RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12108
(665 letters)
>gnl|CDD|185767 cd09244, BRO1_Rhophilin, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin and related domains.
This family contains the Bro1-like domain of
RhoA-binding proteins, Rhophilin-1 and -2, and related
domains. It belongs to the BRO1_Alix_like superfamily
which also includes the Bro1-like domains of mammalian
Alix (apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20
(also known as PalA) from Saccharomyces cerevisiae,
Ustilago maydis Rim23 (also known as PalC), and related
domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound
RhoA. Bro1-like domains are boomerang-shaped, and part
of the domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 and -2, contain an N-terminal Rho-binding
domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Their PDZ domains have limited homology.
Rhophilin-1 and -2 have different activities. The
Drosophila knockout of Rhophilin-1 is embryonic lethal,
suggesting an essential role in embryonic development.
Roles of Rhophilin-2 may include limiting stress fiber
formation or increasing the turnover of F-actin in the
absence of high levels of RhoA signaling activity. The
isolated Bro1-like domain of Rhophilin-1 binds human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. This
family lacks the V-shaped (V) domain found in many
members of the BRO1_Alix _like superfamily.
Length = 350
Score = 534 bits (1379), Expect = 0.0
Identities = 220/386 (56%), Positives = 273/386 (70%), Gaps = 37/386 (9%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLL 176
MIPLGLKETKEID EPFKDFILEHYSED + YED +++F D+RQAMRTP+RD +GI LL
Sbjct: 1 MIPLGLKETKEIDFMEPFKDFILEHYSEDPSLYEDEIADFTDLRQAMRTPSRDEAGIELL 60
Query: 177 FQYYNQLYFIERRFFPPDRSLGIYFE-YDSLTGVPSCQRTIAFEKACVLFNMAAIYTQMA 235
F+YYNQLYF+ERRFFPPDRSLGIYF YDSLTGVPS QR++AFEKA VLFN+ A+YTQ+
Sbjct: 61 FEYYNQLYFVERRFFPPDRSLGIYFHWYDSLTGVPSVQRSVAFEKASVLFNIGALYTQIG 120
Query: 236 AKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPSMDLGPPMLDMLIQLMLAQARECL 295
AKQDR T G++ AVD F RAAG F YL+ENF+NAPSMDL P ML+ LI+LMLAQA+EC+
Sbjct: 121 AKQDRTTEEGIEAAVDAFQRAAGAFNYLRENFSNAPSMDLSPEMLEALIKLMLAQAQECV 180
Query: 296 FQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQVKKE 355
F+KL L + D Q L+LAQEAAQV++ Y + L+ VKDY+P SW+SL++VK E
Sbjct: 181 FEKLVLPGEDSKDIQACLDLAQEAAQVSDCYSEVHKLMNQEPVKDYIPYSWISLVEVKSE 240
Query: 356 HYLALSHYYCASGLLTKSLANLSSTAQTVLSYLHIPQENKKNLILEFEPEDESQRKQLGV 415
HY AL+HYY A GLL +R+ LG
Sbjct: 241 HYKALAHYYAAMGLL------------------------------------LEERRLLGK 264
Query: 416 AHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEEDEFNTMYEAP 475
AHL+ ALL HEE+ R++RMCR LRN +L +VL +AH +L Y+ +EEED+F+ +AP
Sbjct: 265 AHLKEALLLHEEALRLHRMCRFLRNVDSLQEVLKEAHDRSLNKYSSLEEEDDFSDALDAP 324
Query: 476 NITPSTKFQLTLTPPDFAHLPVEDLF 501
+I TK QL + PPDF + V+DLF
Sbjct: 325 DIQAKTKQQLEIIPPDFTQVKVKDLF 350
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 399 bits (1026), Expect = e-134
Identities = 184/390 (47%), Positives = 254/390 (65%), Gaps = 11/390 (2%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLL 176
MIPLGLKETKE+D+ P K+ I EH+ EDGT+YE + E D+RQAMRTP+R +G+ LL
Sbjct: 1 MIPLGLKETKELDLPTPLKELISEHFGEDGTSYEAEIRELEDLRQAMRTPSRSEAGLELL 60
Query: 177 FQYYNQLYFIERRFFPPDRSLGIYFE-YDSLTGVPSCQRTIAFEKACVLFNMAAIYTQMA 235
YYNQL F++ RFFPP +SLG++F YDSLTGVP+ QR +AFEK VLFN+ A++TQ+
Sbjct: 61 MAYYNQLCFLDARFFPPAKSLGLFFHWYDSLTGVPAQQRALAFEKGSVLFNIGALHTQIG 120
Query: 236 AKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPSMDLGPPMLDMLIQLMLAQARECL 295
A+QDR + G +A+D F RAAG F+ L+ENF+NAPS D+ L ML QLM+AQA+EC+
Sbjct: 121 ARQDRSCTEGTRRAIDAFQRAAGAFSLLRENFSNAPSPDMSTASLSMLEQLMVAQAQECI 180
Query: 296 FQKL--QLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQVK 353
F+ L L T + DF L+LAQEAAQVA Y + + P V+DYVP SW +L+ VK
Sbjct: 181 FEGLLLPLLATPQ-DFFAQLQLAQEAAQVAAEYRLVHRTMAQPPVRDYVPFSWTALVHVK 239
Query: 354 KEHYLALSHYYCASGLLTKSLANLS--STAQTVLSYLHIPQENKKNLILEFEPEDESQRK 411
EH+ AL+HY+ A L S A+ +T + H Q +L P++ +R+
Sbjct: 240 AEHFCALAHYHAAMALCDSSPASEGELATQEKAFLQPHTSQPEGPSL-----PQEPEERR 294
Query: 412 QLGVAHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEEDEFNTM 471
+LG AHL+ A+L EE+ R++ +CR LR L VL QA +L Y++++ ED+F
Sbjct: 295 KLGKAHLKRAILGQEEALRLHALCRILRKVDLLQAVLTQALRRSLAKYSELDREDDFFET 354
Query: 472 YEAPNITPSTKFQLTLTPPDFAHLPVEDLF 501
EAP+I P T + + P F+ + V D+F
Sbjct: 355 GEAPDIQPKTHQKPEIRAPSFSQVKVTDIF 384
>gnl|CDD|185772 cd09249, BRO1_Rhophilin_2, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-2. This subfamily
contains the Bro1-like domain of RhoA-binding protein,
Rhophilin-2. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-1, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-2, binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-2 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Roles for Rhophilin-2 may include limiting
stress fiber formation or increasing the turnover of
F-actin in the absence of high levels of RhoA signaling
activity. Rhophilin-2 lacks the V-shaped (V) domain
found in many members of the BRO1_Alix_like superfamily.
