQRLR 223
>gnl|CDD|235152 PRK03705, PRK03705, glycogen debranching enzyme; Provisional.
Length = 658
Score = 26.9 bits (60), Expect = 3.8
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 8 VQNDRYYWISSEGDY 22
+ N YYWI +GDY
Sbjct: 282 IDNRSYYWIREDGDY 296
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 26.9 bits (60), Expect = 3.8
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSEL 102
E ++EE +E KE R E +++ EKL E+ +R L V+ +L EL
Sbjct: 640 EAEFDEARIEEARE--DKE-RAEEYLEQVEEKLDELREERDDLQAEIGAVENELEELEEL 696
Query: 103 HNELQELES 111
+ LE+
Sbjct: 697 RERREALEN 705
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 26.9 bits (60), Expect = 3.9
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 56 EHIRKEIRKELKIKEGAEKLREVARDR------------KSLSDVATIVKKSNSKLSELH 103
+ + ++ + K K AEK + + + L+D+ + + S+ S+L
Sbjct: 162 DDLLAQLDQIAKAKLNAEKKAKQLESQLSELQVKLDELQRQLNDLTSQKSRLQSENSDLT 221
Query: 104 NELQELESQI 113
+L+E E+Q+
Sbjct: 222 RQLEEAEAQV 231
>gnl|CDD|226345 COG3824, COG3824, Predicted Zn-dependent protease [General function
prediction only].
Length = 136
Score = 26.3 bits (58), Expect = 4.0
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 14 YWISSE---GDYIRHPVLYELSHKYG 36
YW +E GD + H +++E+ H +G
Sbjct: 97 YWAENEETLGDQVTHVLIHEIGHHFG 122
>gnl|CDD|219444 pfam07516, SecA_SW, SecA Wing and Scaffold domain. SecA protein
binds to the plasma membrane where it interacts with
proOmpA to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This family is composed of two C-terminal alpha
helical subdomains: the wing and scaffold subdomains.
Length = 213
Score = 26.8 bits (60), Expect = 4.0
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 30 ELSHKYGFITENVAEEALPNKLEELKEHIRKEIRKELKIKE---GAEKLREVAR 80
EL G + EE EELKE + + ++ + KE G E +RE+ R
Sbjct: 93 ELRELLGLDLDIDEEELEGLTEEELKERLIEAAKEAYEEKEAELGEELMREIER 146
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 26.9 bits (60), Expect = 4.2
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREVARD 81
LEELKE +RK + +ELK EK +E D
Sbjct: 262 LEELKEKLRKNLERELKEA-TLEKRKEQLLD 291
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 26.9 bits (59), Expect = 4.3
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 45 EALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDR-KSLSDVATIVKKSNS---KLS 100
L + + L E I++ ++ KIK EK R + D K + V + +KS KL
Sbjct: 274 ANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLE 333
Query: 101 ELHNELQELESQIIMTQGQ 119
+L +E++ E +I Q
Sbjct: 334 KLKSEIELKEEEIKALQSN 352
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 26.9 bits (60), Expect = 4.4
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 18/88 (20%)
Query: 45 EALPNKLEELKEHIRKEIR-KELKI-------------KEGAEKLREVARDRKSLSDVAT 90
E L +LEEL + R+E+ LK+ K A+K+ + R SL +
Sbjct: 158 EELEEELEELLKKEREELGIDSLKLGYNKVHGYYIEVTKSEAKKVPKDFIRRSSLKNTER 217
Query: 91 I----VKKSNSKLSELHNELQELESQII 114
+K+ ++L E E++ LE +I+
Sbjct: 218 FTTPELKELENELLEAKEEIERLEKEIL 245
>gnl|CDD|234866 PRK00927, PRK00927, tryptophanyl-tRNA synthetase; Reviewed.
