RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy124
(60 letters)
>gnl|CDD|214441 MTH00157, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 223
Score = 61.3 bits (150), Expect = 1e-13
Identities = 22/39 (56%), Positives = 30/39 (76%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP IL+P +V+IE N+IRP LAVRL AN++A
Sbjct: 128 LVPQGTPPILMPFMVLIETISNLIRPGTLAVRLAANMIA 166
>gnl|CDD|177190 MTH00132, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 227
Score = 50.6 bits (122), Expect = 1e-09
Identities = 23/39 (58%), Positives = 29/39 (74%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP LIP+++IIE IRP+AL VRLTANL A
Sbjct: 129 LLPEGTPTPLIPVLIIIETISLFIRPLALGVRLTANLTA 167
>gnl|CDD|177230 MTH00179, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 227
Score = 50.3 bits (121), Expect = 2e-09
Identities = 22/39 (56%), Positives = 29/39 (74%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP LIP++V IE +IRP+AL VRLTAN+ A
Sbjct: 129 LLPEGTPTPLIPMLVWIETISLLIRPLALGVRLTANITA 167
>gnl|CDD|177181 MTH00120, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 227
Score = 49.8 bits (120), Expect = 3e-09
Identities = 22/39 (56%), Positives = 29/39 (74%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP LIP +++IE +IRP+AL VRLTANL A
Sbjct: 129 LLPEGTPTPLIPALILIETISLLIRPLALGVRLTANLTA 167
>gnl|CDD|177144 MTH00073, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 227
Score = 48.8 bits (117), Expect = 5e-09
Identities = 24/39 (61%), Positives = 30/39 (76%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP +LIPI++IIE IRP+AL VRLTANL A
Sbjct: 129 LLPEGTPTLLIPILIIIETISLFIRPLALGVRLTANLTA 167
>gnl|CDD|233283 TIGR01131, ATP_synt_6_or_A, ATP synthase subunit 6
(eukaryotes),also subunit A (prokaryotes). Bacterial
forms should be designated ATP synthase, F0 subunit A;
eukaryotic (chloroplast and mitochondrial) forms should
be designated ATP synthase, F0 subunit 6. The F1/F0 ATP
synthase is a multisubunit, membrane associated enzyme
found in bacteria and mitochondria and chloroplast. This
enzyme is principally involved in the synthesis of ATP
from ADP and inorganic phosphate by coupling the energy
derived from the proton electrochemical gradient across
the biological membrane. A brief description of this
multisubunit enzyme complex: F1 and F0 represent two
major clusters of subunits. Individual subunits in each
of these clusters are named differently in prokaryotes
and in organelles e.g., mitochondria and chloroplast.
The bacterial equivalent of subunit 6 is named subunit
'A'. It has been shown that proton is conducted though
this subunit. Typically, deprotonation and reprotonation
of the acidic amino acid side-chains are implicated in
the process [Energy metabolism, ATP-proton motive force
interconversion].
Length = 226
Score = 47.2 bits (113), Expect = 3e-08
Identities = 22/37 (59%), Positives = 27/37 (72%)
Query: 3 PSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
PSGTP LIP +VIIE + RPI+L+VRL AN+ A
Sbjct: 132 PSGTPLPLIPFLVIIETISYLARPISLSVRLFANISA 168
>gnl|CDD|214449 MTH00176, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 229
Score = 46.6 bits (111), Expect = 4e-08
Identities = 23/45 (51%), Positives = 32/45 (71%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLASLVWLG 45
++P GTP +L P +V+IE+ +IRP+ LAVRL ANL A + LG
Sbjct: 131 LVPQGTPPLLNPFLVLIELVSLLIRPLTLAVRLAANLSAGHLLLG 175
>gnl|CDD|177163 MTH00101, ATP6, ATP synthase F0 subunit 6; Validated.