Length = 385
Score = 381 bits (980), Expect = e-127
Identities = 183/391 (46%), Positives = 260/391 (66%), Gaps = 12/391 (3%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLL 176
+IPLGLKETK++D P KDFILEHYSEDG+ YED +++ MD+RQA RTP+RD +G+ LL
Sbjct: 1 LIPLGLKETKDVDFSVPLKDFILEHYSEDGSEYEDEIADLMDLRQACRTPSRDEAGVELL 60
Query: 177 FQYYNQLYFIERRFFPPDRSLGIYFE-YDSLTGVPSCQRTIAFEKACVLFNMAAIYTQMA 235
Y++QL F+E RFFPP R +GI F YDS TGVP Q+ + EKA +LFN+ A+YTQ+
Sbjct: 61 MSYFSQLGFLENRFFPPTRQMGILFTWYDSFTGVPVSQQNLLLEKASILFNIGALYTQIG 120
Query: 236 AKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPSMDLGPPMLDMLIQLMLAQARECL 295
+ +R T GL+ AVD F RAAG YL+E FT+ PS D+ P ML +L+++MLAQA+ECL
Sbjct: 121 TRCNRQTQAGLESAVDAFQRAAGVLNYLKETFTHTPSYDMSPAMLSVLVKMMLAQAQECL 180
Query: 296 FQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQVKKE 355
F+K+ L +F ++++AQEAA+V EVYM + + + VK+ +P SW SL+QVK
Sbjct: 181 FEKISLPGIRN-EFFTLVKMAQEAAKVGEVYMQVHTAMNQAPVKENIPYSWSSLVQVKAH 239
Query: 356 HYLALSHYYCASGLLTKSLANLSS---TAQTVLS--YLHIPQENKKNLILEFEPEDESQR 410
HY AL+HY+ A+ L+ L N S + LS Y H+P+ IL +++ QR
Sbjct: 240 HYNALAHYFVATLLIDHQL-NPSDDEDKQEKALSQLYDHMPEGLTPLTIL----KNKQQR 294
Query: 411 KQLGVAHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEEDEFNT 470
+ LG AHLR A++ HEE+ R +C++LRN L +VL AH +L YA ++ED+F
Sbjct: 295 RLLGKAHLRRAIMHHEEAIREASLCKKLRNIDVLQEVLSAAHNRSLLKYAQHQKEDDFLD 354
Query: 471 MYEAPNITPSTKFQLTLTPPDFAHLPVEDLF 501
+ +AP+I T+ ++ + P F+ + V DLF
Sbjct: 355 LIDAPDIVSKTEKKVEMIIPQFSKVKVTDLF 385
>gnl|CDD|214990 smart01041, BRO1, BRO1-like domain. This domain is found in a
number proteins including Rhophilin and BRO1. It is
known to have a role in endosomal targeting. ESCRT-III
subunit Snf7 binds to a conserved hydrophobic patch in
the BRO1 domain that is required for protein complex
formation and for the protein-sorting function of BRO1.
Length = 381
Score = 338 bits (869), Expect = e-111
Identities = 160/418 (38%), Positives = 226/418 (54%), Gaps = 51/418 (12%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLL 176
+IPL LKETKE+D +P KD+I E YSED ++YED ++E +RQA RTP+RD SG+ LL
Sbjct: 1 LIPLPLKETKEVDFSKPLKDYIKETYSEDSSSYEDEIAELNRLRQAARTPSRDESGLELL 60
Query: 177 FQYYNQLYFIERRFFPPDRSLGIYFE-YDSL-TGVPSCQRTIAFEKACVLFNMAAIYTQM 234
+YY QL +E RF PP+ L + F YDSL TGVPS Q ++AFEKA VLFN+ A+Y+Q+
Sbjct: 61 LKYYGQLEALELRFPPPEGQLKLSFTWYDSLDTGVPSTQSSLAFEKASVLFNLGALYSQI 120
Query: 235 AAKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAP----SMDLGPPMLDMLIQLMLAQ 290
AA+Q+R T GL +A F +AAG F YL+ENF +A S+DL P L L LMLAQ
Sbjct: 121 AAEQNRDTEEGLKEACKAFQQAAGVFNYLKENFLHALSTEPSVDLSPETLSALSSLMLAQ 180
Query: 291 ARECLFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLL-SLITVPEVKDYVPLSWVSL 349
A+EC F+K L + D +A+ AAQ AE Y L +L T VK Y+P SW+ L
Sbjct: 181 AQECFFEKAILDGMKNKDSL----IAKLAAQAAEYYEEALKALQTSEPVKGYIPKSWIKL 236
Query: 350 IQVKKEHYLALSHYYCASGLLTKSLANLSSTAQTVLSYLHIPQENKKNLILEFEPEDESQ 409
+QVK H+ AL+HYY A L E+
Sbjct: 237 VQVKAHHFKALAHYYQALDLE------------------------------------EAN 260
Query: 410 RKQLGVAHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEEDEFN 469
+ +A L+ AL +E+++ + C++L L + L + E + E++++F
Sbjct: 261 KYGEAIARLQEALERLKEAKK-HLRCKKLGKADKLQEDLSGLKDVVEEKLKEAEKDNDFI 319
Query: 470 TMYEAPNITPST---KFQLTLTPPDFAHLPVEDLFKQLGPVAIFSAKHHWTAPRSIQL 524
P+I K L PP L DLF +L P+A+ A ++ ++ +
Sbjct: 320 YHERVPDIVSLPPIKKAPLVKPPPFSEVLKGPDLFAKLVPMAVHEAASLYSEEKAKLV 377
>gnl|CDD|217365 pfam03097, BRO1, BRO1-like domain. This domain is found in a
number proteins including Rhophilin and BRO1. It is
known to have a role in endosomal targeting. ESCRT-III
subunit Snf7 binds to a conserved hydrophobic patch in
the BRO1 domain that is required for protein complex
formation and for the protein-sorting function of BRO1.
