RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15556
(288 letters)
>gnl|CDD|238661 cd01365, KISc_KIF1A_KIF1B, Kinesin motor domain, KIF1_like
proteins. KIF1A (Unc104) transports synaptic vesicles to
the nerve terminal, KIF1B has been implicated in
transport of mitochondria. Both proteins are expressed
in neurons. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
In contrast to the majority of dimeric kinesins, most
KIF1A/Unc104 kinesins are monomeric motors. A
lysine-rich loop in KIF1A binds to the negatively
charged C-terminus of tubulin and compensates for the
lack of a second motor domain, allowing KIF1A to move
processively.
Length = 356
Score = 187 bits (476), Expect = 3e-57
Identities = 71/97 (73%), Positives = 82/97 (84%), Gaps = 4/97 (4%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELST----KKSTFIPYRDSVLTWLLKDSLGGNSK 114
GDRLKEG++INKSL TLG VIS+LA+ S+ KKS+FIPYRDSVLTWLLK++LGGNSK
Sbjct: 260 EGDRLKEGSNINKSLTTLGKVISALADNSSAKSKKKSSFIPYRDSVLTWLLKENLGGNSK 319
Query: 115 TIMIAAISPADVNYSETLSTLRYANRAKNIINKPTVN 151
T MIA ISPAD+NY ETLSTLRYA+RAK I+N VN
Sbjct: 320 TAMIATISPADINYEETLSTLRYADRAKKIVNVAVVN 356
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of organelles
and in cell division.
Length = 335
Score = 164 bits (417), Expect = 1e-48
Identities = 62/93 (66%), Positives = 73/93 (78%), Gaps = 2/93 (2%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
GDRLKE +INKSL LG+VI++LA+ S KS IPYRDS LT LL+DSLGGNSKT+MI
Sbjct: 245 EGDRLKEAGNINKSLSALGNVINALAQHS--KSRHIPYRDSKLTRLLQDSLGGNSKTLMI 302
Query: 119 AAISPADVNYSETLSTLRYANRAKNIINKPTVN 151
A +SP+ N ETLSTLR+A+RAK I NKP VN
Sbjct: 303 ANVSPSSSNLEETLSTLRFASRAKEIKNKPIVN 335
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 160 bits (408), Expect = 2e-47
Identities = 60/86 (69%), Positives = 71/86 (82%), Gaps = 3/86 (3%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
G RLKE A+INKSL LG+VI++LAE +S+ IPYRDS LT LL+DSLGGNSKT+MI
Sbjct: 244 GGRRLKEAANINKSLSALGNVINALAE---NQSSHIPYRDSKLTRLLQDSLGGNSKTLMI 300
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
A ISP+D NY ETLSTLR+A+RAKNI
Sbjct: 301 ANISPSDSNYEETLSTLRFASRAKNI 326
>gnl|CDD|238667 cd01371, KISc_KIF3, Kinesin motor domain, kinesins II or KIF3_like
proteins. Subgroup of kinesins, which form heterotrimers
composed of 2 kinesins and one non-motor accessory
subunit. Kinesins II play important roles in ciliary
transport, and have been implicated in neuronal
transport, melanosome transport, the secretory pathway,
and mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In this group the motor
domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 333
Score = 151 bits (383), Expect = 9e-44
Identities = 62/86 (72%), Positives = 67/86 (77%), Gaps = 3/86 (3%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
TGDRLKE IN SL LG+VIS+L + KST IPYRDS LT LL+DSLGGNSKT+M
Sbjct: 251 TGDRLKEATKINLSLSALGNVISALVD---GKSTHIPYRDSKLTRLLQDSLGGNSKTVMC 307
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
A I PAD NY ETLSTLRYANRAKNI
Sbjct: 308 ANIGPADYNYDETLSTLRYANRAKNI 333
>gnl|CDD|238668 cd01372, KISc_KIF4, Kinesin motor domain, KIF4-like subfamily.
Members of this group seem to perform a variety of
functions, and have been implicated in neuronal
organelle transport and chromosome segregation during
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 341
Score = 147 bits (373), Expect = 4e-42
Identities = 56/86 (65%), Positives = 70/86 (81%), Gaps = 1/86 (1%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
TGDRLKEG IN L+ LG+VIS+L + +KK + +PYRDS LT LL+DSLGGNS T+MI
Sbjct: 256 TGDRLKEGISINSGLLALGNVISALGD-ESKKGSHVPYRDSKLTRLLQDSLGGNSHTLMI 314
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
A +SPAD N+ ETL+TL+YANRA+NI
Sbjct: 315 ACVSPADSNFEETLNTLKYANRARNI 340
>gnl|CDD|238666 cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup.
