Query 026259
Match_columns 241
No_of_seqs 159 out of 281
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:40:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026259.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026259hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14379 Myb_CC_LHEQLE: MYB-CC 99.9 3.8E-27 8.3E-32 167.5 7.1 51 71-121 1-51 (51)
2 PLN03162 golden-2 like transcr 98.7 3.5E-09 7.6E-14 101.5 1.6 26 1-26 266-291 (526)
3 TIGR01557 myb_SHAQKYF myb-like 98.0 2.1E-06 4.7E-11 62.1 1.4 23 2-24 34-56 (57)
4 PF14379 Myb_CC_LHEQLE: MYB-CC 94.1 0.13 2.8E-06 37.2 5.0 35 86-121 6-40 (51)
5 PF15235 GRIN_C: G protein-reg 80.3 1.3 2.7E-05 37.9 2.2 19 93-111 71-89 (137)
6 cd07645 I-BAR_IMD_BAIAP2L1 Inv 51.1 1.5E+02 0.0032 27.4 9.3 70 71-143 63-141 (226)
7 PF01519 DUF16: Protein of unk 49.7 91 0.002 25.6 7.0 25 94-118 68-92 (102)
8 cd07646 I-BAR_IMD_IRSp53 Inver 48.8 1.8E+02 0.0038 27.1 9.5 70 71-143 65-143 (232)
9 PF06548 Kinesin-related: Kine 35.5 5.1E+02 0.011 26.6 11.1 64 72-135 294-372 (488)
10 PF00435 Spectrin: Spectrin re 31.9 1.8E+02 0.0039 20.4 7.2 49 94-145 42-90 (105)
11 PRK10803 tol-pal system protei 31.2 1.6E+02 0.0035 26.8 6.4 43 79-121 54-96 (263)
12 KOG2620 Prohibitins and stomat 30.5 2.5E+02 0.0054 27.0 7.6 51 68-118 153-209 (301)
13 KOG0994 Extracellular matrix g 29.6 3.6E+02 0.0079 31.1 9.6 73 74-147 1410-1483(1758)
14 PF00752 XPG_N: XPG N-terminal 28.2 24 0.00052 26.8 0.5 14 4-18 1-14 (101)
15 KOG4466 Component of histone d 27.0 4.1E+02 0.0089 25.5 8.4 38 94-137 69-106 (291)
16 KOG1916 Nuclear protein, conta 22.9 4.5E+02 0.0098 29.6 8.7 44 80-123 898-951 (1283)
17 PF08898 DUF1843: Domain of un 22.6 1.5E+02 0.0032 21.8 3.7 34 108-141 18-51 (53)
18 COG5665 NOT5 CCR4-NOT transcri 22.6 7E+02 0.015 25.4 9.4 52 74-131 117-168 (548)
19 KOG0804 Cytoplasmic Zn-finger 22.2 5E+02 0.011 26.7 8.4 46 73-119 321-366 (493)
20 COG5420 Uncharacterized conser 22.0 3.8E+02 0.0082 20.7 6.5 47 83-141 10-68 (71)
21 PF03816 LytR_cpsA_psr: Cell e 21.4 78 0.0017 26.1 2.3 18 100-117 131-148 (149)
22 PF01815 Rop: Rop protein; In 20.8 87 0.0019 23.5 2.2 21 85-105 38-59 (60)
23 PF00517 GP41: Retroviral enve 20.4 3.3E+02 0.0071 24.1 6.2 39 73-111 22-64 (204)
24 PF07889 DUF1664: Protein of u 20.4 5.2E+02 0.011 21.7 7.1 52 94-145 62-113 (126)
No 1
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=99.94 E-value=3.8e-27 Score=167.51 Aligned_cols=51 Identities=88% Similarity=1.125 Sum_probs=49.1
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 026259 71 GYQVTEALRVQMEVQRRLHEQLEVQRRLQLRIEAQGKYLQSILEKACKALN 121 (241)
Q Consensus 71 ~~qI~EALrmQmEVQrRLhEQLEvQR~LQlRIEaQGkYLq~iLEKAqe~La 121 (241)
|++|+||||+||||||||||||||||+||+|||||||||++|||||+++++
T Consensus 1 g~~i~EALr~QmEvQrrLhEQLEvQr~Lqlrieaqgkyl~~ilek~~~~~s 51 (51)
T PF14379_consen 1 GMQITEALRMQMEVQRRLHEQLEVQRHLQLRIEAQGKYLQSILEKAQKALS 51 (51)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999999999999999874
No 2
>PLN03162 golden-2 like transcription factor; Provisional
Probab=98.72 E-value=3.5e-09 Score=101.50 Aligned_cols=26 Identities=46% Similarity=0.676 Sum_probs=24.4
Q ss_pred CcccCCCCchHHHHHHHhhhhhhccc
Q 026259 1 MRTMGVKGLTLYHLKSHLQKYRLGKQ 26 (241)
Q Consensus 1 lRLMGVkGLTLYHLKSHLQKYRLgK~ 26 (241)
|++|+|+|||++||||||||||+.++
T Consensus 266 LelMnV~GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 266 LELMGVQCLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred HHHcCCCCcCHHHHHHHHHHHHHhcc
Confidence 57999999999999999999999875
No 3