Length = 374
Score = 327 bits (841), Expect = e-106
Identities = 144/413 (34%), Positives = 216/413 (52%), Gaps = 62/413 (15%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTP--NRDNSGIS 174
++PL LKETKE+D+ +P KD+IL Y ED + +ED ++E +RQ + D SG+
Sbjct: 1 LLPLPLKETKEVDLSKPLKDYILSTYGEDPSLFEDDLAELNKLRQDAVNVPGSPDESGLE 60
Query: 175 LLFQYYNQLYFIERRFFPPDRSLGIYFE-YDSL-TGVPSCQRTIAFEKACVLFNMAAIYT 232
LL++YY QL +E+RF PD LG+ F YD+ TG P Q ++AFEKA VLFN+AA+Y+
Sbjct: 61 LLYRYYGQLEALEKRF--PDDQLGVEFTWYDAFDTGSPVTQSSLAFEKASVLFNLAALYS 118
Query: 233 QMAAKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPSMDLGPPMLDMLIQLMLAQAR 292
Q+AA Q+R T GL A D F +AAG F YL+ENF ++PS+DL P L L LMLAQA+
Sbjct: 119 QIAASQNRDTDEGLKAACDYFQKAAGAFEYLKENFLHSPSVDLSPETLKFLESLMLAQAQ 178
Query: 293 ECLFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQV 352
EC F+K L + L +A+ AAQV+++Y L + VK +P W+ +Q+
Sbjct: 179 ECFFEKAILDGK-----KDSL-IAKLAAQVSDLYEEALEALQESPVKTGIPKEWIKHVQL 232
Query: 353 KKEHYLALSHYYCASGLLTKSLANLSSTAQTVLSYLHIPQENKKNLILEFEPEDESQRKQ 412
K+ ++ AL+HYY A L LE ++K+
Sbjct: 233 KQHYFKALAHYYHA-------------------------------LALE-------EKKK 254
Query: 413 LG--VAHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEEDEFNT 470
G +A L+ AL +E+ ++ L + L + L E + E++++F
Sbjct: 255 YGEAIARLQKALSALKEALKL----APLSSSSELLEDLKGLKDRIKEKLKEAEKDNDFIY 310
Query: 471 MYEAPNI---TPSTKFQLT--LTPPDFAHLP-VEDLFKQLGPVAIFSAKHHWT 517
E P+ P L + P + DLFK+L P+A+ A ++
Sbjct: 311 HEEVPDEVSLPPIKPAPLVKPIPPNELTESVKGPDLFKKLVPIAVHEALSAYS 363
>gnl|CDD|185765 cd09242, BRO1_ScBro1_like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
proteins Rhophilin-1 and -2, Brox, Saccharomyces
cerevisiae Rim20 (also known as PalA), Ustilago maydis
Rim23 (also known as PalC), and related domains. Alix,
HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system. Bro1 participates in endosomal
trafficking. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: Snf7 in the case of Bro1. Snf7
binds to a conserved hydrophobic patch on the middle of
the concave side of the Bro1 domain. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain contains a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. The
Alix V-domain is also a dimerization domain. The
C-terminal portion (V-domain and proline rich-region) of
Bro1 interacts with Doa4, a protease that
deubiquitinates integral membrane proteins sorted into
the lumenal vesicles of late-endosomal multivesicular
bodies. It interacts with a YPxL motif in the Doa4
catalytic domain to stimulate its deubiquitination
activity.
Length = 348
Score = 190 bits (484), Expect = 9e-55
Identities = 86/254 (33%), Positives = 138/254 (54%), Gaps = 7/254 (2%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLL 176
+I L LK+T+E+D ++P ++ Y YE+ ++EF +RQ D +G LL
Sbjct: 1 LISLPLKDTEEVDWKKPLSSYLKRSYGSSTFYYEEEIAEFDRLRQDANGVLADETGRDLL 60
Query: 177 FQYYNQLYFIERRFFPPDRSLGIYFE-YDSLTG-VPSCQRTIAFEKACVLFNMAAIYTQM 234
++YY QL +E RF ++ L + F YD+ Q ++AFEKA VLFN+ A+ +Q+
Sbjct: 61 YKYYGQLELLELRFPFNNKELKVDFTWYDAFYKSKKVKQHSLAFEKASVLFNIGALLSQL 120
Query: 235 AAKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPSMDLGPPMLDMLIQLMLAQAREC 294
AA++ R L +A+ N +AAG F Y+ ENF +APS+DL + L++LMLAQA+E
Sbjct: 121 AAEKYREDEDDLKEAITNLQQAAGCFQYINENFLHAPSVDLQQENVKFLVKLMLAQAQEI 180
Query: 295 LFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLIT--VPEVKDYVPLSWVSLIQV 352
KL + +++ A+ A +Y S + + + Y W+SL+Q
Sbjct: 181 FLLKL---INGDDAQKKASLISKLASATANLYESCVEFLKEIQEKGISYGDPKWISLVQC 237
Query: 353 KKEHYLALSHYYCA 366
K +Y +L+ YY A
Sbjct: 238 KAHYYKSLAAYYHA 251
>gnl|CDD|185761 cd09034, BRO1_Alix_like, Protein-interacting Bro1-like domain of
mammalian Alix and related domains. This superfamily
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also
known as PalA) from Saccharomyces cerevisiae, and
related domains. Alix, HD-PTP, Brox, Bro1 and Rim20
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1),
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP functions in cell
migration and endosomal trafficking, Bro1 in endosomal
trafficking, and Rim20 in the response to the external
pH via the Rim101 pathway. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4
(in the case of Alix, HD-PTP, and Brox) and Snf7 (in the
case of yeast Bro1, and Rim20). The single domain
protein human Brox, and the isolated Bro1-like domains
of Alix, HD-PTP and Rhophilin can bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V)
domain, which in the case of Alix, has been shown to be
a dimerization domain and to contain a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in this superfamily. Alix,
HD-PTP and Bro1 also have a proline-rich region (PRR);
the Alix PRR binds multiple partners. Rhophilin-1, and
-2, in addition to this Bro1-like domain, have an
N-terminal Rho-binding domain and a C-terminal PDZ
(PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded
by the PTPN23 gene, a tumor suppressor gene candidate
frequently absent in human kidney, breast, lung, and
cervical tumors. This protein has a C-terminal,
catalytically inactive tyrosine phosphatase domain.
Length = 345
Score = 169 bits (429), Expect = 5e-47
Identities = 94/374 (25%), Positives = 158/374 (42%), Gaps = 55/374 (14%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSE-DGTAYEDSVSEFMDMRQAMRTPNRD----NS 171
I L LK+TKE+DV+ P FI ++Y E + TA ED + + +R + T + +
Sbjct: 1 FIGLPLKKTKEVDVKVPLSKFIPKNYGELEATAVEDLIEKLSKLRNNIVTEQNNDTTCEN 60
Query: 172 GISLLFQYYNQLYFIERRFFPPDRSLGIYFE-YDSLTGVPSCQRTIAFEKACVLFNMAAI 230
+ L +Y L +E++ + F DS ++ +E +LFN+AA+
Sbjct: 61 LLEALKEYLPYLLGLEKKLPFQKLRDNVEFTWTDSFDTKKESATSLRYELLSILFNLAAL 120
Query: 231 YTQMAAKQDRLTST-GLDQAVDNFLRAAGTFTYLQENFTNAPSM----DLGPPMLDMLIQ 285
+Q+A ++ S L QA+ + +AAG F YL+E+ P DL +L L
Sbjct: 121 ASQLANEKLITGSEEDLKQAIKSLQKAAGYFEYLKEHVLPLPPDELPVDLTEAVLSALSL 180
Query: 286 LMLAQARECLFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLS 345
+MLAQA+EC K + +K + LA EAA+ E + LS + E +P
Sbjct: 181 IMLAQAQECFLLKAEED--KKAKLSLLARLACEAAKYYEEALKCLSGV-DLETIKNIPKK 237
Query: 346 WVSLIQVKKEHYLALSHYYCASGLLTKSLANLSSTAQTVLSYLHIPQENKKNLILEFEPE 405
W+ ++ KK + AL++YY L
Sbjct: 238 WLLFLKWKKCIFKALAYYYHGLKL------------------------------------ 261
Query: 406 DESQRKQLGVAHLRSALLFHEESQRIYRMCRELRNKQALFQVLVQAHTLTLEMYADVEEE 465
DE+ + +A L++AL +ES+R+ + ++ L + + E E
Sbjct: 262 DEANKIGEAIARLQAALELLKESERLCKSF-----LLDVWGNLKKLKEKIEKELEKAERE 316
Query: 466 DEFNTMYEAPNITP 479
++F E P P
Sbjct: 317 NDFIYFEEVPPEDP 330
>gnl|CDD|185762 cd09239, BRO1_HD-PTP_like, Protein-interacting, N-terminal,
Bro1-like domain of mammalian His-Domain type N23
protein tyrosine phosphatase and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian His-Domain type N23 protein tyrosine
phosphatase (HD-PTP) and related domains. It belongs to
the BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains. Alix,
also known as apoptosis-linked gene-2 interacting
protein 1 (AIP1), HD-PTP, Brox, Bro1, Rim20, and Rim23,
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. HD-PTP participates in
cell migration and endosomal trafficking. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of HD-PTP. The Bro1-like
domain of HD-PTP can also bind human immunodeficiency
virus type 1 (HIV-1) nucleocapsid. HD-PTP, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain contains a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the V-domain
superfamily. HD-PTP is encoded by the PTPN23 gene, a
tumor suppressor gene candidate frequently absent in
human kidney, breast, lung, and cervical tumors. This
family also contains Drosophila Myopic which promotes
epidermal growth factor receptor (EGFR) signaling, and
Caenorhabditis elegans (enhancer of glp-1) EGO-2 which
promotes Notch signaling.