The yeast kinesin KIP3 plays a role in positioning the
mitotic spindle. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 338
Score = 147 bits (372), Expect = 5e-42
Identities = 55/86 (63%), Positives = 68/86 (79%), Gaps = 1/86 (1%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
G RLKEGA+IN+SL+ LG+ I++L + KK+ IPYRDS LT LLKDSLGGN KT+MI
Sbjct: 254 RGQRLKEGANINRSLLALGNCINALVDGK-KKNKHIPYRDSKLTRLLKDSLGGNCKTVMI 312
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
A ISP+ +Y ET +TL+YANRAKNI
Sbjct: 313 ANISPSSSHYEETHNTLKYANRAKNI 338
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 328
Score = 143 bits (363), Expect = 8e-41
Identities = 56/84 (66%), Positives = 66/84 (78%), Gaps = 2/84 (2%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
GDRLKE +INKSL LG+VIS+L+ +K IPYRDS LT LL+DSLGGNSKT+MI
Sbjct: 247 EGDRLKEAKNINKSLSALGNVISALSSG--QKKKHIPYRDSKLTRLLQDSLGGNSKTLMI 304
Query: 119 AAISPADVNYSETLSTLRYANRAK 142
A ISP+ NY ETLSTLR+A+RAK
Sbjct: 305 ANISPSSENYDETLSTLRFASRAK 328
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type), N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 352
Score = 135 bits (341), Expect = 2e-37
Identities = 56/94 (59%), Positives = 69/94 (73%), Gaps = 4/94 (4%)
Query: 60 GDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMIA 119
R +E +IN+SL+TLG VI++L E KS IPYR+S LT LL+DSLGG +KT +IA
Sbjct: 263 NKRAREAGNINQSLLTLGRVINALVE----KSPHIPYRESKLTRLLQDSLGGRTKTSIIA 318
Query: 120 AISPADVNYSETLSTLRYANRAKNIINKPTVNED 153
ISPA +N ETLSTL YA+RAKNI NKP VN+
Sbjct: 319 TISPASINLEETLSTLEYAHRAKNIKNKPEVNQK 352
>gnl|CDD|238662 cd01366, KISc_C_terminal, Kinesin motor domain,
KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a
spindle motor protein necessary for chromosome
segregation in meiosis. KIFC2/KIFC3-like kinesins have
been implicated in motility of the Golgi apparatus as
well as dentritic and axonal transport in neurons. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In this subgroup the motor domain is found at
the C-terminus (C-type). C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 329
Score = 130 bits (329), Expect = 9e-36
Identities = 49/86 (56%), Positives = 63/86 (73%), Gaps = 4/86 (4%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
TGDRLKE INKSL LG VIS+L K + +PYR+S LT+LL+DSLGGNSKT+M
Sbjct: 245 TGDRLKEAQAINKSLSALGDVISALR----SKDSHVPYRNSKLTYLLQDSLGGNSKTLMF 300
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
ISP + N SETL +LR+A+R +++
Sbjct: 301 VNISPLESNLSETLCSLRFASRVRSV 326
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 130 bits (327), Expect = 9e-34
Identities = 66/119 (55%), Positives = 84/119 (70%), Gaps = 7/119 (5%)
Query: 60 GDRLKEGAHINKSLVTLGSVISSLAELS-TKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
GDRLKE +IN+SL LG++I+ LAE+S T K IPYRDS LT+LL++SLGGN+K M+
Sbjct: 349 GDRLKEAGNINRSLSQLGNLINILAEISQTGKQRHIPYRDSRLTFLLQESLGGNAKLAMV 408
Query: 119 AAISPADVNYSETLSTLRYANRAKNIINKPTVNE----DPN--TRIIRELHDEITKLKA 171
AISP+ SET STLR+A RAK I NK VNE D N +IR+L DE+ ++KA
Sbjct: 409 CAISPSQSCKSETFSTLRFAQRAKAIKNKAVVNEVMQDDVNFLREVIRQLRDELQRVKA 467
>gnl|CDD|238670 cd01374, KISc_CENP_E, Kinesin motor domain, CENP-E/KIP2-like
subgroup, involved in chromosome movement and/or spindle
elongation during mitosis. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type). N-type kinesins are (+) end-directed motors,
i.e. they transport cargo towards the (+) end of the
microtubule. Kinesin motor domains hydrolyze ATP at a
rate of about 80 per second, and move along the
microtubule at a speed of about 6400 Angstroms per
second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 321
Score = 122 bits (307), Expect = 1e-32
Identities = 48/88 (54%), Positives = 65/88 (73%), Gaps = 2/88 (2%)
Query: 57 SITGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTI 116
+ G+R KEG+ INKSL+TLG+VIS L+E K S IPYRDS LT +L+ SL GN++T
Sbjct: 236 TGAGERRKEGSFINKSLLTLGTVISKLSE--GKNSGHIPYRDSKLTRILQPSLSGNARTA 293
Query: 117 MIAAISPADVNYSETLSTLRYANRAKNI 144
+I ISPA + ETL+TL++A+RAK +
Sbjct: 294 IICTISPASSHVEETLNTLKFASRAKKV 321
>gnl|CDD|227392 COG5059, KIP1, Kinesin-like protein [Cytoskeleton].
Length = 568
Score = 122 bits (307), Expect = 2e-31
Identities = 65/184 (35%), Positives = 95/184 (51%), Gaps = 15/184 (8%)
Query: 60 GDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMIA 119
G RLKEGA INKSL+TLG+VI++L KKS IPYR+S LT LL+DSLGGN T +I
Sbjct: 254 GTRLKEGASINKSLLTLGNVINAL--GDKKKSGHIPYRESKLTRLLQDSLGGNCNTRVIC 311
Query: 120 AISPADVNYSETLSTLRYANRAKNIINKPTVNEDPNTRIIRELH----------DEITKL 169
ISP+ ++ ET++TL++A+RAK+I NK VN ++ RE+ EI L
Sbjct: 312 TISPSSNSFEETINTLKFASRAKSIKNKIQVNS--SSDSSREIEEIKFDLSEDRSEIEIL 369
Query: 170 KAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKIL 229
S S + + + Q + + + + + T E + +E
Sbjct: 370 VFREQSQLSQS-SLSGIFAYMQSLKKETETLKSRIDLIMKSIISGTFERKKLLKEEGWKY 428
Query: 230 QEQQ 233
+
Sbjct: 429 KSTL 432
>gnl|CDD|238665 cd01369, KISc_KHC_KIF5, Kinesin motor domain, kinesin heavy chain
(KHC) or KIF5-like subgroup. Members of this group have
been associated with organelle transport. This catalytic
(head) domain has ATPase activity and belongs to the
larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 325
Score = 118 bits (298), Expect = 2e-31
Identities = 49/85 (57%), Positives = 60/85 (70%), Gaps = 3/85 (3%)
Query: 60 GDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMIA 119
G L+E INKSL LG+VI++L + KST IPYRDS LT +L+DSLGGNS+T +I
Sbjct: 244 GQTLEEAKKINKSLSALGNVINALTD---GKSTHIPYRDSKLTRILQDSLGGNSRTTLII 300
Query: 120 AISPADVNYSETLSTLRYANRAKNI 144
SP+ N SETLSTLR+ RAK I
Sbjct: 301 CCSPSSYNESETLSTLRFGARAKTI 325
>gnl|CDD|238669 cd01373, KISc_KLP2_like, Kinesin motor domain, KLP2-like subgroup.