Length = 333
Score = 26.6 bits (60), Expect = 4.5
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 45 EALPNKLEELKEHIRKEIRKELK-----IKEGAEKLREVAR 80
EA+ L ++E +E+ + + EGAEK R VA
Sbjct: 279 EAVVEFLAPIRER-YEELLADPAYLDEILAEGAEKARAVAS 318
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 26.7 bits (59), Expect = 4.6
Identities = 25/130 (19%), Positives = 48/130 (36%), Gaps = 20/130 (15%)
Query: 21 DYIRH--PVLYELSHKYGFITENVAEEALPNKLEELKEHIRKEIRKELKIKEG--AEKLR 76
+H L E KY + + K++EL E K+++ + + G K+
Sbjct: 240 SNKQHSLDYLIENHPKYQIV------ADIREKIDELIEERNKKLKPSPQKRRGLSDIKIL 293
Query: 77 EVARDRKSLSDVATIVKKS-------NSKLSELHNELQELESQI---IMTQGQTVTSPTA 126
A ++ + ++ S N + L L E+E +I I+ + V S +
Sbjct: 294 RKALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTNS 353
Query: 127 ANHEHGKSSD 136
+ G D
Sbjct: 354 SAGLKGWEFD 363
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 27.0 bits (60), Expect = 4.9
Identities = 14/48 (29%), Positives = 24/48 (50%)
Query: 38 ITENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSL 85
I+ +EE + LEEL E + R E +I+E +L + ++L
Sbjct: 414 ISTIPSEEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEAL 461
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 26.7 bits (59), Expect = 5.0
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 40 ENVAEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKL 99
E L K+E L E I K+I + ++ + K+ + + K S +
Sbjct: 640 EQTPPPNLQEKIESLNEEINKKIERVIRSSDLKSKIELLK---------LEVAKASKTPD 690
Query: 100 SELHNELQELESQI 113
+++ LE QI
Sbjct: 691 VTEKEKIEALEQQI 704
>gnl|CDD|212013 cd11623, HR1_PKN_2, Second 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
second HR1 domain of PKN. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family.
Length = 71
Score = 25.3 bits (56), Expect = 5.4
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 44 EEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKS 84
E A ++L L+ K++ ELK+K+GAE + ++ + KS
Sbjct: 1 ENAQNSRLAGLE----KQLNIELKVKQGAENMIQMYSNGKS 37
>gnl|CDD|217899 pfam04108, APG17, Autophagy protein Apg17. Apg17 is required for
activating Apg1 protein kinases.
Length = 408
Score = 26.5 bits (59), Expect = 5.5
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 75 LREVARDRKSLSDVATIVKKSNSKLSELHNELQELESQIIMTQG 118
L EV R R + I+K N +L +L E Q+ Q + G
Sbjct: 348 LLEVERRRAVRKKMEKILKFCNEQLDKLQEEDQKRRQQFLAEYG 391
>gnl|CDD|220175 pfam09316, Cmyb_C, C-myb, C-terminal. Members of this family are
predominantly found in the proto-oncogene c-myb and the
viral transforming protein myb. Truncation of the domain
results in 'activation' of c-myb and subsequent
tumourigenesis.
Length = 168
Score = 26.3 bits (58), Expect = 5.5
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 48 PNKLEE-LKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNEL 106
P+ LEE +KE I++E ++L I E E +K +V + +KK L+ E
Sbjct: 95 PSHLEEDIKEVIKQETGEDLIIVEEVE-----PPLKKIKQEVESPMKKVRKSLALDIWEG 149
Query: 107 QELESQIIMTQG 118
++L +Q++
Sbjct: 150 EDLNAQLLTPDS 161
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 26.6 bits (60), Expect = 5.6
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 50 KLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNELQEL 109
+LEEL+ R + KE+ + + E VK+ ++ L EL EL
Sbjct: 43 ELEELQ-AERNALSKEIGQAKRKGEDAEALIAE---------VKELKEEIKALEAELDEL 92
Query: 110 ESQI 113
E+++
Sbjct: 93 EAEL 96
>gnl|CDD|198034 smart00966, SpoVT_AbrB, SpoVT / AbrB like domain. This domain is
found in AbrB from Bacillus subtilis. The product of
the abrB gene is an ambiactive repressor and activator
of the transcription of genes expressed during the
transition state between vegetative growth and the
onset of stationary phase and sporulation. AbrB is
thought to interact directly with the transcription
initiation regions of genes under its control. AbrB
contains a helix-turn-helix structure, but this domain
ends before the helix-turn-helix begins. The product of
the B. subtilis gene spoVT is another member of this
family and is also a transcriptional regulator.