Length = 361
Score = 147 bits (373), Expect = 4e-39
Identities = 81/260 (31%), Positives = 129/260 (49%), Gaps = 14/260 (5%)
Query: 113 PVMPMIPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSG 172
P +PM+ L LK + E + K +ILE+Y ED Y + + +RQ P RD G
Sbjct: 4 PRLPMLWLQLKSSGEFTFQPALKKYILENYGEDPELYSEELKSLEQLRQEAVNPPRDFEG 63
Query: 173 ISLLFQYYNQLYFIERRF-FPPDRSLGIYFEY-DSLTGVPSCQRTIAFEKACVLFNMAAI 230
S+L +YY QL+ ++ RF + + F + D +G I FE+A VL+N+ A+
Sbjct: 64 CSVLKRYYGQLHLLQSRFPMGAGQEAAVPFTWTDIFSGSEVTHEDIKFEEASVLYNIGAL 123
Query: 231 YTQMAAKQDRLTSTGLDQAVDNFLRAAGTFTYLQENFTNAPS-MDLGPPMLDMLIQLMLA 289
++Q+ A R + G+ A +F AA F YL+E++ +D+ +L LMLA
Sbjct: 124 HSQLGASDKRDSEEGMKVACTHFQCAAWAFAYLREHYPQVYGAVDMSSQLLSFNYSLMLA 183
Query: 290 QARECLFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLS---- 345
QA+ECL +K L D + A+ +AQV E Y L + E + L
Sbjct: 184 QAQECLLEKSLL------DNRKSHITAKVSAQVVEYYKEALRALENWESNSKIILGKIQK 237
Query: 346 -WVSLIQVKKEHYLALSHYY 364
W L+Q+K +Y +++H +
Sbjct: 238 EWRKLVQMKIAYYASIAHLH 257
>gnl|CDD|185769 cd09246, BRO1_Alix_like_1, Protein-interacting, N-terminal,
Bro1-like domain of an Uncharacterized family of the
BRO1_Alix_like superfamily. This domain family is
comprised of uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: CHMP4 (in the case of Alix,
Brox and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. In addition to this Bro1-like
domain, Alix, Bro1, Rim20, HD_PTP, and proteins
belonging to this uncharacterized family, also have a
V-shaped (V) domain. The Alix V-domain is a dimerization
domain, and contains a binding site for the retroviral
late assembly (L) domain YPXnL motif, which is partially
conserved in the BRO1_Alix_like superfamily. Many
members of this superfamily also have a proline-rich
region (PRR), a protein interaction domain.
Length = 353
Score = 146 bits (370), Expect = 8e-39
Identities = 84/270 (31%), Positives = 130/270 (48%), Gaps = 24/270 (8%)
Query: 117 MIPLGLKETKEIDVREPFKDFILEHYSE-DGTAYEDSVSEFMDMRQAMRTPNRDNSGI-S 174
M+ + K+T+ +D+ P + +I E YSE + ED ++E +R +RT ++
Sbjct: 1 MLSIHRKKTETVDLVSPLRAYISETYSEREAQDAEDDLAELQQLRSEVRTLQEKHAASRE 60
Query: 175 LLFQYYNQLYFIERRFFPPDRSLG---IYFE-YDSLTGVP-SCQRTIAFEKACVLFNMAA 229
LL +YY L +E RF P G + F YD+ + Q + FEKA VLFN+ A
Sbjct: 61 LLLRYYRALCAVESRF-PISEESGHARVSFSWYDAFRPHRKATQANVHFEKAAVLFNLGA 119
Query: 230 IYTQMAAKQDRLTSTGLDQAVDNFLRAAGTFTYLQEN----FTNAPSMDLGPPMLDMLIQ 285
+ +Q+ +QDR T+ G+ QA F AAG F +L++ + DL L ML
Sbjct: 120 LSSQLGLQQDRTTAEGIKQACHAFQAAAGAFAHLRDKVSGKTGGFRTPDLTAECLGMLES 179
Query: 286 LMLAQARECLFQKL---QLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYV 342
LMLAQA+EC ++K +LA+ Q Y L + P +K +
Sbjct: 180 LMLAQAQECFYEKAVADGKSPAVCS------KLAK---QARSYYEEALEALDSPPLKGHF 230
Query: 343 PLSWVSLIQVKKEHYLALSHYYCASGLLTK 372
SWV+ +Q+K ++ A + Y A L K
Sbjct: 231 DKSWVAHVQLKAAYFRAEALYRAAKDLHEK 260
>gnl|CDD|185763 cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like
domain of mammalian Alix and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), also called apoptosis-linked gene-2
interacting protein 1 (AIP1). It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4,
in the case of Alix. The Alix Bro1-like domain can also
bind human immunodeficiency virus type 1 (HIV-1)
nucleocapsid and Rab5-specfic GAP (RabGAP5, also known
as Rab-GAPLP). In addition to this Bro1-like domain,
Alix has a middle V-shaped (V) domain. The Alix V-domain
is a dimerization domain, and carries a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1) and the
apoptotic protein ALG-2.