Members of this subgroup seem to play a role in mitosis
and meiosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 337
Score = 117 bits (295), Expect = 7e-31
Identities = 49/86 (56%), Positives = 64/86 (74%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
G RLKE +INKSL TLG VI +L +++ K +PYRDS LT+LL+DSLGGN+KT +I
Sbjct: 252 EGVRLKEAKNINKSLSTLGHVIMALVDVAHGKQRHVPYRDSKLTFLLRDSLGGNAKTTII 311
Query: 119 AAISPADVNYSETLSTLRYANRAKNI 144
A +SP+ + ETLSTL++A RAK I
Sbjct: 312 ANVSPSSKCFGETLSTLKFAQRAKLI 337
>gnl|CDD|238663 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
KIF2 is a protein expressed in neurons, which has been
associated with axonal transport and neuron development;
alternative splice forms have been implicated in
lysosomal translocation. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In this
subgroup the motor domain is found in the middle
(M-type) of the protein chain. M-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second (KIF2 may be slower). To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 322
Score = 100 bits (250), Expect = 2e-24
Identities = 41/82 (50%), Positives = 52/82 (63%), Gaps = 4/82 (4%)
Query: 61 DRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMIAA 120
KEGA INKSL+ L I +LA +P+R S LT +L+DS GNSKT+MIA
Sbjct: 245 QTRKEGAEINKSLLALKECIRALA----SNKAHVPFRGSKLTQVLRDSFIGNSKTVMIAT 300
Query: 121 ISPADVNYSETLSTLRYANRAK 142
ISP+ + TL+TLRYA+R K
Sbjct: 301 ISPSASSCEHTLNTLRYADRVK 322
>gnl|CDD|238671 cd01375, KISc_KIF9_like, Kinesin motor domain, KIF9-like subgroup;
might play a role in cell shape remodeling. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 334
Score = 90.2 bits (224), Expect = 7e-21
Identities = 44/85 (51%), Positives = 57/85 (67%), Gaps = 3/85 (3%)
Query: 58 ITGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIM 117
++G LKE +INKSL L VI++L+E K T +PYR+S LT +L+DSLGGN KT+M
Sbjct: 253 VSGQVLKEAKYINKSLSFLEQVINALSE---KARTHVPYRNSKLTHVLRDSLGGNCKTVM 309
Query: 118 IAAISPADVNYSETLSTLRYANRAK 142
+A I N ETLSTLR+A R
Sbjct: 310 LATIWVEPSNLDETLSTLRFAQRVA 334
>gnl|CDD|238672 cd01376, KISc_KID_like, Kinesin motor domain, KIF22/Kid-like
subgroup. Members of this group might play a role in
regulating chromosomal movement along microtubules in
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 319
Score = 88.3 bits (219), Expect = 3e-20
Identities = 43/84 (51%), Positives = 54/84 (64%), Gaps = 4/84 (4%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMI 118
G RLKE A IN SL L V+ +L K IPYR+S LT LL+DSLGG S+ IM+
Sbjct: 240 EGIRLKESAAINSSLFVLSKVVDAL----NKGLPRIPYRESKLTRLLQDSLGGGSRCIMV 295
Query: 119 AAISPADVNYSETLSTLRYANRAK 142
A I+P Y +TLSTL +A+R+K
Sbjct: 296 ANIAPERSFYQDTLSTLNFASRSK 319
>gnl|CDD|238659 cd01363, Motor_domain, Myosin and Kinesin motor domain. These
ATPases belong to the P-loop NTPase family and provide
the driving force in myosin and kinesin mediated
processes.
Length = 186
Score = 85.3 bits (211), Expect = 4e-20
Identities = 41/69 (59%), Positives = 52/69 (75%), Gaps = 4/69 (5%)
Query: 55 FYSITGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSK 114
F G RL E A+INKSL TLG+VIS+LAE + + +PYR+S LT LL+DSLGGNS+
Sbjct: 122 FSGAEGSRLTETANINKSLSTLGNVISALAE----RDSHVPYRESKLTRLLQDSLGGNSR 177
Query: 115 TIMIAAISP 123
T+M+A ISP
Sbjct: 178 TLMVACISP 186
>gnl|CDD|238664 cd01368, KISc_KIF23_like, Kinesin motor domain, KIF23-like
subgroup. Members of this group may play a role in
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 345
Score = 78.6 bits (194), Expect = 1e-16
Identities = 36/86 (41%), Positives = 51/86 (59%), Gaps = 2/86 (2%)
Query: 59 TGDRLKEGAHINKSLVTLGSVISSLAE--LSTKKSTFIPYRDSVLTWLLKDSLGGNSKTI 116
TG+RLKE +IN SL+TLG I L E LS + +PYRDS LT L ++ G K
Sbjct: 260 TGERLKEAGNINTSLMTLGKCIEVLRENQLSGSTNKMVPYRDSKLTHLFQNYFDGEGKAR 319
Query: 117 MIAAISPADVNYSETLSTLRYANRAK 142
MI ++P +Y ETL ++++ A+
Sbjct: 320 MIVNVNPCASDYDETLHVMKFSAIAQ 345
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 35.6 bits (82), Expect = 0.030
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 155 NTRIIRELHDEITKLKAMLTSVKVNSVA--RQQLLSKAQQTQGNQPQMLAALQAKQEQEK 212
+ L +EI KLK++L S K +A R L + Q + LA L++K E EK
Sbjct: 575 ADKDKEALMEEILKLKSLL-STKREQIATLRTVLKANKQTAEV----ALANLKSKYENEK 629
Query: 213 VLTEEWAEKWRETQKILQEQQA 234
+ E K R K L+E A
Sbjct: 630 AMVTETMMKLRNELKALKEDAA 651
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 34.8 bits (80), Expect = 0.046
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 183 RQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQ 233
RQQ K+ + Q + QA++ Q+K E+ K E +++ ++Q
Sbjct: 66 RQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQ 116
Score = 28.2 bits (63), Expect = 5.6
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 177 KVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQA 234
++ + +++L ++ Q+ Q + AAL+ KQ EE A K K E +A
Sbjct: 102 RLKQLEKERLAAQEQKKQAEEAAKQAALKQKQA------EEAAAKAAAAAKAKAEAEA 153
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 34.4 bits (79), Expect = 0.079
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 159 IRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEW 218
+ EL EI +L+ L ++ ++LL K + + + L L+ K E+ + EE
Sbjct: 293 LEELEREIEELEEELEGLRALLEELEELLEKLKSLE----ERLEKLEEKLEKLESELEEL 348
Query: 219 AEKWRETQKILQEQQAL 235
AE+ E K+L+E+
Sbjct: 349 AEEKNELAKLLEERLKE 365
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 31.8 bits (73), Expect = 0.37
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 164 DEITKLKAMLTSVKVNSVARQQLLSK------AQQTQGNQPQMLAA--LQAKQEQEKVLT 215
+E+ +L L + KVN Q+ K ++ + +M+ L+A E+E+
Sbjct: 4 EELRELNEKLRAAKVNKERDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERER 63
Query: 216 EEWAEKWRETQKILQEQ 232
+ E+ RE + +LQEQ
Sbjct: 64 KRKEER-REGRAVLQEQ 79
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 32.0 bits (73), Expect = 0.39
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 182 ARQQLLSKAQQTQGNQPQMLAALQAKQEQEK-VLTEEWAEKWRETQKILQEQQA 234
ARQ+ +++ +QT+ A L+ KQ Q+K +L E+ A++ QK+ Q +
Sbjct: 167 ARQETIAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQ----QKLEQARNE 216
>gnl|CDD|172948 PRK14473, PRK14473, F0F1 ATP synthase subunit B; Provisional.