DNA-binding activity in this AbrB homologue requires
hexamerisation. Another family member has been isolated
from the Sulfolobus solfataricus and has been
identified as a homologue of bacterial repressor-like
proteins. The Escherichia coli family member SohA or
Prl1F appears to be bifunctional and is able to
regulate its own expression as well as relieve the
export block imposed by high-level synthesis of
beta-galactosidase hybrid proteins.
Length = 45
Score = 24.4 bits (54), Expect = 5.9
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 58 IRKEIRKELKIKEGAEKLREVARDR 82
I KE+R++L IKEG E EV D
Sbjct: 11 IPKEVREKLGIKEGDEVELEVDGDG 35
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 26.4 bits (59), Expect = 6.0
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 62 IRKELKIKEGAEKLREVARDRKSL--SDVATIV 92
IR++ KI E EK VAR K++ +DV +V
Sbjct: 236 IRRKGKITESVEKY-SVARTLKAIERADVVLLV 267
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 26.3 bits (59), Expect = 6.1
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLS 86
A E + + L+ L + + K+L +KE E L+E +SL
Sbjct: 195 AMEIISDHLDLLARRDFRTLAKKLGVKE--EDLQEALDLIRSLD 236
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 26.4 bits (58), Expect = 6.1
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 45 EALPNKLEEL---KEHIRKEI-RKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLS 100
E L KLEEL KE + KE+ E + +E E+L+ + S + ++KK ++
Sbjct: 138 EELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRL---EVENSRLEEMLKKLPGEVY 194
Query: 101 ELHNELQELESQI 113
+L ELE +
Sbjct: 195 DLKKRWDELEPGV 207
>gnl|CDD|212568 cd11695, DHR2_DOCK_C, Dock Homology Region 2, a GEF domain, of
Class C Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided into
four classes (A-D) based on sequence similarity and
domain architecture; class C, also called the
Zizimin-related (Zir) subfamily, includes Dock6, 7 and
8. Class C DOCKs have been shown to have GEF activity
for both Rac and Cdc42. Dock6 regulates neurite
outgrowth. Dock7 plays a critical roles in the early
stages of axon formation, neuronal polarity, and
myelination. Dock8 regulates T and B cell numbers and
functions, and plays essential roles in humoral immune
responses and the proper formation of B cell
immunological synapses. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Class C
Docks, which contains the catalytic GEF activity for Rac
and Cdc42.
Length = 368
Score = 26.5 bits (59), Expect = 6.4
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 94 KSNSKLSELHNELQELESQIIMTQG 118
+ KL+E+H +LQ+ ++I QG
Sbjct: 72 RDYKKLAEIHGKLQDAFTKIEKQQG 96
>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 = 26.1 bits (58), Expect = 6.5
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREV 78
LEELKE +RK++ +E K E +
Sbjct: 2 LEELKEKLRKQLEEEKKEATAEELKEAI 29
>gnl|CDD|212021 cd11631, HR1_PKN2_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N2. PKN2, also called PKNgamma or
Protein-kinase C-related kinase 2 (PRK2), is a
serine/threonine protein kinase and an effector of the
small GTPase Rho/Rac. It regulates G2/M cell cycle
progression and the exit from cytokinesis. It also
phosphorylates hepatitis C virus (HCV) RNA polymerase
and thus, plays a role in HCV RNA replication. PKN2
shares a common domain architecture with other PKNs,
containing three HR1 domains, a C2 domain, and a kinase
domain. In addition, PKN2 contains a proline-rich
region in between its C2 and kinase domains and has
been shown to associate with SH3 domain containing
proteins like NCK and Grb4. This model characterizes
the second HR1 domain of PKN2. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; PKN2 specifically binds to
RhoA GTPase in a GTP-dependent manner. The HR1 domains
of PKN2, together with its C2 domain, also facilitate
the recruitment of PKN2 to primordial junctions at
nascent cell-cell contacts, where it promotes
junctional maturation.