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.01 E-value=2.1e-06 Score=62.07 Aligned_cols=23 Identities=57% Similarity=0.699 Sum_probs=21.3
Q ss_pred cccCCCCchHHHHHHHhhhhhhc
Q 026259 2 RTMGVKGLTLYHLKSHLQKYRLG 24 (241)
Q Consensus 2 RLMGVkGLTLYHLKSHLQKYRLg 24 (241)
.+|++++||..||+|||||||+-
T Consensus 34 ~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 34 ELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred HHcCCCCCCHHHHHHHHHHHHcc
Confidence 57999999999999999999984
No 4
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=94.12 E-value=0.13 Score=37.17 Aligned_cols=35 Identities=43% Similarity=0.499 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 026259 86 RRLHEQLEVQRRLQLRIEAQGKYLQSILEKACKALN 121 (241)
Q Consensus 86 rRLhEQLEvQR~LQlRIEaQGkYLq~iLEKAqe~La 121 (241)
--|..|+||||+|.=.+|.| |-|+.=+|..-+-|.
T Consensus 6 EALr~QmEvQrrLhEQLEvQ-r~Lqlrieaqgkyl~ 40 (51)
T PF14379_consen 6 EALRMQMEVQRRLHEQLEVQ-RHLQLRIEAQGKYLQ 40 (51)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHH
Confidence 45789999999999999999 677766666655543
No 5
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=80.28 E-value=1.3 Score=37.87 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHhHHHHH
Q 026259 93 EVQRRLQLRIEAQGKYLQS 111 (241)
Q Consensus 93 EvQR~LQlRIEaQGkYLq~ 111 (241)
-||+||+++||+|++....
T Consensus 71 AIQkHLE~qi~e~~~q~~~ 89 (137)
T PF15235_consen 71 AIQKHLERQIEEHERQRAP 89 (137)
T ss_pred HHHHHHHHHHHHhhhcccc
Confidence 4899999999999988754
No 6
>cd07645 I-BAR_IMD_BAIAP2L1 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 1. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. BAIAP2L1 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 1) is also known as IRTKS (Insulin Receptor Tyrosine Kinase Substrate). It is widely expressed, serves as a substrate for the insulin receptor, and binds the small GTPase Rac. It plays a role in regulating the actin cytoskeleton and colocalizes with F-actin, cortactin, VASP, and vinculin. BAIAP2L1 expression leads to the formation of short actin bundles, distinct from filopodia-like protrusions induced by the expression of the related protein IRSp53. It contains an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The IMD domain of
Probab=51.05 E-value=1.5e+02 Score=27.44 Aligned_cols=70 Identities=19% Similarity=0.293 Sum_probs=54.6
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHH
Q 026259 71 GYQVTEALRVQMEVQRRLHEQLEV---------QRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREELSELA 141 (241)
Q Consensus 71 ~~qI~EALrmQmEVQrRLhEQLEv---------QR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~ 141 (241)
+..|.++|.-=-||+|+++.|||. =..|.-.+|..-||+...+.+=+.. +-.-..+||-+.++|--+-
T Consensus 63 SkeLG~~L~qi~ev~r~i~~~le~~lK~Fh~Ell~~LE~k~elD~kyi~a~~Kkyq~E---~k~k~dsLeK~~seLKK~R 139 (226)
T cd07645 63 SKELGHVLMEISDVHKKLNDSLEENFKKFHREIIAELERKTDLDVKYMTATLKRYQTE---HKNKLDSLEKSQADLKKIR 139 (226)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Confidence 456778885445999999998873 3578999999999999988875443 4455678999999988887
Q ss_pred HH
Q 026259 142 IK 143 (241)
Q Consensus 142 s~ 143 (241)
-+
T Consensus 140 RK 141 (226)
T cd07645 140 RK 141 (226)
T ss_pred hc
Confidence 66
No 7
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=49.68 E-value=91 Score=25.57 Aligned_cols=25 Identities=40% Similarity=0.419 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHH
Q 026259 94 VQRRLQLRIEAQGKYLQSILEKACK 118 (241)
Q Consensus 94 vQR~LQlRIEaQGkYLq~iLEKAqe 118 (241)
.=+.||.+|.+||+-|++|++.-+.