Length = 164
Score = 30.7 bits (69), Expect = 0.48
Identities = 27/96 (28%), Positives = 51/96 (53%), Gaps = 10/96 (10%)
Query: 147 KPTVNE-DPNTRIIRELHDEITKLKAMLTSVKVN-----SVARQQ---LLSKAQQTQGNQ 197
+P +N + TR I E + K++ L + K + + ARQ+ ++++AQ+ Q
Sbjct: 31 RPVLNLLNERTRRIEESLRDAEKVREQLANAKRDYEAELAKARQEAAKIVAQAQERARAQ 90
Query: 198 PQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQ 233
+ A QA++E EK+ E A+ +E Q++L E +
Sbjct: 91 EAEIIA-QARREAEKIKEEARAQAEQERQRMLSELK 125
>gnl|CDD|184696 PRK14474, PRK14474, F0F1 ATP synthase subunit B; Provisional.
Length = 250
Score = 30.9 bits (70), Expect = 0.57
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 185 QLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQALGLRMGKDGT 244
Q++ K QQ N+ Q Q + QE AE++R+ Q+ L++Q+A + ++
Sbjct: 32 QVMKKRQQRIANRWQDAEQRQQEAGQE-------AERYRQKQQSLEQQRASFMAQAQEAA 84
Query: 245 GVVLDSDRPHLV 256
D R HL+
Sbjct: 85 ----DEQRQHLL 92
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 31.1 bits (70), Expect = 0.67
Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 159 IRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQA-----KQEQEKV 213
+ + +E L+ ++ S+K ++ L + ++ +G + ++L+A K E+E
Sbjct: 268 LEKAAEEEKSLRNLVESLKQELEEEKKELEELREKEGEAEEAASSLEAELNRTKSEKESK 327
Query: 214 LTEEWAEKWRETQKILQE 231
E+ E + Q+ E
Sbjct: 328 AREKMVEIPLKLQQASSE 345
>gnl|CDD|226055 COG3524, KpsE, Capsule polysaccharide export protein [Cell envelope
biogenesis, outer membrane].
Length = 372
Score = 30.2 bits (68), Expect = 1.2
Identities = 28/125 (22%), Positives = 49/125 (39%), Gaps = 20/125 (16%)
Query: 115 TIMIA--AISPADVNYSETLSTLRYANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAM 172
T+ A + A+ + + L R KN + P + ++ +L DE+ ++A
Sbjct: 180 TVRFAEEEVQKAEERVKKASNDLT-DYRIKNGVFDPKAQAEVQMSLVSKLEDELIVIQAQ 238
Query: 173 LTSVK----------------VNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE 216
L +VK + S+ R+QLL + Q + QA + Q L
Sbjct: 239 LDTVKSVMNPENPQIPGLKARIESL-RKQLLQEKQAISAGGSSQSLSNQAAEFQRLYLEN 297
Query: 217 EWAEK 221
+AEK
Sbjct: 298 TFAEK 302
>gnl|CDD|213755 TIGR02977, phageshock_pspA, phage shock protein A. Members of this
family are the phage shock protein PspA, from the phage
shock operon. This is a narrower family than the set of
PspA and its homologs, sometimes several in a genome, as
described by pfam04012. PspA appears to maintain the
protonmotive force under stress conditions that include
overexpression of certain phage secretins, heat shock,
ethanol, and protein export defects [Cellular processes,
Adaptations to atypical conditions].
Length = 219
Score = 29.9 bits (68), Expect = 1.2
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 159 IRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQE 211
+ +L ++I KL+A L + ARQ+ L+ Q ++ + L + + E
Sbjct: 115 LAKLQEDIAKLQAKLAEAR----ARQKALAIRHQAASSRLDVRRQLDSGRSDE 163
>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 = 30.4 bits (69), Expect = 1.3
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 168 KLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQK 227
KL+ + K A QL Q + Q A L+A ++ + L E KW+ +
Sbjct: 671 KLELAIAERK--QQAETQLRQLDAQLKQLLEQQQAFLEALKDDFRELRTERLAKWQVVEG 728
Query: 228 ILQEQQAL 235
L Q A
Sbjct: 729 ELDNQLAQ 736
Score = 29.7 bits (67), Expect = 2.2
Identities = 21/126 (16%), Positives = 46/126 (36%), Gaps = 25/126 (19%)
Query: 159 IRELHDEITKLKAM---LTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLT 215
I +L ++ +L ++ L + VA ++ L++ Q+ + A ++Q + L
Sbjct: 248 IEKLQEDFEQLLSLELRLQHLHGELVADEERLAEEQE------ERQEAKNRLRQQLRTLE 301
Query: 216 EEWAEKWRETQKILQEQQALGLRMGKDGTGVVLDSDRPHLVRIDDDLYSTGVTLYDSVLP 275
++ E E + L A L +DR L ++D D+ +
Sbjct: 302 DQLKEARDELNQELSAANAK------------LAADRSELELLEDQKG----AFEDADIE 345
Query: 276 SFALHM 281
+
Sbjct: 346 QLQADL 351
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 30.3 bits (68), Expect = 1.3
Identities = 26/117 (22%), Positives = 48/117 (41%), Gaps = 18/117 (15%)
Query: 137 YANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAMLTSVKVNSVARQ-------QLLSK 189
A + +N + DPNT+++R+ L+ M+ ++ ++AR QLLS+
Sbjct: 543 LAQQLRNNPQQLARPLDPNTKVLRQ-----QDLQNMMD--QIENLARSGDRDQAKQLLSQ 595
Query: 190 AQQTQGN----QPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQALGLRMGKD 242
QQ N QP + + + + E R+ Q++ E L +D
Sbjct: 596 LQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQRRD 652
>gnl|CDD|203394 pfam06133, DUF964, Protein of unknown function (DUF964). This
family consists of several relatively short bacterial
and archaeal hypothetical sequences. The function of
this family is unknown.