Length = 74
Score = 25.0 bits (54), Expect = 6.5
Identities = 14/47 (29%), Positives = 31/47 (65%), Gaps = 5/47 (10%)
Query: 58 IRKEIRKELKIKEGAEKLREV-----ARDRKSLSDVATIVKKSNSKL 99
++K++ ELK+K+GAE + ++ ++DRK L+ +++ S +K+
Sbjct: 14 LKKQLDIELKVKQGAENMIQMYSNGSSKDRKLLATAQQMLQDSKTKI 60
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 26.3 bits (59), Expect = 7.0
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 49 NKLEELKEHIRKEIRKELKIKEGAEKLREVARDR------KSLSDVATIVKKSNSKLSEL 102
NK++ + E IR I + KE E+L E+ D + L+ ++K ++ EL
Sbjct: 347 NKIDFVIEVIRGSIDLKKAKKELIEELSEIQADYLLDMRLRRLT--KEEIEKLEKEIEEL 404
Query: 103 HNELQELES 111
E+ ELE
Sbjct: 405 EKEIAELEK 413
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 26.5 bits (58), Expect = 7.1
Identities = 13/67 (19%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 48 PNKLEELKEHIRK-EIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHNEL 106
P+KL+ + ++K E R++ + + + K + ++ ++K N + L N++
Sbjct: 708 PDKLKSTESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNKLQKVNRDIQRLKNDI 767
Query: 107 QELESQI 113
+E E+ +
Sbjct: 768 EEQETLL 774
>gnl|CDD|169427 PRK08402, PRK08402, replication factor A; Reviewed.
Length = 355
Score = 25.9 bits (57), Expect = 7.6
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 43 AEEALPNKLEELKEHIRKEIRKELKIKEGAEKLRE 77
A E L + EE+ E +++ I L KE A KL E
Sbjct: 267 AAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAE 301
>gnl|CDD|173938 cd08179, NADPH_BDH, NADPH-dependent butanol dehydrogenase involved
in the butanol and ethanol formation pathway in
bacteria. NADPH-dependent butanol dehydrogenase (BDH)
is involved in the butanol and ethanol formation pathway
of some bacteria. The fermentation process is
characterized by an acid producing growth phase,
followed by a solvent producing phase. The latter phase
is associated with the induction of solventogenic
enzymes such as butanol dehydrogenase. The activity of
the enzymes require NADPH as cofactor, as well as
divalent ions zinc or iron. This family is a member of
the iron-containing alcohol dehydrogenase superfamily.
Protein structure has a dehydroquinate synthase-like
fold.
Length = 375
Score = 26.1 bits (58), Expect = 7.8
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 33 HKYGFITENVAEEALPNKLEELKE--HIRKEIRKELKIKEGA--EKLREVARDRKSLSDV 88
+Y + + E L + EL + I KE I E EKL E+A ++ D
Sbjct: 295 KRYAGLAKEEGVEDLIEAVRELNKKLGIPACF-KEYGIDEQEFLEKLDELA--ENAIKDA 351
Query: 89 AT 90
T
Sbjct: 352 CT 353
>gnl|CDD|233770 TIGR02188, Ac_CoA_lig_AcsA, acetate--CoA ligase. This model
describes acetate-CoA ligase (EC 6.2.1.1), also called
acetyl-CoA synthetase and acetyl-activating enzyme. It
catalyzes the reaction ATP + acetate + CoA = AMP +
diphosphate + acetyl-CoA and belongs to the family of
AMP-binding enzymes described by pfam00501.