T Consensus 68 qIkel~~e~k~qgktL~~I~~~L~~ 92 (102)
T PF01519_consen 68 QIKELQVEQKAQGKTLQLILKTLQS 92 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3378999999999999999875443
No 8
>cd07646 I-BAR_IMD_IRSp53 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Insulin Receptor tyrosine kinase Substrate p53. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. IRSp53 (Insulin Receptor tyrosine kinase Substrate p53) is also known as BAIAP2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2). It is a scaffolding protein that takes part in many signaling pathways including Cdc42-induced filopodia formation, Rac-mediated lamellipodia extension, and spine morphogenesis. IRSp53 exists as multiple splicing variants that differ mainly at the C-termini. One variant (T-form) is expressed exclusively in human breast cancer cells. The gene encoding IRSp53 is a putative susceptibility gene for Gilles de la Tourette syndrome. IRSp53 contains an N-terminal IMD, a CRIB (Cdc42 and Rac interactive binding motif), an SH3 domain, and a WASP
Probab=48.78 E-value=1.8e+02 Score=27.07 Aligned_cols=70 Identities=27% Similarity=0.392 Sum_probs=53.4
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHH
Q 026259 71 GYQVTEALRVQMEVQRRLHEQLEVQ---------RRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREELSELA 141 (241)
Q Consensus 71 ~~qI~EALrmQmEVQrRLhEQLEvQ---------R~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~ 141 (241)
+..|..||.-=-||+|.++.+||++ ..|+.++|..-|||...+.+=+-. +-.-..++|-+++||-.|-
T Consensus 65 SkeLG~~L~~m~~~hr~i~~~le~~lk~Fh~eli~pLE~k~E~D~k~i~a~~Kky~~e---~k~k~~sleK~qseLKKlR 141 (232)
T cd07646 65 SKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLTAALKKYQTE---HRSKGESLEKCQAELKKLR 141 (232)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Confidence 4567788855458888888888744 479999999999999876665443 4455678999999998877
Q ss_pred HH
Q 026259 142 IK 143 (241)
Q Consensus 142 s~ 143 (241)
-+
T Consensus 142 rK 143 (232)
T cd07646 142 KK 143 (232)
T ss_pred Hh
Confidence 55
No 9
>PF06548 Kinesin-related: Kinesin-related; InterPro: IPR010544 This entry represents a domain within kinesin-related proteins from higher plants. Many proteins containing this domain also contain the IPR001752 from INTERPRO domain. Kinesins are ATP-driven microtubule motor proteins that produce directed force []. Some family members are associated with the phragmoplast, a structure composed mainly of microtubules that executes cytokinesis in higher plants [].
Probab=35.46 E-value=5.1e+02 Score=26.59 Aligned_cols=64 Identities=31% Similarity=0.475 Sum_probs=43.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHhHHHHHHH---HHHHHHhhhhhhhhhchHHHHH
Q 026259 72 YQVTEALRVQMEVQRRLHEQLE------------VQRRLQLRIEAQGKYLQSIL---EKACKALNDQAIVAAGLEAARE 135 (241)
Q Consensus 72 ~qI~EALrmQmEVQrRLhEQLE------------vQR~LQlRIEaQGkYLq~iL---EKAqe~La~~~~~~~glEaak~ 135 (241)
+.++|-||+-+|..|.|-|-+| ++--||.-|+-|.|.|.--- ||--.-++.|...-.||+-.|.