Length = 346
Score = 139 bits (353), Expect = 2e-36
Identities = 82/261 (31%), Positives = 135/261 (51%), Gaps = 26/261 (9%)
Query: 122 LKETKEIDVREPFKDFILEHYS--EDGTAYEDSVSEFMDMRQA--MRTPNRDNSGISLLF 177
LK++ E+D+ +P + FI YS E+ Y++++ E +R R ++ S + LL
Sbjct: 8 LKKSSEVDLVKPLEKFIKNTYSSGEEQADYKEAIKELNKLRNNAVCRPLDKHESSLELLL 67
Query: 178 QYYNQLYFIERRFFPPDRSLGIYFEYD------SLTG--VPSCQRTIAFEKACVLFNMAA 229
+YY+QL IE +F + + + F + SL G ++ +EK CVLFN+AA
Sbjct: 68 RYYDQLCAIEPKFPFSESQIQVTFTWKDAFDKGSLFGGSKKLALSSLGYEKVCVLFNIAA 127
Query: 230 IYTQMAAKQDRLTSTGLDQAVDNFLRAAGTFTYLQE----NFTNAPSMDLGPPMLDMLIQ 285
+ +Q+AA+Q+ T GL A F +AAG F +L+E P+ DL P L L
Sbjct: 128 LQSQIAAEQNLDTDEGLKLAAKLFQQAAGIFNHLKETVLSALQQEPTPDLSPDTLSALSA 187
Query: 286 LMLAQARECLFQKLQLQTTEKCDFQHMLE--LAQEAAQVAEVYMSLLSLITVPEVKDYVP 343
LMLAQA+E + K T +K M + +A+ AAQ A+ Y +V+ +P
Sbjct: 188 LMLAQAQEVFYLK---ATRDK-----MKDAIIAKLAAQAADYYGDAFKQCQREDVRSLLP 239
Query: 344 LSWVSLIQVKKEHYLALSHYY 364
W+ ++ K+ ++ AL+ Y+
Sbjct: 240 KDWIPVLAGKQAYFHALAEYH 260
>gnl|CDD|185764 cd09241, BRO1_ScRim20-like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 (also
known as PalA) and related proteins. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox,
Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23
(also known as PalC), and related domains. Alix, HD-PTP,
Brox, Bro1, Rim20, and Rim23, interact with the ESCRT
(Endosomal Sorting Complexes Required for Transport)
system. Rim20 and Rim23 participate in the response to
the external pH via the Rim101 pathway. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: Snf7 in the case of Rim20. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain is a dimerization domain that
also contains a binding site for the retroviral late
assembly (L) domain YPXnL motif, which is partially
conserved in the V-domain superfamily. Rim20 localizes
to endosomes under alkaline pH conditions. By binding
Snf7, it may bring the protease Rim13 (a YPxL-containing
transcription factor) into proximity with Rim101, and
thus aid in the proteolytic activation of the latter.
Rim20 and other intermediates in the Rim101 pathway play
roles in the pathogenesis of fungal corneal infection
during Candida albicans keratitis.
Length = 355
Score = 139 bits (352), Expect = 3e-36
Identities = 84/261 (32%), Positives = 136/261 (52%), Gaps = 19/261 (7%)
Query: 118 IPLGLKETKEIDVREPFKDFILEHYSEDGTAYEDSVSEFMDMRQAMRTPNRDNSGISLLF 177
IP K T +D+++ +++I HY + +++ED ++E +R P +G+SLL
Sbjct: 5 IPF--KRTLPVDLKDALRNYISNHYFQTPSSFEDDLAEIDKLRNDAINPEPSVNGLSLLK 62
Query: 178 QYYNQLYFIERRFFPPDRSLGI-YFE--YDSLTGVPSCQRTIAFEKACVLFNMAAIYTQM 234
+YY QL + ++F PD L ++ +G P ++ FE+A +L+N+ A+Y+Q+
Sbjct: 63 EYYAQLVVLSKKF--PDDQLEFTWYPTLGYKSSG-PVSLSSLKFERANILYNLGALYSQL 119
Query: 235 AAKQDRLTSTGLDQAVDNFLRAAGTFTYL--QENFTNAPSMDLGPPMLDMLIQLMLAQAR 292
A ++R T GL +A F +AG F Y+ T +P DL L L LMLAQA+
Sbjct: 120 ALSENRYTDEGLKRACSYFQASAGCFEYILQHLLPTLSPPPDLDENTLKALESLMLAQAQ 179
Query: 293 ECLFQKLQLQTTEKCDFQHMLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQV 352
EC +QK T + L +A+ AAQV++ Y L D + W++ ++V
Sbjct: 180 ECFWQKAISDGT-----KDSL-IAKLAAQVSDYYQEALKYA---NKSDLIRSDWINHLKV 230
Query: 353 KKEHYLALSHYYCASGLLTKS 373
KK H+ A +HY A L KS
Sbjct: 231 KKHHFKAAAHYRMALVALEKS 251
>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 = 83.7 bits (207), Expect = 1e-19
Identities = 35/46 (76%), Positives = 44/46 (95%)
Query: 31 QATTNRKLKETVALELSFVNSNLQLLKEQLAELNSSVELYQNDKRS 76
+AT+N+K++ETVALELSFVNSNLQLLKE+LAELNSSVE+YQ+D +
Sbjct: 39 KATSNKKVRETVALELSFVNSNLQLLKEELAELNSSVEIYQSDSEA 84
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases.