Length = 625
Score = 26.1 bits (58), Expect = 8.0
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 35 YGFITENVAEEALPNKLEELKEHIRKEI 62
Y F+T E +EL++H+RKEI
Sbjct: 541 YAFVTLKDGYEPDDELRKELRKHVRKEI 568
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 26.3 bits (58), Expect = 8.4
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 42 VAEEALPNKLEELKEHIRKEIRK-ELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLS 100
++++AL K ELK +R + E K K+ +KL SL + +I N +L
Sbjct: 37 LSDDALREKGMELKSRVRGALEPIEQKKKDLEKKLD---NPDISLEEAESI----NEELD 89
Query: 101 ELHNELQE 108
L E +E
Sbjct: 90 TLAKEYEE 97
>gnl|CDD|217206 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 25.7 bits (57), Expect = 8.4
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 38 ITENVAE--EALPNKLEELKE--HIRKEIRKELKIKEGA---EKLREVA 79
I + A+ EAL + +E R E++++L KE EKLRE+A
Sbjct: 103 INDKFAKLSEALYIAERKAREEVRQRAELQRQLAEKEKQEKEEKLRELA 151
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
with domain III, which is central to the structure of
Thermus aquaticus MutS as characterized in.
Length = 290
Score = 25.8 bits (57), Expect = 8.7
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 13/72 (18%)
Query: 52 EELKEHIRKEIRKELK-----------IKEGAEKLREVARDRKSLSDVATIVK--KSNSK 98
EEL E +R+E+R+ LK + G R++ R SL + + K S
Sbjct: 59 EELLEDLREELREALKGIPDLERLLSRLALGRASPRDLLALRSSLEALPALRKLLASAPL 118
Query: 99 LSELHNELQELE 110
L++L ++L E
Sbjct: 119 LADLADQLPLPE 130
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 25.8 bits (58), Expect = 9.2
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 16/70 (22%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREVARDRKSLSD---VA----TIVKKSNSKLSELH 103
+E + KE+ K EK E+ R K LS+ VA +V+K KL+E
Sbjct: 809 VEAELARLEKELAK-------LEK--EIERVEKKLSNEGFVAKAPEEVVEKEREKLAEYE 859
Query: 104 NELQELESQI 113
+L +L+ ++
Sbjct: 860 EKLAKLKERL 869
>gnl|CDD|240286 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone]
flavoprotein subunit; Provisional.
Length = 617
Score = 25.9 bits (57), Expect = 9.5
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 14/68 (20%)
Query: 63 RKELKIKEGAEKLREVARDRKSLSDVATIVKKS---NSKLSELHNELQELESQIIMTQG- 118
R ++EG EK++E+ D DV I KS N+ L E LE + ++TQ
Sbjct: 497 RIGESLQEGVEKIKEIYSD---FKDVK-IKDKSLVWNTDLIET------LELENLLTQAK 546
Query: 119 QTVTSPTA 126
QT+ S A
Sbjct: 547 QTILSAEA 554
>gnl|CDD|179847 PRK04424, PRK04424, fatty acid biosynthesis transcriptional
regulator; Provisional.
Length = 185
Score = 25.6 bits (57), Expect = 9.5
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 16/66 (24%)
Query: 52 EELKEH-------IRKEIRKELKIKEGAEKLREVARDRKSLSDVATIVKKSNSKLSELHN 104
EEL E IR + R EL I E E+++ VA K+ V ++ E+
Sbjct: 25 EELAEKFGVSIQTIRLD-RMELGIPELRERIKHVA--EKNYDKVKSLP------EEEVVG 75
Query: 105 ELQELE 110
EL +LE
Sbjct: 76 ELIDLE 81
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 26.0 bits (58), Expect = 9.6
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 51 LEELKEHIRKEIRKELKIKEGAEKLREV 78
LEELK IRK + +E K + + ++
Sbjct: 252 LEELKADIRKNLEREKKERAKNKLKEQL 279
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
0.310 0.128 0.351
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,133,991
Number of extensions: 649584
Number of successful extensions: 1788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1704
Number of HSP's successfully gapped: 385
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.4 bits)