T Consensus 294 IsLteeLR~dle~~r~~aek~~~EL~~Ek~c~eEL~~al~~A~~GhaR~lEqYadLqEk~~~Ll~~Hr~i~egI~dVKk 372 (488)
T PF06548_consen 294 ISLTEELRVDLESSRSLAEKLEMELDSEKKCTEELDDALQRAMEGHARMLEQYADLQEKHNDLLARHRRIMEGIEDVKK 372 (488)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6688999999999999888765 55678888888877765432 2222334555555556654433
No 10
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=31.91 E-value=1.8e+02 Score=20.36 Aligned_cols=49 Identities=24% Similarity=0.338 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHHHHhh
Q 026259 94 VQRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREELSELAIKVS 145 (241)
Q Consensus 94 vQR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~s~v~ 145 (241)
-.+.++-.|..+..-+..|.+.++.-.... +..-..-+..+.+|.....
T Consensus 42 ~~~~~~~ei~~~~~~l~~l~~~~~~L~~~~---~~~~~~i~~~~~~l~~~w~ 90 (105)
T PF00435_consen 42 KHKELQEEIESRQERLESLNEQAQQLIDSG---PEDSDEIQEKLEELNQRWE 90 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HTTHHHHHHHHHHHHHHHH
T ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHcC---CCcHHHHHHHHHHHHHHHH
Confidence 334455566777777888888877774433 3344555666666665543
No 11
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=31.20 E-value=1.6e+02 Score=26.85 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Q 026259 79 RVQMEVQRRLHEQLEVQRRLQLRIEAQGKYLQSILEKACKALN 121 (241)
Q Consensus 79 rmQmEVQrRLhEQLEvQR~LQlRIEaQGkYLq~iLEKAqe~La 121 (241)
++|.|+|.+|.+.-.==+.|.=.||.+..-|+.|.+++.+--.
T Consensus 54 ~~~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~ 96 (263)
T PRK10803 54 QLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYL 96 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888888664333356788899999999999998777543
No 12
>KOG2620 consensus Prohibitins and stomatins of the PID superfamily [Energy production and conversion]
Probab=30.53 E-value=2.5e+02 Score=27.00 Aligned_cols=51 Identities=24% Similarity=0.158 Sum_probs=38.8
Q ss_pred CCCCccHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH---HHHhHHHHHHHHHHHH
Q 026259 68 PNDGYQVTEALRVQMEVQRRLHEQL---EVQRRLQLRI---EAQGKYLQSILEKACK 118 (241)
Q Consensus 68 ~~~~~qI~EALrmQmEVQrRLhEQL---EvQR~LQlRI---EaQGkYLq~iLEKAqe 118 (241)
..-.-++.+|.+||-|.+|+=.-++ |--|.+|+.+ |++.|||.+.=.+++.
T Consensus 153 I~pp~~V~~AM~~q~~AeR~krAailesEger~~~InrAEGek~s~iL~seg~~~qr 209 (301)
T KOG2620|consen 153 IEPPPSVKRAMNMQNEAERMKRAAILESEGERIAQINRAEGEKESKILASEGIARQR 209 (301)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHhhhhhcchhhhHHhhhHHHHHHH
Confidence 3334578999999999999766553 4778888877 6889999887666554
No 13
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=29.60 E-value=3.6e+02 Score=31.10 Aligned_cols=73 Identities=22% Similarity=0.244 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHHHHhhcC
Q 026259 74 VTEALRVQMEVQRRLHEQL-EVQRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREELSELAIKVSND 147 (241)
Q Consensus 74 I~EALrmQmEVQrRLhEQL-EvQR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~s~v~~~ 147 (241)
-.+||.+=++++.+|.+-+ |+++-|++--||-- --...-++|+++|..-+.+..-.+.+.++|.+|...|.++
T Consensus 1410 A~~A~~~A~~~~~~l~~~~ae~eq~~~~v~ea~~-~aseA~~~Aq~~~~~a~as~~q~~~s~~el~~Li~~v~~F 1483 (1758)
T KOG0994|consen 1410 AGGALLMAGDADTQLRSKLAEAEQTLSMVREAKL-SASEAQQSAQRALEQANASRSQMEESNRELRNLIQQVRDF 1483 (1758)
T ss_pred cchHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3478888888877776643 57777766544432 2224556777777777777777889999999999988863
No 14
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=28.19 E-value=24 Score=26.75 Aligned_cols=14 Identities=50% Similarity=0.674 Sum_probs=7.3
Q ss_pred cCCCCchHHHHHHHh
Q 026259 4 MGVKGLTLYHLKSHL 18 (241)
Q Consensus 4 MGVkGLTLYHLKSHL 18 (241)
|||+||+-| +|.+.