Length = 226
Score = 45.7 bits (109), Expect = 9e-08
Identities = 23/38 (60%), Positives = 29/38 (76%)
Query: 2 IPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
+P GTP LIP++VIIE I+P+ALAVRLTAN+ A
Sbjct: 129 LPQGTPTPLIPMLVIIETISLFIQPMALAVRLTANITA 166
>gnl|CDD|214448 MTH00173, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 231
Score = 44.9 bits (107), Expect = 2e-07
Identities = 18/39 (46%), Positives = 26/39 (66%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P+G P L P +V+IE +IRP+ L VRL AN+ A
Sbjct: 131 LVPAGAPAGLNPFLVLIETVSILIRPLTLTVRLLANISA 169
>gnl|CDD|177110 MTH00035, ATP6, ATP synthase F0 subunit 6; Validated.
Length = 229
Score = 44.6 bits (106), Expect = 2e-07
Identities = 20/39 (51%), Positives = 27/39 (69%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P GTP+ LIP++V IE +PIAL +RL ANL A
Sbjct: 132 LVPQGTPSFLIPLMVWIETLSLFAQPIALGLRLAANLTA 170
>gnl|CDD|109186 pfam00119, ATP-synt_A, ATP synthase A chain.
Length = 217
Score = 44.1 bits (105), Expect = 3e-07
Identities = 18/38 (47%), Positives = 25/38 (65%)
Query: 2 IPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
+P GTP LIP +V IE+ RP++L +RL N+LA
Sbjct: 123 VPPGTPLFLIPFLVPIELISLFARPLSLGLRLFGNILA 160
>gnl|CDD|214447 MTH00172, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 232
Score = 40.8 bits (96), Expect = 6e-06
Identities = 20/39 (51%), Positives = 26/39 (66%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++PSG P L P++V+IE I R I+L VRL ANL A
Sbjct: 131 LMPSGAPLGLAPLLVLIETVSYISRAISLGVRLAANLSA 169
>gnl|CDD|164583 MTH00005, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 231
Score = 39.7 bits (93), Expect = 1e-05
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLASLVWLG 45
++P G P+ L P +V+IE ++RPI L+ RL AN+ A + L
Sbjct: 133 LLPGGAPDWLNPFLVLIETISILVRPITLSFRLAANMSAGHIVLS 177
>gnl|CDD|177228 MTH00175, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 244
Score = 36.1 bits (84), Expect = 3e-04
Identities = 18/39 (46%), Positives = 26/39 (66%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
++P G P +L P +V+IE +IR I+L VRL AN+ A
Sbjct: 142 LMPGGAPLVLAPFLVLIETLSYLIRAISLGVRLAANISA 180
>gnl|CDD|177125 MTH00050, ATP6, ATP synthase F0 subunit 6; Validated.
Length = 170
Score = 32.9 bits (76), Expect = 0.003
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVR 32
+P GTP + P + I E IIRP+ L +R
Sbjct: 82 FVPVGTPLYICPFVCIAETISYIIRPVVLILR 113
>gnl|CDD|133799 MTH00174, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 252
Score = 32.6 bits (74), Expect = 0.004
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 1 MIPSGTPNILIPIIVIIEITRNIIRPIALAVRLTANL 37
++P G P L P++ IIE I R I+L VRL AN+
Sbjct: 150 LMPQGAPLALAPLLTIIETLSYISRAISLGVRLAANI 186
>gnl|CDD|223433 COG0356, AtpB, F0F1-type ATP synthase, subunit a [Energy production
and conversion].
Length = 246
Score = 31.1 bits (71), Expect = 0.014
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 7 PNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
P L P+++ +EI + +PI+L++RL N+LA
Sbjct: 155 PFPLAPLMLPLEIVSELAKPISLSLRLFGNILA 187
>gnl|CDD|177152 MTH00087, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 195
Score = 30.7 bits (70), Expect = 0.019
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 15 VIIEITRNIIRPIALAVRLTANLLA 39
+ +EI + RP+AL +RLT NL+
Sbjct: 124 LFVEIVSELSRPLALTLRLTVNLMV 148
>gnl|CDD|237380 PRK13417, PRK13417, F0F1 ATP synthase subunit A; Provisional.