Length = 82
Score = 79.5 bits (197), Expect = 2e-18
Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 6/84 (7%)
Query: 519 PRSIQLQRANNSDTGFGFSVRG----DAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDV 574
R++ L++ + G GFS+RG + V+ V+ G A+ GG++ GD I+ + V
Sbjct: 1 VRTVTLRK--DPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSV 58
Query: 575 KWSPHEEVVQLIKDAGKCLSLKLV 598
+ HEE V+L+K++G ++L +
Sbjct: 59 EGLTHEEAVELLKNSGDEVTLTVR 82
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 68.9 bits (169), Expect = 1e-14
Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 7/86 (8%)
Query: 519 PRSIQLQRANNSDTGFGFSVRG----DAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDV 574
PR ++L++ G GFS+ G V+V+SV GS A G++ GD I+ + V
Sbjct: 2 PRLVELEK---GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSV 58
Query: 575 KWSPHEEVVQLIKDAGKCLSLKLVTP 600
+ H E V L+K AG ++L ++
Sbjct: 59 EGLTHLEAVDLLKKAGGKVTLTVLRG 84
>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 = 65.7 bits (160), Expect = 2e-13
Identities = 30/44 (68%), Positives = 36/44 (81%)
Query: 30 LQATTNRKLKETVALELSFVNSNLQLLKEQLAELNSSVELYQND 73
+AT N K+KETV LELSFVNS LQLLKE+L +NSS+E+YQN
Sbjct: 32 FKATKNTKVKETVRLELSFVNSQLQLLKEELEGINSSLEVYQNV 75
>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 = 64.3 bits (156), Expect = 6e-13
Identities = 31/47 (65%), Positives = 39/47 (82%)
Query: 30 LQATTNRKLKETVALELSFVNSNLQLLKEQLAELNSSVELYQNDKRS 76
L+ATTN K++E V LELSFVNS+LQLLKE+L LN SVE+YQN + +
Sbjct: 35 LKATTNNKVREQVLLELSFVNSDLQLLKEELEGLNISVEVYQNTEEA 81
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 55.7 bits (135), Expect = 6e-10
Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 6/81 (7%)
Query: 521 SIQLQRANNSDTGFGFSVRG----DAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKW 576
+ L+++ G GFS+ G D + V+ V G A+ GG+++GD I++I +D++
Sbjct: 1 EVTLEKSGRG--GLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLEN 58
Query: 577 SPHEEVVQLIKDAGKCLSLKL 597
H+E V +K +G ++L +
Sbjct: 59 LSHDEAVLALKGSGGEVTLTI 79
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 55.4 bits (134), Expect = 6e-10
Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 532 TGFGFSVRGDAP--VIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPHEEVVQLIKDA 589
G GFS+RG V+V SV+ GS A+ G++ GD I+A+ DVK E+V +L+K
Sbjct: 1 GGLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKE 60
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 90
Score = 43.0 bits (102), Expect = 2e-05
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 522 IQLQRANNSD--TGFGFSVRGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPH 579
+ +Q +G V+VASVD GS A G+K GD I+A+ + VK S
Sbjct: 5 VTVQDLTPDLAEELGLKDTKG---VLVASVDPGSPAAKAGLKPGDVILAVNGKPVK-SV- 59
Query: 580 EEVVQLIKDAGK 591
++ + + +
Sbjct: 60 ADLRRALAELKP 71
>gnl|CDD|185766 cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of
human Brox1 and related proteins. This family contains
the Bro1-like domain of a single-domain protein, human
Brox, and related domains. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of Brox. Human Brox can bind
to human immunodeficiency virus type 1 (HIV-1)
nucleocapsid. In addition to a Bro1-like domain, Brox
also has a C-terminal thioester-linkage site for
isoprenoid lipids (CaaX motif). This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 353
Score = 45.4 bits (108), Expect = 6e-05
Identities = 56/189 (29%), Positives = 84/189 (44%), Gaps = 27/189 (14%)
Query: 199 IYFEY-DSL-TGVPSCQRTIAFEKACVLFNMAAIYTQMAAKQDRLTSTGLDQA--VDNFL 254
I F++ DSL PS Q+ FE A +LFN+A YT+ A+K D+A V L
Sbjct: 85 INFKWTDSLLGNEPSVQQDAIFELASMLFNVALWYTKHASKLAGKEDITEDEAKDVHKSL 144
Query: 255 R-AAGTFTYLQENF-----TNAPS-MDLGPPMLDMLIQLMLAQARECLFQKLQLQTTEKC 307
R AAG F +++EN+ A DL P +L+ I A+A+E +
Sbjct: 145 RTAAGIFQFVKENYIPKLIEPAEKGSDLDPRVLEAYINQCTAEAQE-------VTVARAI 197
Query: 308 DFQH----MLELAQEAAQVAEVYMSLLSLITVPEVKDYVPLSWVSLIQVKKEHYLALSHY 363
+ +H + LA E A++ + LS + W +Q+K YLA ++
Sbjct: 198 ELKHNAGLISALAYETAKLFQKADDSLS-----SLDPEYSGKWRKYLQLKSVFYLAYAYC 252
Query: 364 YCASGLLTK 372
Y LL K
Sbjct: 253 YHGETLLAK 261
>gnl|CDD|216921 pfam02185, HR1, Hr1 repeat.
Length = 60
Score = 39.4 bits (93), Expect = 2e-04
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 25 RNVAQLQATTNRKLKETVALELSFVNSNLQLLKEQLAELNS 65
N+ + T N+K+ + EL N ++LLKEQL +L
Sbjct: 20 ENMLRALETDNKKVLQEAESELRESNQKIELLKEQLEKLQK 60
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 39.9 bits (94), Expect = 2e-04
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 533 GFGFSV-RGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVK-WSPHEEVVQLIKDAG 590
GF ++ V GS A G+K GD I+AI + +K W E++V +++
Sbjct: 2 ILGFVPGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSW---EDLVDAVQENP 58
Query: 591 K 591
Sbjct: 59 G 59
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 39.2 bits (92), Expect = 5e-04
Identities = 16/46 (34%), Positives = 20/46 (43%)
Query: 530 SDTGFGFSVRGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVK 575
D G V V SV GS A G+K GD I++I + V
Sbjct: 1 GDIGVRVVQNEGTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVN 46
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 40.7 bits (96), Expect = 0.002
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 544 VIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPHEEVVQLIKDAGKCLSLKL 597
V+V V SGS A G++ GD I+++ + V S E+ +++ A K + L
Sbjct: 364 VVVTKVVSGSPAARAGLQPGDVILSVNQQPVS-SV-AELRKVLARAKKGGRVAL 415
Score = 34.1 bits (79), Expect = 0.21
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 544 VIVASVDSGSLAQFGGMKDGDFIVAIGDRDVK 575
+VA V GS A+ G+K GD I ++ + +
Sbjct: 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPIS 290
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 37.2 bits (87), Expect = 0.002
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 532 TGFG--FSVRGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPHEEVVQLIK-D 588
G G VI + + A+ G+K GD IVAI V E+VV+L++
Sbjct: 2 GGIGLELKYDDGGLVITSVLPGSPAAK-AGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGK 60
Query: 589 AGKCLSLKL 597
AG + L L
Sbjct: 61 AGTKVRLTL 69
>gnl|CDD|185768 cd09245, BRO1_UmRIM23-like, Protein-interacting, Bro1-like domain
of Ustilago maydis Rim23 (PalC), and related domains.
This family contains the Bro1-like domain of Ustilago
maydis Rim23 (also known as PalC), and related proteins.
It belongs to the BRO1_Alix_like superfamily which
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, and related
domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Rim20 and Rim23
participate in the response to the external pH via the
Rim101 pathway. Through its Bro1-like domain, Rim23
allows the interaction between the endosomal and plasma
membrane complexes. Bro1-like domains are
boomerang-shape, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure.
Intermediates in the Rim101 pathway may play roles in
the pathogenesis of fungal corneal infection during
Candida albicans keratitis. This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 413
Score = 37.8 bits (88), Expect = 0.015
Identities = 25/114 (21%), Positives = 38/114 (33%), Gaps = 20/114 (17%)
Query: 215 TIAFEKACVLFNMAAIYTQMA---------AKQDRLTST--------GLDQAVDNFLRAA 257
+ +E A VL A + +A + DR S L A +AA
Sbjct: 111 GLHYELAFVLLTYAYALSNLARSILAPLGAYETDRSISDASRKQRDERLKAATKLLCKAA 170
Query: 258 GTFTYLQEN--FTNAPSMDLGPPMLDMLIQLMLAQARECLFQKLQLQTTEKCDF 309
G F YL + PP D+ +++ A + L + L K D
Sbjct: 171 GIFDYLATRVLPQWESNRGGAPPPPDLSPEVLSALSSLALAEA-TLLAVRKLDP 223
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 36.2 bits (84), Expect = 0.059
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 544 VIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPHEEVVQLIK 587
V V S GS A G+K GD I+ I + V +E V+LI+
Sbjct: 114 VKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIR 157
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 35.3 bits (81), Expect = 0.090
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 529 NSDTGFGFSVRGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWS 577
+D G V A +V V GS A G+K GD I A+ + V
Sbjct: 259 TADIALGLPV--AAGAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASL 305
>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 = 31.8 bits (73), Expect = 0.090
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 30 LQATTN-RKLKETVALELSFVNSNLQLLKEQLAE 62
+ T+N RK+ L N L LLKE+L +
Sbjct: 24 RKLTSNDRKVLSEAQSMLRESNQKLDLLKEELEK 57
>gnl|CDD|225130 COG2220, COG2220, Predicted Zn-dependent hydrolases of the
beta-lactamase fold [General function prediction only].