T Consensus 1 MGI~gL~~~-l~~~~ 14 (101)
T PF00752_consen 1 MGIKGLWQL-LKPAA 14 (101)
T ss_dssp ---TTHHHH-CHHHE
T ss_pred CCcccHHHH-HHhhc
Confidence 999999876 44443
No 15
>KOG4466 consensus Component of histone deacetylase complex (breast carcinoma metastasis suppressor 1 protein in human) [Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=27.04 E-value=4.1e+02 Score=25.54 Aligned_cols=38 Identities=16% Similarity=0.295 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHH
Q 026259 94 VQRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREEL 137 (241)
Q Consensus 94 vQR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eL 137 (241)
+|+.++.||+--|.|.+-+++.++.-.- .-++||++++
T Consensus 69 L~~~~kerl~~aely~e~~~e~v~~eYe------~E~~aAk~e~ 106 (291)
T KOG4466|consen 69 LDESRKERLRVAELYREYCVERVEREYE------CEIKAAKKEY 106 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHH
Confidence 8999999999999999999888776543 2345555553
No 16
>KOG1916 consensus Nuclear protein, contains WD40 repeats [General function prediction only]
Probab=22.87 E-value=4.5e+02 Score=29.60 Aligned_cols=44 Identities=39% Similarity=0.414 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHH----------HHHHHHHHHHHHhHHHHHHHHHHHHHhhhh
Q 026259 80 VQMEVQRRLHEQLE----------VQRRLQLRIEAQGKYLQSILEKACKALNDQ 123 (241)
Q Consensus 80 mQmEVQrRLhEQLE----------vQR~LQlRIEaQGkYLq~iLEKAqe~La~~ 123 (241)
-|-|+|+||.-||+ |.|-|.-+-+|.-+-|+.-|-|-++++.++
T Consensus 898 sQ~el~~~l~~ql~g~le~~l~~~iEk~lks~~d~~~~rl~e~la~~e~~~r~~ 951 (1283)
T KOG1916|consen 898 SQKELQRQLSNQLTGPLEVALGRMIEKSLKSNADALWARLQEELAKNEKALRDL 951 (1283)
T ss_pred hHHHHHHHHHHhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhhhhHH
Confidence 36788888888876 456666777777777777776666655543
No 17
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=22.65 E-value=1.5e+02 Score=21.81 Aligned_cols=34 Identities=24% Similarity=0.395 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHH
Q 026259 108 YLQSILEKACKALNDQAIVAAGLEAAREELSELA 141 (241)
Q Consensus 108 YLq~iLEKAqe~La~~~~~~~glEaak~eLseL~ 141 (241)
.|++++-.|.+.|+.+..-...++..++|...|.