Length = 108
Score = 28.6 bits (65), Expect = 1.5
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 157 RIIRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE 216
+ IRE +E K ++K + A Q+L+ + Q+ Q +Q KQ K + +
Sbjct: 11 KAIRES-EEYKAYKEAKAAIKADEEA-QKLIDEFQKLQ-------EEIQEKQMFGKEIPK 61
Query: 217 EWAEKWRETQKILQE 231
E +K +E ++ +
Sbjct: 62 EVQQKIQELKREIDL 76
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 29.9 bits (67), Expect = 1.5
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 79 VISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKTIMIAAISPADV 126
+I + LS K+ +RD+V+T L+ +S + I +AA AD+
Sbjct: 373 IIDPMQPLSFKQEEDTEFRDTVVTLLIDNSGSMRGRPITVAATC-ADI 419
>gnl|CDD|165307 PHA03006, PHA03006, hypothetical protein; Provisional.
Length = 323
Score = 29.6 bits (66), Expect = 2.1
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 140 RAKNIINKPTVNEDP-----NTRIIRELHDEITKLKAMLTSVKVNSVARQQLLSK 189
+ KN+IN+ +DP T II++L DE +LK ++ S +L+ K
Sbjct: 135 KLKNVINQFEKKQDPIKDLSKTEIIKKLKDENKELKKKQKKME-KSENLNELIKK 188
>gnl|CDD|233933 TIGR02568, LcrE, type III secretion regulator YopN/LcrE/InvE/MxiC.
This protein is found in type III secretion operons and,
in Yersinia is localized to the cell surface and is
involved in the Low-Calicium Response (LCR), possibly by
sensing the calcium concentration. In Salmonella, the
gene is known as InvE and is believed to perform an
essential role in the secretion process and interacts
with the proteins SipBCD and SicA.//Altered name to
reflect regulatory role. Added GO and role IDs. Negative
regulation of type III secretion in Y pestis is mediated
in part by a multiprotein complex that has been proposed
to act as a physical impediment to type III secretion by
blocking the entrance to the secretion apparatus prior
to contact with mammalian cells. This complex is
composed of YopN, its heterodimeric secretion chaperone
SycN-YscB, and TyeA. PMID: 15701523[SS 6/3/05] [Protein
fate, Protein and peptide secretion and trafficking,
Cellular processes, Pathogenesis].
Length = 240
Score = 29.3 bits (66), Expect = 2.3
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 2/77 (2%)
Query: 168 KLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRET-Q 226
KLK + + + +QLL+ A+ + AL+A Q L + E Q
Sbjct: 63 KLKELRAELSGQAAGLEQLLALARGAFPDPSDQALALRAAL-QRLELDPAERKALEEAAQ 121
Query: 227 KILQEQQALGLRMGKDG 243
+L+ + +R G +
Sbjct: 122 ALLELEDGPTIRAGINT 138
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 29.3 bits (66), Expect = 2.3
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 12/65 (18%)
Query: 182 ARQQLLSKAQQTQGNQP--QMLAALQAKQEQEKVLTEEWAEKWRETQKIL----QEQQAL 235
+QQ QT N L ALQ QE +K +E ++ K L ++Q AL
Sbjct: 58 GKQQA---QNQTATNDALANQLTALQKAQESQK---QELEGILKQQAKALDQANRQQAAL 111
Query: 236 GLRMG 240
++
Sbjct: 112 AKQLD 116
>gnl|CDD|219330 pfam07201, HrpJ, HrpJ-like domain. This family represents a
conserved region approximately 200 residues long within
a number of bacterial hypersensitivity response
secretion protein HrpJ and similar proteins. HrpJ forms
part of a type III secretion system through which, in
phytopathogenic bacterial species, virulence factors are
thought to be delivered to plant cells. This family also
includes the InvE invasion protein from Salmonella. This
protein is involved in host parasite interactions and
mutations in the InvE gene render Salmonella typhimurium
non-invasive. InvE S. typhimurium mutants fail to elicit
a rapid Ca2+ increase in cultured cells, an important
event in the infection procedure and internalisation of
S. typhimurium into epithelial cells. This family
includes bacterial SepL and SsaL proteins. SepL plays an
essential role in the infection process of
enterohemorrhagic Escherichia coli and is thought to be
responsible for the secretion of EspA, EspD, and EspB.
SsaL of Salmonella typhimurium is thought to be a
component of the type III secretion system.
Length = 161
Score = 28.5 bits (64), Expect = 2.4
Identities = 25/121 (20%), Positives = 46/121 (38%), Gaps = 9/121 (7%)
Query: 160 RELHDE-ITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEW 218
R L E KL+ + +K + QLL+ + + AL+A +Q + L
Sbjct: 34 RVLDLEAEEKLRELRQLLKSGRSSLPQLLAYLESLFPDPSDQDLALRALLQQARPLKRAL 93
Query: 219 AEKWRETQKILQEQQALGLRMGKDGTGV-----VLDSDRPHLVRIDDDLYSTGVTLYDSV 273
E + + L+++ +R G + +D +R DLY V+ S+
Sbjct: 94 KELLEQALEQLEQEDGKAIRAGINIALAAALFSQVDPGSLQALR---DLYRQAVSGDQSL 150
Query: 274 L 274
Sbjct: 151 S 151
>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO. This family
contains the bacterial type III secretion protein YscO,
which is approximately 150 residues long. YscO has been
shown to be required for high-level expression and
secretion of the anti-host proteins V antigen and Yops
in Yersinia pestis.
Length = 152
Score = 28.2 bits (63), Expect = 2.8
Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 15/78 (19%)
Query: 165 EITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE-------- 216
E+ K + + ++ N + +Q L++A+Q ++ A Q ++ + L E
Sbjct: 68 ELEKWQQQVGLLRENEASLEQQLAEAKQ------RLEAERQRLRQARQQLQEARKAQEKF 121
Query: 217 -EWAEKWRETQKILQEQQ 233
E A + + + ++
Sbjct: 122 AELARQEQAEAQAQRQYL 139
>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 548
Score = 29.0 bits (65), Expect = 2.8
Identities = 16/86 (18%), Positives = 26/86 (30%), Gaps = 12/86 (13%)
Query: 149 TVNEDPNTRIIRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQ 208
+ T I + KL + V +Q A+QT+ + +
Sbjct: 227 ENEAEKETEIAIAEANRDAKLVELE-------VEQQPAGKTAEQTREVKIILAETEAEVA 279
Query: 209 EQEKVLTEEWAEKWRETQKILQEQQA 234
+ E E E +IL EQ
Sbjct: 280 AWKA---ETRREA--EQAEILAEQAI 300
>gnl|CDD|180482 PRK06233, PRK06233, hypothetical protein; Provisional.