Length = 258
Score = 34.8 bits (80), Expect = 0.11
Identities = 26/114 (22%), Positives = 34/114 (29%), Gaps = 15/114 (13%)
Query: 496 PVEDLFKQLGPVAIFSAKHHWTAPRSIQLQRANNSDTGFGFSVRGDAPVIVASVDSGSLA 555
+ DL P SA+H P G+ + + + D+G L
Sbjct: 112 ELGDLEITAVPAYHVSARHL---PGRGIRPTGLWV----GYVIETPGGRVYHAGDTGYLF 164
Query: 556 QFGGMKDGDFIVA---IGDRDVKWS-PHEEVVQLIKDAGKCLSLKLVTPMHKNN 605
DG VA IG P E V + L K V PMH
Sbjct: 165 LIIEELDGPVDVALLPIGGYPNATMMPPEAAVAAAEV----LRPKRVIPMHYGP 214
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 32.9 bits (75), Expect = 0.50
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 534 FGFSVRGDAPV---IVASVDSGSLAQFGGMKDGDFIVAIGDRDVK 575
F V G PV +V V S A G++ GD IVA+ V
Sbjct: 118 VLFFVIGLVPVASPVVGEVAPKSAAALAGLRPGDRIVAVDGEKVA 162
>gnl|CDD|233316 TIGR01217, ac_ac_CoA_syn, acetoacetyl-CoA synthase. This enzyme
catalyzes the first step of the mevalonate pathway of
IPP biosynthesis. Most bacteria do not use this pathway,
but rather the deoxyxylulose pathway [Central
intermediary metabolism, Other].
Length = 652
Score = 32.9 bits (75), Expect = 0.57
Identities = 24/106 (22%), Positives = 39/106 (36%), Gaps = 20/106 (18%)
Query: 421 ALLFHEESQRIYRMC-RELRNKQALFQVLVQAHTLTLEMYADVEEEDEFNTMYEAPNITP 479
ALL+ +E+ + ELR + A ++A V D + PNI
Sbjct: 102 ALLYVDETHEPAPVTWAELRRQVASLAAALRAL--------GVRPGDRVSGYL--PNIPQ 151
Query: 480 STKFQL---------TLTPPDFAHLPVEDLFKQLGPVAIFSAKHHW 516
+ L + PDF V D F+Q+ P +F+ +
Sbjct: 152 AVVAMLATASVGAIWSSCSPDFGARGVLDRFQQIEPKLLFTVDGYR 197
>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 = 29.5 bits (67), Expect = 0.64
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 32 ATTNRKLKETVALELSFVNSNLQLLKEQLAELNSSV 67
ATT++K V L N L+ L ++L EL + +
Sbjct: 31 ATTDKKSLAHVESILKKSNRKLEDLHQELQELEAHI 66
>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 = 29.6 bits (67), Expect = 0.64
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 30 LQATTN---RKLKETVALELSFVNSNLQLLKEQLAELNSSV 67
L+ +N +K V L L + LLK QL N+ V
Sbjct: 28 LKLYSNPKVKKDLAEVQLNLKESKEKIDLLKRQLERYNALV 68
>gnl|CDD|221005 pfam11153, DUF2931, Protein of unknown function (DUF2931). Some
members in this family of proteins are annotated as
lipoproteins however this cannot be confirmed.
Currently, there is no known function.
Length = 170
Score = 30.0 bits (68), Expect = 2.3
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 158 DMRQAMRTPNRDNSGISLLFQYYNQLYF 185
D+RQ MRTP + Y + +
Sbjct: 77 DLRQRMRTPADYTCRDGDIECYRDNIVL 104
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the
family being composed of Afadin- and alpha
-Actinin-Binding Proteins Localised at Cell-Cell
Adherens Junctions.
Length = 149
Score = 29.6 bits (67), Expect = 2.6
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 24 QRNVAQLQA--TTNRKLKETVALELSFVNSNLQLLKEQLAELNSSVELYQNDKRSL 77
R++ ++ T RKL+ E+ + + ++ LK QL +L + L Q +R L
Sbjct: 46 DRDLEFRESLEETLRKLEA----EIERLQNTIERLKTQLEDLERELALLQAKERQL 97
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 30.4 bits (69), Expect = 3.1
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 532 TGFGFSV-RGDAPVIVASVDSGSLAQFGGMKDGDFIVAIGDRDVKWSPHEEVVQLIK-DA 589
G G V D +++ S GS A+ G+K GD I+ I + V ++ V LI+
Sbjct: 51 EGIGIQVGMDDGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKK 110
Query: 590 GKCLSLKLVTP 600
G +SL+++
Sbjct: 111 GTKVSLEILRA 121
>gnl|CDD|185770 cd09247, BRO1_Alix_like_2, Protein-interacting Bro1-like domain of
an Uncharacterized family of the BRO1_Alix_like
superfamily. This domain family is comprised of
uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. These domains bind components of
the ESCRT-III complex: CHMP4 (in the case of Alix, Brox
and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. This family lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_like
superfamily.
Length = 346
Score = 29.7 bits (67), Expect = 4.9
Identities = 26/109 (23%), Positives = 40/109 (36%), Gaps = 18/109 (16%)
Query: 198 GIYFEYDSLTGVPSCQRT-----IAFEKACVLFNMAAIYTQMAAKQDRLTSTG-LDQAVD 251
+ F + S G + + FE VLF A + A+ + T +A
Sbjct: 85 QLSFRWTSGLGSSKGPKAFQSDSLRFELGMVLFLYGAALRERAS---EVLPTEDFKEAAT 141
Query: 252 NFLRAAGTFTYLQEN----FTNAPSMD-----LGPPMLDMLIQLMLAQA 291
+ RAAG F +L + A S D P + + L LA+A
Sbjct: 142 HLRRAAGVFEFLAHDELPRLRGALSADERPPECTPSLALAMSLLCLAEA 190
>gnl|CDD|222417 pfam13851, GAS, Growth-arrest specific micro-tubule binding.