T Consensus 18 ~MK~l~~~aeq~L~~~~~i~~al~~Lk~EIaklE 51 (53)
T PF08898_consen 18 QMKALAAQAEQQLAEAGDIAAALEKLKAEIAKLE 51 (53)
T ss_pred HHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHh
Confidence 4677888999999988877788888898887764
No 18
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=22.60 E-value=7e+02 Score=25.45 Aligned_cols=52 Identities=27% Similarity=0.376 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchH
Q 026259 74 VTEALRVQMEVQRRLHEQLEVQRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLE 131 (241)
Q Consensus 74 I~EALrmQmEVQrRLhEQLEvQR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glE 131 (241)
|..|| -|+||+| ||+|.| .|.-|||.| ++-+.-||---+-|...-..+..++
T Consensus 117 i~~~~---~el~~q~-e~~ea~-e~e~~~erh-~~h~~~le~i~~~l~n~~~~pe~v~ 168 (548)
T COG5665 117 IHDCL---DELQKQL-EQYEAQ-ENEEQTERH-EFHIANLENILKKLQNNEMDPEPVE 168 (548)
T ss_pred HHHHH---HHHHHHH-HHHHHH-HhHHHHHHH-HHHHHHHHHHHHHHhccCCChhhHH
Confidence 55555 4788877 889998 788999988 6666667766666665444444443
No 19
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=22.19 E-value=5e+02 Score=26.66 Aligned_cols=46 Identities=26% Similarity=0.359 Sum_probs=33.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 026259 73 QVTEALRVQMEVQRRLHEQLEVQRRLQLRIEAQGKYLQSILEKACKA 119 (241)
Q Consensus 73 qI~EALrmQmEVQrRLhEQLEvQR~LQlRIEaQGkYLq~iLEKAqe~ 119 (241)
+-+--|--|+|-||+.-||. +=+-.|-.+|-|..|+...+.+|...
T Consensus 321 ~~s~ll~sqleSqr~y~e~~-~~e~~qsqlen~k~~~e~~~~e~~~l 366 (493)
T KOG0804|consen 321 EYSPLLTSQLESQRKYYEQI-MSEYEQSQLENQKQYYELLITEADSL 366 (493)
T ss_pred ecchhhhhhhhHHHHHHHHH-HHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 33446667999999999953 33344568888999998888877663
No 20
>COG5420 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=22.00 E-value=3.8e+02 Score=20.69 Aligned_cols=47 Identities=38% Similarity=0.592 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH---------h---HHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHH
Q 026259 83 EVQRRLHEQLEVQRRLQLRIEAQ---------G---KYLQSILEKACKALNDQAIVAAGLEAAREELSELA 141 (241)
Q Consensus 83 EVQrRLhEQLEvQR~LQlRIEaQ---------G---kYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~ 141 (241)
|+|+|. |+||.|--+- | +|. .|.+-|-+++.-+ +-|+++|.||..|.
T Consensus 10 eiqkKv-------rkLqsrAg~akm~LhDLAEgLP~~wt-ei~~VA~kt~~~y----aeLD~~k~ELakle 68 (71)
T COG5420 10 EIQKKV-------RKLQSRAGQAKMELHDLAEGLPVKWT-EIMAVAEKTFEAY----AELDAAKRELAKLE 68 (71)
T ss_pred HHHHHH-------HHHHHHHHHHHhhHHHHhccCCccHH-HHHHHHHHHHHHH----HHHHHHHHHHHHhh
Confidence 567776 6777764322 1 343 2444444444433 36788899887764
No 21
>PF03816 LytR_cpsA_psr: Cell envelope-related transcriptional attenuator domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.; PDB: 3PE5_B 3QFI_A 3NRO_B 3OKZ_B 3OWQ_C 3MEJ_A 4DE9_A 3TEP_A 3TEL_A 3TFL_A ....
Probab=21.39 E-value=78 Score=26.07 Aligned_cols=18 Identities=39% Similarity=0.434 Sum_probs=15.9
Q ss_pred HHHHHHhHHHHHHHHHHH
Q 026259 100 LRIEAQGKYLQSILEKAC 117 (241)
Q Consensus 100 lRIEaQGkYLq~iLEKAq 117 (241)
-|++.|.+||.++++|+.