Length = 372
Score = 28.9 bits (65), Expect = 2.9
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 13/79 (16%)
Query: 165 EITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRE 224
E T+ KA V S R + L +A++ A + Q+Q + E
Sbjct: 1 ETTQTKAPFRFDIVGSFLRPERLKEAREQ-------FAIGEISQDQLLKIQHA------E 47
Query: 225 TQKILQEQQALGLRMGKDG 243
+++++EQ LGL+ DG
Sbjct: 48 IKRLVKEQVELGLKAVTDG 66
>gnl|CDD|221452 pfam12168, DNA_pol3_tau_4, DNA polymerase III subunits tau domain
IV DnaB-binding. This domain family is found in
bacteria, and is approximately 80 amino acids in length.
The family is found in association with pfam00004.
Domains I-III are shared between the tau and the gamma
subunits, while most of the DnaB-binding Domain IV and
all of the alpha-interacting Domain V are unique to tau.
Length = 80
Score = 27.0 bits (60), Expect = 2.9
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 190 AQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQE 231
A T+ QP+ A ++ ++K E + +WR TQ + +E
Sbjct: 33 ASVTERVQPRQAAKSAEQKPKKK---EAY--RWRPTQPVEKE 69
>gnl|CDD|237467 PRK13676, PRK13676, hypothetical protein; Provisional.
Length = 114
Score = 27.6 bits (62), Expect = 3.2
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 19/90 (21%)
Query: 157 RIIRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE 216
R +REL E LK +VK + A ++L + + Q +Q KQ + +TE
Sbjct: 14 RALREL-PEYKALKEAKEAVKADEEA-KKLFDEFRALQLE-------IQQKQMTGQEITE 64
Query: 217 EWAEKWRET-QKI---------LQEQQALG 236
E +K +E QKI ++ +Q L
Sbjct: 65 EEQQKAQELGQKIQQNELLSKLMEAEQRLS 94
>gnl|CDD|218559 pfam05335, DUF745, Protein of unknown function (DUF745). This
family consists of several uncharacterized Drosophila
melanogaster proteins of unknown function.
Length = 188
Score = 28.4 bits (64), Expect = 3.3
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 169 LKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQE 209
LKA+L + + N +Q+ S AQQ + Q+L A + + E
Sbjct: 114 LKALLKNAQANLENIEQVASGAQQELAEKTQLLEAAKRRVE 154
>gnl|CDD|216225 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins
involved in steps 4 and 6 of the histidine biosynthesis
pathway are contained in this family. Histidine is
formed by several complex and distinct biochemical
reactions catalyzed by eight enzymes. The enzymes in
this Pfam entry are called His6 and His7 in eukaryotes
and HisA and HisF in prokaryotes. The structure of HisA
is known to be a TIM barrel fold. In some archaeal HisA
proteins the TIM barrel is composed of two tandem
repeats of a half barrel . This family belong to the
common phosphate binding site TIM barrel family.
Length = 230
Score = 28.6 bits (65), Expect = 3.3
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 10/95 (10%)
Query: 159 IRELHDEITKLKAMLTSVKVNSVA--RQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE 216
IR L D L A V + + A +L+ +A + G+Q ++ A+ AK+E KV
Sbjct: 82 IRSLEDAERLLSAGADKVIIGTAAVKNPELIKEAAEKFGSQ-CIVVAIDAKREDGKVAIN 140
Query: 217 EWAEKW-RETQKILQEQQALGLR------MGKDGT 244
W E+ + + ++ + LG + +DGT
Sbjct: 141 GWREETGIDAVEWAKKLEELGAGEILLTDIDRDGT 175
>gnl|CDD|150787 pfam10154, DUF2362, Uncharacterized conserved protein (DUF2362).
This is a family of proteins conserved from nematodes to
humans. The function is not known.
Length = 501
Score = 29.0 bits (65), Expect = 3.3
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 7/93 (7%)
Query: 125 DVNYSETLSTL-----RYANRAKNIINKPTVN-EDPNTRIIRELHDEITKLKAMLTSVKV 178
+ +S L TL Y +I + + N E++ ++ +L LT V
Sbjct: 99 QLIHSPALETLLNLEHNYFKSISELIQERDSEVKKLNELQQSEMNKQMQELGKSLTDQDV 158
Query: 179 NSVARQQLLSKAQQTQGNQPQMLAALQAKQEQE 211
N++A Q + L L Q+QE
Sbjct: 159 NNLAAQH-NENQNSIEKKYSSELEQLSGIQKQE 190
>gnl|CDD|224755 COG1842, PspA, Phage shock protein A (IM30), suppresses
sigma54-dependent transcription [Transcription / Signal
transduction mechanisms].
Length = 225
Score = 28.4 bits (64), Expect = 3.9
Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 8/97 (8%)
Query: 151 NEDPNTRI---IRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGN-QPQMLAALQA 206
EDP + IR++ E+ K + L ++ L +AQ + + ALQA
Sbjct: 22 AEDPEKMLEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQARAEKLEEKAELALQA 81
Query: 207 KQEQ--EKVLTEE--WAEKWRETQKILQEQQALGLRM 239
E + L E+ + + + LQ+ + ++
Sbjct: 82 GNEDLAREALEEKQSLEDLAKALEAELQQAEEQVEKL 118
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 28.7 bits (65), Expect = 3.9
Identities = 24/124 (19%), Positives = 39/124 (31%), Gaps = 22/124 (17%)
Query: 120 AISPADVNYSETLSTLRYANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAMLTSVKVN 179
A+ A+ E L + K K + + EL DE+ +LK +L
Sbjct: 93 ALLQAENALPEWKKELEKPSEPKEEEPKAAAESKVVQKELDELRDELKELKNLLEDQL-- 150
Query: 180 SVARQQLLSKAQQTQGNQPQMLAALQAK-QEQE----------KVLTEEWAEKWRETQKI 228
S +Q + P A L + + K+L E + R +
Sbjct: 151 --------SGLRQVE-RIPPEFAELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRY 201
Query: 229 LQEQ 232
L E
Sbjct: 202 LLEL 205
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 28.5 bits (63), Expect = 4.2
Identities = 40/159 (25%), Positives = 68/159 (42%), Gaps = 13/159 (8%)
Query: 67 AHINKSLVTLGSVISSLAELSTKKS--TFIPYRDSVLTWLLKDSLGGNSKTIMIAAISPA 124
+ N LV G+V S+L S +S F YR S + K +I +SP
Sbjct: 78 QYENHGLVPDGAVCSNLPYASWFESFCQFAKYRCSNHVYYAKRVPCSQPVSI----LSPN 133
Query: 125 DVNYSETLSTLRYANRAKNIINKPTVNEDPNTRII-RELHDEITK-LKAMLTS-----VK 177
+ +E + ++ I PT+ E+ + + LH+ + + L++ L+ VK