Length = 352
Score = 30.2 bits (68), Expect = 0.029
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 2 IPSGTPNILIPIIVIIE-ITRNIIRPIALAVRLTANLLASLV 42
+P+G P +L PI+ +E I + + AL VRL AN+ A V
Sbjct: 253 VPNGVPLLLYPIMWPLEFIVSPMAKTFALTVRLLANMTAGHV 294
>gnl|CDD|237381 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
Length = 342
Score = 30.1 bits (68), Expect = 0.040
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 5 GTPNILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
GT L I++ IE +P AL VRL AN+ A
Sbjct: 234 GTHWSLWIIMIPIEFIGLFTKPFALTVRLFANMTA 268
>gnl|CDD|235617 PRK05815, PRK05815, F0F1 ATP synthase subunit A; Validated.
Length = 227
Score = 29.8 bits (68), Expect = 0.044
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 11 IPIIVIIEITRNIIRPIALAVRLTANLLA 39
P+++ IEI RPI+L++RL N+LA
Sbjct: 139 HPLLLPIEIISEFSRPISLSLRLFGNMLA 167
>gnl|CDD|227605 COG5280, COG5280, Phage-related minor tail protein [Function
unknown].
Length = 634
Score = 28.6 bits (64), Expect = 0.13
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 10 LIPIIVIIEITRNIIRPIALAVRLTANLLASLVWLGD 46
+IP ++++ IIRP+A + + A + W
Sbjct: 549 VIPSLILVAGILAIIRPLAAGIGTVGSWGAIMDWDAL 585
>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 = 27.7 bits (62), Expect = 0.31
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 7/51 (13%)
Query: 13 IIVIIEITRNIIRPIALA------VRLTANLLASL-VWLGDLKQRLDQLNL 56
+ + ++ + + +L L L W+ DL +R+ QL
Sbjct: 503 ELTMTNDLEDLAKALFKGRVPASWAKLAYPSLKPLGSWVTDLLRRIRQLQD 553
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 26.9 bits (60), Expect = 0.45
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 24 IRPIALAVRLTANLLASLVWLGDLKQRLDQLNLAGGL 60
IR I VR A L LG + ++ GGL
Sbjct: 276 IRDIKTGVREAARFYVELRKLG---ANIKYFDVGGGL 309
>gnl|CDD|197327 cd09093, INPP5c_INPP5B, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of Type II inositol
polyphosphate 5-phosphatase I, Oculocerebrorenal
syndrome of Lowe 1, and related proteins. This
subfamily contains the INPP5c domain of type II inositol
polyphosphate 5-phosphatase I (INPP5B),
Oculocerebrorenal syndrome of Lowe 1 (OCRL-1), and
related proteins. It belongs to a family of
Mg2+-dependent inositol polyphosphate 5-phosphatases,
which hydrolyze the 5-phosphate from the inositol ring
of various 5-position phosphorylated phosphoinositides
(PIs) and inositol phosphates (IPs), and to the large
EEP (exonuclease/endonuclease/phosphatase) superfamily
that contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. INPP5B and OCRL1 preferentially hydrolyze the
5-phosphate of phosphatidylinositol (4,5)- bisphosphate
[PI(4,5)P2] and phosphatidylinositol (3,4,5)-
trisphosphate [PI(3,4,5)P3]. INPP5B can also hydrolyze
soluble inositol (1,4,5)-trisphosphate [I(1,4,5)P3] and
inositol (1,3,4,5)-tetrakisphosphate [I(1,3,4,5)P4].
INPP5B participates in the endocytic pathway and in the
early secretory pathway. In the latter, it may function
in retrograde ERGIC (ER-to-Golgi intermediate
compartment)-to-ER transport; it binds specific RAB
proteins within the secretory pathway. In the endocytic
pathway, it binds RAB5 and during endocytosis, may
function in a RAB5-controlled cascade for converting
PI(3,4,5)P3 to phosphatidylinositol 3-phosphate (PI3P).