T Consensus 131 ~R~~rQ~~~l~al~~k~~ 148 (149)
T PF03816_consen 131 GRIQRQQEVLKALLEKLK 148 (149)
T ss_dssp HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 489999999999999974
No 22
>PF01815 Rop: Rop protein; InterPro: IPR000769 The Rop protein regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor. Processing of the precursor, RNAII, is inhibited by hydrogen bonding of RNAII to its complementary sequence in RNAI. Rop increases the affinity of RNAI for RNAII and thus decreases the rate of replication initiation events. The 3D structure of Rop has been determined by X-ray crystallography and refined to 1.7A resolution. The 63 amino acid protein is a homodimer, each monomer consisting almost entirely of two alpha-helices, the whole molecule forming a highly regular four-alpha-helix bundle []. This can be approximated by a four-stranded rope, with radius 7.0 A, a left-handed helical twist, and pitch 172.5 A. A very compact packing of side chains in the helix interfaces of the Rop coiled-coil structure is presumed to account for its high stability []. The overall details of the structure have been confirmed by proton NMR [, ].; PDB: 1GTO_C 2IJH_A 2IJJ_B 1GMG_A 1ROP_A 1NKD_A 1QX8_A 1F4M_D 2GHY_B 3K79_A ....
Probab=20.77 E-value=87 Score=23.50 Aligned_cols=21 Identities=38% Similarity=0.526 Sum_probs=16.2
Q ss_pred HHHHHHHHH-HHHHHHHHHHHH
Q 026259 85 QRRLHEQLE-VQRRLQLRIEAQ 105 (241)
Q Consensus 85 QrRLhEQLE-vQR~LQlRIEaQ 105 (241)
=-||||+-| +.++|..|++..
T Consensus 38 CE~LHe~AE~L~~~l~~r~~~e 59 (60)
T PF01815_consen 38 CERLHELAEQLYRSLSARLGEE 59 (60)
T ss_dssp HHHHHHHHHHHHHHHHHHHT-T
T ss_pred HHHHHHHHHHHHHHHHHHhccC
Confidence 358999977 789999998764
No 23
>PF00517 GP41: Retroviral envelope protein; InterPro: IPR000328 This entry represents envelope proteins from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from Human immunodeficiency virus (HIV) and Simian-Human immunodeficiency virus (SIV), which mediate membrane fusion during viral entry []. It has a core composed of a six-helix bundle and is folded by its trimeric N- and C-terminal heptad-repeats (NHR and CHR) []. Derivatives of this protein prevent HIV-1 from entering cell lines and primary human CD4+ cells in vitro [], making it an attractive subject of gene therapy studies against HIV and related retroviruses. The entry also represents envelop proteins from Bovine immunodeficiency virus, Feline immunodeficiency virus and Equine infectious anemia virus (EIAV) [, ], as well as the Gp36 protein from Mouse mammary tumor virus (MMTV) and Human endogenous retrovirus (HERV).; GO: 0005198 structural molecule activity, 0019031 viral envelope; PDB: 2EZO_B 2EZQ_B 2EZR_A 2JNR_B 1F23_D 2EZP_A 1JEK_A 2Q7C_A 2Q5U_A 2Q3I_A ....
Probab=20.39 E-value=3.3e+02 Score=24.08 Aligned_cols=39 Identities=31% Similarity=0.321 Sum_probs=27.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhHHHHH
Q 026259 73 QVTEALRVQMEVQRRLHEQLEVQRR----LQLRIEAQGKYLQS 111 (241)
Q Consensus 73 qI~EALrmQmEVQrRLhEQLEvQR~----LQlRIEaQGkYLq~ 111 (241)
+.+.+|+.|-..|..|.-++--=++ ||-|+.|=.+||+.
T Consensus 22 ~~~~ll~~~e~~~~lL~l~v~gik~~V~~L~aRV~alE~~l~d 64 (204)
T PF00517_consen 22 QQSNLLRAQEAQQHLLQLTVWGIKQGVKQLQARVLALERYLKD 64 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 3456777777777777766654444 88888888888743
No 24
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=20.39 E-value=5.2e+02 Score=21.67 Aligned_cols=52 Identities=13% Similarity=0.186 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchHHHHHHHHHHHHHhh
Q 026259 94 VQRRLQLRIEAQGKYLQSILEKACKALNDQAIVAAGLEAAREELSELAIKVS 145 (241)
Q Consensus 94 vQR~LQlRIEaQGkYLq~iLEKAqe~La~~~~~~~glEaak~eLseL~s~v~ 145 (241)
..|||..||+.=++-|....|-++.+-.+=+.....++..+.++..+...|.
T Consensus 62 tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~ 113 (126)
T PF07889_consen 62 TKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVE 113 (126)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 6789999999988888877776655544333334444444555444444443
Done!