Sbjct: 134 TLKEAEPSAEVQPTTMTLPIAEHPTITENQSFQPWPERLHNNVEELLQSSLSLGGSVQVK 193
Query: 178 VNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTE 216
++QLLSK Q+ Q +QE+E+V E
Sbjct: 194 APKPKQEQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEE 232
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 28.5 bits (64), Expect = 4.3
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 159 IRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGN-QPQMLAALQAKQEQEKV---- 213
I+ L ++ +LK M+ ++ S +++L SK ++ ++ + K+++EK
Sbjct: 286 IKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQI 345
Query: 214 -LTEEWAEKWRETQKILQE---QQALG 236
EE EK E Q +E ALG
Sbjct: 346 ERLEERIEKL-EVQATDKEENKTVALG 371
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 28.5 bits (64), Expect = 4.6
Identities = 15/106 (14%), Positives = 41/106 (38%), Gaps = 4/106 (3%)
Query: 127 NYSETLSTLRYANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAMLTSVKVNSVARQQL 186
E +S N + I + + +D + +I +E+ +L L +K +
Sbjct: 137 VVQELVSIF---NDLIDSIKEDNLKDDLES-LIASAKEELDQLSKKLAELKAEEEEELER 192
Query: 187 LSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQ 232
K ++ + L + +E L ++ ++ ++ L+++
Sbjct: 193 ALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKEELRKK 238
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 27.7 bits (62), Expect = 4.6
Identities = 7/52 (13%), Positives = 22/52 (42%)
Query: 188 SKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQALGLRM 239
+K + + + ++E+E+ + AE +E ++ +++ L
Sbjct: 68 AKEKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKAEAKLMK 119
>gnl|CDD|220450 pfam09869, DUF2096, Uncharacterized protein conserved in archaea
(DUF2096). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 169
Score = 27.8 bits (62), Expect = 4.9
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 130 ETLSTLRYANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAML 173
E + LR A I+N ++ N +R+ E+ +++ +L
Sbjct: 25 EVIEKLRLAR---AILNFYLLDPHANFEELRDAEKELNRVQEIL 65
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.5 bits (64), Expect = 4.9
Identities = 10/54 (18%), Positives = 24/54 (44%)
Query: 182 ARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQAL 235
AR + + + T + A + A+Q + L E + + ++L+E++
Sbjct: 158 ARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKT 211
>gnl|CDD|239482 cd03388, PAP2_SPPase1, PAP2_like proteins,
sphingosine-1-phosphatase subfamily.
Sphingosine-1-phosphatase is an intracellular enzyme
located in the endoplasmic reticulum, which regulates
the level of sphingosine-1-phosphate (S1P), a bioactive
lipid. S1P acts as a second messenger in the cell, and
extracellularly by binding to G-protein coupled
receptors of the endothelial differentiation gene
family.
Length = 151
Score = 27.6 bits (62), Expect = 5.5
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 19 FPWFVSGWVT-----IWSHGDFWGQYLKGLF 44
W +V + + G + GQ++K LF
Sbjct: 26 LFWNGDPYVGRDLVVVLALGMYIGQFIKDLF 56
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 26.8 bits (60), Expect = 6.0
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 183 RQQLLSKAQQTQGNQPQMLAALQAKQEQE--------KVLTEE 217
R++L +Q Q Q +A+ + E ++LT E
Sbjct: 8 RRKLEELQKQAQEQQQAQEEQEEAQAQAEAQKQAILRQILTPE 50
>gnl|CDD|150081 pfam09293, RNaseH_C, T4 RNase H, C terminal. Members of this
family are found in T4 RNaseH ribonuclease, and adopt a
SAM domain-like fold, consisting of a bundle of
four/five helices. These residues may have a role in
providing a docking site for other proteins or enzymes
in the replication fork.
Length = 122
Score = 27.0 bits (60), Expect = 6.4
Identities = 8/37 (21%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 197 QPQM----LAALQAKQEQEKVLTEEWAEKWRETQKIL 229
P + L A+ +++ + +LTEE ++ E ++++
Sbjct: 39 APSIRTKELEAIFDREDPKVLLTEEEYARYDENRELI 75
>gnl|CDD|213711 TIGR02453, TIGR02453, TIGR02453 family protein. Members of this
family are widely (though sparsely) distributed
bacterial proteins about 230 residues in length. All
members have a motif RxxRDxRFxxx[DN]KxxY. The function
of this protein family is unknown. In several fungi,
this model identifies a conserved region of a longer
protein. Therefore, it may be incorrect to speculate
that all members share a common function.
Length = 217
Score = 27.7 bits (62), Expect = 6.9
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 74 VTLGSVISSLAELSTKKSTFIPYRDS 99
L + L + K S F YRD
Sbjct: 45 ARLAKISPELRGDAKKGSLFRIYRDV 70
>gnl|CDD|225664 COG3122, COG3122, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 27.6 bits (61), Expect = 7.1
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 12/65 (18%)
Query: 172 MLTSVKVNS--VARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKIL 229
+L + V S A+ Q L+K + + +AA + K EQ + R+ Q
Sbjct: 49 LLKAGLVTSKKRAKVQRLAKKSRVDAREAYRIAAEENKAEQLE----------RDKQLSE 98
Query: 230 QEQQA 234
Q++QA
Sbjct: 99 QQKQA 103
>gnl|CDD|215974 pfam00529, HlyD, HlyD family secretion protein.
Length = 304
Score = 27.8 bits (62), Expect = 7.2
Identities = 19/95 (20%), Positives = 30/95 (31%), Gaps = 6/95 (6%)
Query: 173 LTSVKVNSVARQQLLSKAQQTQGN-----QPQMLAALQAKQEQEKVLTEEWAEKWRETQK 227
L S + +Q T G Q Q LAA E L + AE R +
Sbjct: 113 LRSALALLPISLGRIGASQATLGALLNNLQAQGLAARAQLDEAYLQLAQTAAELLRLIRA 172
Query: 228 ILQ-EQQALGLRMGKDGTGVVLDSDRPHLVRIDDD 261
Q E+ ++ G + P + + +
Sbjct: 173 PAQGERVQSEAQLRSVQVGEEVGVGSPLMGVVPFN 207
>gnl|CDD|222882 PHA02567, rnh, RnaseH; Provisional.