This cascade may link growth factor signaling and
membrane dynamics. Mutation in OCRL1 is implicated in
Lowe syndrome, an X-linked recessive multisystem
disorder, which includes defects in eye, brain, and
kidney function, and in Type 2 Dent's disease, a
disorder with only the renal symptoms. OCRL-1 may have a
role in membrane trafficking within the endocytic
pathway and at the trans-Golgi network, and may
participate in actin dynamics or signaling from
endomembranes. OCRL1 and INPP5B have overlapping
functions: deletion of both 5-phosphatases in mice is
embryonic lethal, deletion of OCRL1 alone has no
phenotype, and deletion of Inpp5b alone has only a mild
phenotype (male sterility). Several of the proteins that
interact with OCRL1 also bind INPP5B, for examples,
inositol polyphosphate phosphatase interacting protein
of 27kDa (IPIP27)A and B (also known as Ses1 and 2), and
endocytic signaling adaptor APPL1. OCRL1, but not
INPP5B, binds clathrin heavy chain, the plasma membrane
AP2 adaptor subunit alpha-adaptin. In addition to this
INPP5c domain, most proteins in this subfamily have a
C-terminal RhoGAP (GTPase-activator protein [GAP] for
Rho-like small GTPases) domain.
Length = 292
Score = 25.0 bits (55), Expect = 2.6
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 41 LVWLGDLKQRLDQLN 55
+ WLGDL R+ +L
Sbjct: 176 VFWLGDLNYRIQELP 190
>gnl|CDD|206160 pfam13990, YjcZ, YjcZ-like protein. This family of proteins is
functionally uncharacterized. The family includes the
YjcZ protein from E. coli. This family of proteins is
found in enteric bacteria. Proteins in this family are
approximately 300 amino acids in length. There are two
conserved sequence motifs: FGD and MPR.
Length = 270
Score = 24.7 bits (54), Expect = 3.2
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 24 IRPIALAVRLTANLLASLVWLGDLKQRLDQLNLA 57
R A+ L L A L WL L LD +LA
Sbjct: 37 ERQWAMNGNLAQGLEARLQWLEKLTSSLDPGHLA 70
>gnl|CDD|236112 PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed.
Length = 466
Score = 24.8 bits (55), Expect = 3.3
Identities = 12/19 (63%), Positives = 13/19 (68%), Gaps = 2/19 (10%)
Query: 24 IRPIALAV--RLTANLLAS 40
I PIALAV RLT + LA
Sbjct: 422 ILPIALAVQNRLTVDDLAQ 440
>gnl|CDD|233325 TIGR01238, D1pyr5carbox3, delta-1-pyrroline-5-carboxylate
dehydrogenase (PutA C-terminal domain). This model
represents one of several related branches of
delta-1-pyrroline-5-carboxylate dehydrogenase. Members
of this branch are the C-terminal domain of the PutA
bifunctional proline dehydrogenase /
delta-1-pyrroline-5-carboxylate dehydrogenase [Energy
metabolism, Amino acids and amines].
Length = 500
Score = 24.1 bits (52), Expect = 5.9
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 7 PNILIPIIVIIEITRNIIRPIALAVRLTANLLASLVWLGDLKQRLDQLNLAG 58
L + I E++ + P+ VR A L +V DQ+N G
Sbjct: 389 APTLFELDDIAELSEEVFGPVLHVVRYKARELDQIV---------DQINQTG 431
>gnl|CDD|237382 PRK13420, PRK13420, F0F1 ATP synthase subunit A; Provisional.
Length = 226
Score = 23.9 bits (52), Expect = 6.5
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 4/31 (12%)
Query: 9 ILIPIIVIIEITRNIIRPIALAVRLTANLLA 39
L+P +I EITR + ALAVRL N+++
Sbjct: 141 FLLPFHLISEITRTL----ALAVRLFGNIMS 167
>gnl|CDD|222278 pfam13638, PIN_4, PIN domain. Members of this family of
bacterial domains are predicted to be RNases (from
similarities to 5'-exonucleases).
Length = 129
Score = 23.3 bits (51), Expect = 9.4
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 8 NILIPIIVIIEI----TRNIIRPIALAVRLTANLLASLV 42
+++IPI V+ E+ R+ +R + R L L+
Sbjct: 23 DVVIPITVLEELDKLKKRSDLRELGRNAREAIRFLDELL 61
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
0.327 0.146 0.419
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,202,046
Number of extensions: 237301
Number of successful extensions: 369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 41
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)