This family is the highly conserved central region of a
number of metazoan proteins referred to as
growth-arrest proteins. In mouse, Gas8 is predominantly
a testicular protein, whose expression is
developmentally regulated during puberty and
spermatogenesis. In humans, it is absent in infertile
males who lack the ability to generate gametes. The
localisation of Gas8 in the motility apparatus of
post-meiotic gametocytes and mature spermatozoa,
together with the detection of Gas8 also in cilia at
the apical surfaces of epithelial cells lining the
pulmonary bronchi and Fallopian tubes suggests that the
Gas8 protein may have a role in the functioning of
motile cellular appendages. Gas8 is a
microtubule-binding protein localised to regions of
dynein regulation in mammalian cells.
Length = 201
Score = 29.1 bits (66), Expect = 5.0
Identities = 14/55 (25%), Positives = 29/55 (52%)
Query: 31 QATTNRKLKETVALELSFVNSNLQLLKEQLAELNSSVELYQNDKRSLDSVESVYR 85
N KL +A E + L+ +E++ EL ++ Y+ DK+SL ++++ +
Sbjct: 42 NEEHNEKLMAEIAQENKRLVEPLKKAEEEVEELRKKLKDYEKDKQSLKNLKARLK 96
>gnl|CDD|220916 pfam10962, DUF2764, Protein of unknown function (DUF2764). This
bacterial family of proteins has no known function.
Length = 271
Score = 29.3 bits (66), Expect = 6.6
Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 12/106 (11%)
Query: 68 ELYQNDKRSLDSVESVYRLFSLMILFMLSTRDRKTPRSFKYFSKEPVMPMIPLGLKETKE 127
L + DK+ +D + Y F L P +++ + +I +E+ +
Sbjct: 35 NLSEKDKKLIDLL---YLKFDNENLLAFLWDGEPLPDPRGRITQDELEELISA-QRESDK 90
Query: 128 IDVREP--FKDFILEHY---SEDGTAYEDS-VSEFMDMRQAMRTPN 167
D P FKDF+LE+ +E+ ++ED + + + AM+ N
Sbjct: 91 PDDEFPDYFKDFLLEYLAKSAEERISHEDRLAALYYE--YAMKCGN 134
>gnl|CDD|234370 TIGR03838, queuosine_YadB, glutamyl-queuosine tRNA(Asp) synthetase.
This protein resembles a shortened glutamyl-tRNA
ligase, but its purpose is to modify tRNA(Asp) at a
queuosine position in the anticodon rather than to
charge a tRNA with its cognate amino acid [Protein
synthesis, tRNA and rRNA base modification].
Length = 271
Score = 29.0 bits (66), Expect = 7.8
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 484 QLTLTPPDFAHLPV------EDLFKQLGPVAI 509
L L PP + HLP+ E L KQ G A+
Sbjct: 207 LLGLPPPRYLHLPLVVNADGEKLSKQNGAPAL 238
>gnl|CDD|150690 pfam10044, Ret_tiss, Retinal tissue protein. Rtp is a family of
proteins of approximately 112 amino acids in length
which is conserved from nematodes to humans. The
proposed tertiary structure is of almost entirely alpha
helix interrupted only by loops located at proline
residues. Three sites in the protein sequence reveal two
types of possible post-translation modification. A
serine residue, at position 41, is a candidate for
protein kinase C phosphorylation. Glycine residues at
position 69 and 91 are probable sites for acetylation by
covalent amide linkage of myristate via N-myristoyl
transferase. Rtp is differentially expressed in the
trout retina between parr and smolt developmental stages
(smoltification). It is likely to be a house-keeping
protein.
Length = 95
Score = 27.4 bits (61), Expect = 7.8
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 6/41 (14%)
Query: 466 DEFNTMYEAPNITPSTKFQLTLTPPD------FAHLPVEDL 500
DEF +M + P T K+ LT D L L
Sbjct: 23 DEFLSMNDNPMYTSPPKWTSGLTKDDMDKINELGSLTTSGL 63
>gnl|CDD|235835 PRK06589, PRK06589, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 489
Score = 29.0 bits (65), Expect = 9.3
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 217 AFEKACVLFNMAAIYTQMAAKQ-DRLTSTG 245
+F K C+ ++M +IY+ Q D+L T
Sbjct: 342 SFAKICLFYSMGSIYSLKKEDQVDKLHGTS 371
>gnl|CDD|200530 cd11269, Sema_6D, The Sema domain, a protein interacting module, of
semaphorin 6D (Sema6D). Sema6D is expressed
predominantly in the nervous system during embryogenesis
and it uses Plexin-A1 as a receptor. It displays
repellent activity for dorsal root ganglion axons.
Sema6D also acts as a regulator of late phase primary
immune responses. In addition, Sema6D is overexpressed
in gastric carcinoma, indicating that it may have an
important role in the occurrence and development of the
cancer. Sema6D is a member of the class 6 semaphorin
family of proteins, which are membrane associated
semaphorins. Semaphorins are regulatory molecules
involved in the development of the nervous system and in
axonal guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 465
Score = 28.8 bits (64), Expect = 9.3
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 630 NQSPSSSITPSRKQIWNPFKKHQRDHELC 658
N+ P + +TPSRK W + Q+D E C
Sbjct: 35 NEVPKTEVTPSRKLTW---RSRQQDRENC 60
>gnl|CDD|226582 COG4097, COG4097, Predicted ferric reductase [Inorganic ion
transport and metabolism].
Length = 438
Score = 29.0 bits (65), Expect = 9.9
Identities = 20/80 (25%), Positives = 25/80 (31%), Gaps = 8/80 (10%)
Query: 501 FKQLGPVAIFSAKHHWTAPRSIQLQRANNSDTG-FGF-------SVRGDAPVIVASVDSG 552
F LG V + T +I LQ G F F P +A G
Sbjct: 214 FPYLGKVTAPQRGNVDTLEITIGLQGPWLYQAGQFAFLKIEIEEFRMRPHPFTIACSHEG 273
Query: 553 SLAQFGGMKDGDFIVAIGDR 572
S +F GDF + D
Sbjct: 274 SELRFSIKALGDFTKTLKDN 293
>gnl|CDD|233230 TIGR01000, bacteriocin_acc, bacteriocin secretion accessory
protein. This family represents an accessory protein
that works with the bacteriocin maturation and ABC
transport secretion protein described by TIGR01193
[Transport and binding proteins, Other].
Length = 457
Score = 28.9 bits (65), Expect = 10.0
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 25 RNVAQLQATTNRKLKETVALELSFVNSNLQLL-------KEQLAELNSSVELYQNDKRSL 77
+ ++++Q+T+N +KE E FV L+ + Q L ++ ++ K+SL
Sbjct: 57 KILSKIQSTSNNAIKENYLKENKFVKKGDLLVVYDNGNEENQKQLLEQQLDNLKDQKKSL 116
Query: 78 D 78
D
Sbjct: 117 D 117
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.377
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,032,775
Number of extensions: 3225878
Number of successful extensions: 2942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2893
Number of HSP's successfully gapped: 56
Length of query: 665
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 562
Effective length of database: 6,369,140
Effective search space: 3579456680
Effective search space used: 3579456680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.7 bits)