Length = 304
Score = 27.7 bits (62), Expect = 7.3
Identities = 9/37 (24%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 197 QPQM----LAALQAKQEQEKVLTEEWAEKWRETQKIL 229
P + L A+ ++ + +LTEE E++ E ++++
Sbjct: 221 APSISTKELEAIADAEDPKVLLTEEEYERYDENRELI 257
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 27.4 bits (61), Expect = 7.4
Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 157 RIIRELHDEITKLKAMLTSVKVN-------SVARQQLLSKAQQTQGNQPQMLAALQAKQE 209
++I E H + +++ L + + R+Q L +A Q Q +E
Sbjct: 65 QLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRDADDLEQWLEE 124
Query: 210 QEKVL-TEEWAEKWRETQKILQEQQAL 235
+E L +E+ + +++L++ + L
Sbjct: 125 KEAALASEDLGKDLESVEELLKKHKEL 151
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 27.7 bits (62), Expect = 7.7
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 13/78 (16%)
Query: 158 IIRELHDEITKLKAMLTSVKVNSVA-RQQLLSKAQQTQGNQPQMLAALQA---------- 206
I+ L + +L+A L ++K + ++ K Q+ + Q + L ALQ+
Sbjct: 172 AIKNLAARLQQLQAELDNLKSDEANLEAKIERKKQELERTQ-KRLQALQSVRPAFMEEYE 230
Query: 207 KQEQE-KVLTEEWAEKWR 223
K E+E + L + + EK+R
Sbjct: 231 KLEEELQKLYQTYFEKFR 248
>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 = 27.4 bits (61), Expect = 7.9
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 169 LKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQK 227
L+A LT + +A +Q SK QQ + + + + QEQ ++ EK E +K
Sbjct: 1 LEAELTELIS-KLAEKQAKSKLQQLERARDKQEKKAEEYQEQ----IKKAIEKAEEAKK 54
>gnl|CDD|219540 pfam07730, HisKA_3, Histidine kinase. This is the dimerisation and
phosphoacceptor domain of a sub-family of histidine
kinases. It shares sequence similarity with pfam00512
and pfam07536.
Length = 64
Score = 25.7 bits (57), Expect = 8.3
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 156 TRIIRELHDEI--------TKLKAMLTSVKVNSVARQQLLSKAQQT 193
RI RELHD + +L+ + + ++ L + ++
Sbjct: 3 ARIARELHDSVGQSLSAIKLQLELARRLLARDPEEAREQLDEIREL 48
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 27.6 bits (61), Expect = 8.4
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 184 QQLLSKAQQTQGNQPQMLAAL--QAKQEQEKVLTEEWAEKWRETQKILQEQQA 234
+Q+ + + Q + + L L + + QE+ E AEK + ++ QE+QA
Sbjct: 86 EQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQA 138
>gnl|CDD|193562 cd08014, M20_Acy1_like4, M20 Peptidase Aminoacylase 1 subfamily.
Peptidase M20 family, Uncharacterized subfamily of
uncharacterized bacterial proteins predicted as putative
amidohydrolases. These are a class of zinc binding
homodimeric enzymes involved in hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 372
Score = 27.6 bits (62), Expect = 8.5
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 220 EKWRETQKILQEQQALGL--RMGKDGTGVVLD 249
E+ R T I + +A GL R+ GTG++ D
Sbjct: 17 EEHRTTAFIAERLEAAGLKPRLLPAGTGLICD 48
>gnl|CDD|227661 COG5366, COG5366, Protein involved in propagation of M2 dsRNA
satellite of L-A virus [General function prediction
only].
Length = 531
Score = 27.6 bits (61), Expect = 9.1
Identities = 13/69 (18%), Positives = 21/69 (30%), Gaps = 5/69 (7%)
Query: 56 YSITGDRLKEGAHINKSLVTLGSVISSLAELSTKKSTFIPYRDSVLTWLLKDSLGGNSKT 115
+T L +G NK T + +L K+ T YR + W +
Sbjct: 74 NGVTMIWLWDGIGFNKLQGTSSGGLGTLLTSGFKEYTQENYRKAGKLW-----RNFIMQK 128
Query: 116 IMIAAISPA 124
+ S
Sbjct: 129 SEMDVASKI 137
>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
Length = 208
Score = 27.2 bits (61), Expect = 9.5
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 11/51 (21%)
Query: 129 SETLSTLRYANRAKNI-------INKPTVNEDPNTRIIRELHDEITKLKAM 172
+ ++ ++ ANR K+I ++KP +E+ + R L D I++ K
Sbjct: 87 RQIITAIKTANRQKHIPLNSYVSLDKPIYDEESD----RTLLDVISEAKVT 133
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 27.7 bits (61), Expect = 9.6
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 183 RQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWAEKWRETQKILQEQQ 233
Q L + TQ + AAL A Q ++KVL ++ ++ E + ++ +
Sbjct: 679 LQARLERLTHTQSDIAIAKAALDAAQTRQKVLERQYQQEVTECAGLKKDLK 729
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 27.7 bits (61), Expect = 9.6
Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 14/87 (16%)
Query: 160 RELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGNQPQMLAALQAKQEQEKVLTEEWA 219
+EI KL ML S + L +KA++ + + + +Q +VL E+
Sbjct: 152 DARDEEIKKLLEMLQS--------KGLSAKAEEEDSERLGRIREAEDQQSHLEVLLEQK- 202
Query: 220 EKWRETQKI-LQEQQALGLRMGKDGTG 245
E + + L+E+ L+M +D
Sbjct: 203 ----EKEHMMLREEIHQKLQMERDDAK 225
>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 = 27.4 bits (61), Expect = 9.8
Identities = 18/99 (18%), Positives = 33/99 (33%), Gaps = 3/99 (3%)
Query: 137 YANRAKNIINKPTVNEDPNTRIIRELHDEITKLKAMLTSVKVNSVARQQLLSKAQQTQGN 196
N +K + PN+ ++ L + +A L + + Q L+ AQ
Sbjct: 236 SYIADGNKFDKTPIPNTPNS--LKALQAALATAQADLAAAQTALNTAQAALTTAQTAYAA 293
Query: 197 QPQMLAALQAKQEQEKVLTEEWAEK-WRETQKILQEQQA 234
LA Q + + + A+ Q L +A
Sbjct: 294 AQAALATAQKELANAQAQALQTAQNNLATAQAALANAEA 332
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
0.317 0.132 0.387
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,414,590
Number of extensions: 1350696
Number of successful extensions: 1759
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1720
Number of HSP's successfully gapped: 124
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.0 bits)