Query 048122
Match_columns 125
No_of_seqs 127 out of 666
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:28:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048122hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02519 Auxin_inducible: Auxi 100.0 4.7E-38 1E-42 224.1 10.1 98 1-101 1-100 (100)
2 PLN03090 auxin-responsive fami 100.0 1.1E-36 2.5E-41 219.0 10.4 90 4-100 12-103 (104)
3 PLN03220 uncharacterized prote 100.0 9.6E-32 2.1E-36 193.5 9.7 64 35-98 31-101 (105)
4 PLN03219 uncharacterized prote 100.0 8.8E-32 1.9E-36 194.6 9.6 87 12-99 13-104 (108)
5 PRK02899 adaptor protein; Prov 87.8 0.46 9.9E-06 37.4 2.6 24 63-86 38-62 (197)
6 PRK02315 adaptor protein; Prov 84.1 0.83 1.8E-05 36.7 2.4 24 63-86 38-62 (233)
7 PF02214 BTB_2: BTB/POZ domain 83.1 0.57 1.2E-05 31.4 0.9 53 51-103 7-63 (94)
8 PF05389 MecA: Negative regula 77.4 0.74 1.6E-05 36.1 0.0 24 63-86 38-62 (220)
9 cd05992 PB1 The PB1 domain is 67.2 12 0.00027 23.9 4.0 52 47-102 7-70 (81)
10 smart00666 PB1 PB1 domain. Pho 67.1 11 0.00023 24.4 3.7 50 47-101 8-69 (81)
11 PF00651 BTB: BTB/POZ domain; 63.8 21 0.00045 23.5 4.7 57 44-103 13-74 (111)
12 PF14317 YcxB: YcxB-like prote 57.7 20 0.00044 21.2 3.5 33 39-71 27-59 (62)
13 PF11822 DUF3342: Domain of un 44.7 46 0.001 28.5 4.8 52 51-105 13-70 (317)
14 cd06407 PB1_NLP A PB1 domain i 44.2 43 0.00093 22.8 3.8 47 45-95 5-64 (82)
15 PF08948 DUF1859: Domain of un 41.8 12 0.00026 27.7 0.7 28 40-67 86-123 (126)
16 COG0826 Collagenase and relate 40.7 28 0.00061 29.7 2.9 63 38-101 22-86 (347)
17 PF03460 NIR_SIR_ferr: Nitrite 39.6 33 0.00072 21.5 2.5 56 40-101 6-67 (69)
18 COG1759 5-formaminoimidazole-4 39.2 15 0.00031 32.0 1.0 75 36-111 87-196 (361)
19 COG4923 Predicted nuclease (RN 36.4 51 0.0011 27.0 3.6 15 82-96 87-101 (245)
20 cd06396 PB1_NBR1 The PB1 domai 35.0 1.1E+02 0.0024 21.1 4.7 56 45-103 5-70 (81)
21 PF06849 DUF1246: Protein of u 34.6 1.8 3.8E-05 32.4 -4.6 23 36-58 67-92 (124)
22 PF12058 DUF3539: Protein of u 34.3 6.3 0.00014 27.9 -1.6 13 59-71 4-16 (88)
23 TIGR02527 dot_icm_IcmQ Dot/Icm 34.1 38 0.00082 26.9 2.5 55 11-65 78-146 (182)
24 cd06397 PB1_UP1 Uncharacterize 33.9 93 0.002 21.8 4.1 46 47-96 7-64 (82)
25 PF01799 Fer2_2: [2Fe-2S] bind 32.8 99 0.0021 20.8 4.1 51 63-123 12-64 (75)
26 PF00564 PB1: PB1 domain; Int 30.8 82 0.0018 20.1 3.4 49 49-101 10-70 (84)
27 COG0623 FabI Enoyl-[acyl-carri 30.0 80 0.0017 26.4 3.9 41 56-100 35-75 (259)
28 KOG1290 Serine/threonine prote 29.9 30 0.00064 31.9 1.5 19 39-57 62-83 (590)
29 cd06401 PB1_TFG The PB1 domain 29.6 1E+02 0.0022 21.4 3.8 43 45-90 5-62 (81)
30 PRK13277 5-formaminoimidazole- 29.2 22 0.00049 30.8 0.6 26 36-63 87-115 (366)
31 TIGR03193 4hydroxCoAred 4-hydr 29.2 1.5E+02 0.0033 22.5 5.0 62 52-123 67-135 (148)
32 cd04751 Commd3 COMM_Domain con 29.1 45 0.00098 23.1 2.0 29 81-110 64-92 (95)
33 PRK06029 3-octaprenyl-4-hydrox 28.7 1.6E+02 0.0034 22.9 5.2 45 52-96 117-165 (185)
34 PF04332 DUF475: Protein of un 28.3 39 0.00084 28.7 1.8 16 2-17 6-21 (294)
35 smart00540 LEM in nuclear memb 28.0 51 0.0011 20.3 1.9 18 68-86 10-27 (44)
36 TIGR03849 arch_ComA phosphosul 27.1 19 0.00042 29.4 -0.2 53 43-101 54-110 (237)
37 COG4862 MecA Negative regulato 27.0 46 0.001 27.3 2.0 26 62-87 37-63 (224)
38 PF04019 DUF359: Protein of un 26.9 1.1E+02 0.0024 22.4 3.8 28 75-102 90-117 (121)
39 PF07429 Glyco_transf_56: 4-al 26.8 1.2E+02 0.0026 26.5 4.5 90 9-103 149-266 (360)
40 PF11046 HycA_repressor: Trans 26.6 1.7E+02 0.0036 22.6 4.8 58 40-101 58-124 (148)
41 PF02209 VHP: Villin headpiece 26.3 30 0.00065 20.4 0.6 18 60-77 1-19 (36)
42 PF01976 DUF116: Protein of un 26.0 1.1E+02 0.0025 23.1 3.9 22 80-101 107-128 (158)
43 PF11834 DUF3354: Domain of un 26.0 56 0.0012 21.8 1.9 16 64-79 26-42 (69)
44 smart00153 VHP Villin headpiec 25.3 35 0.00075 20.1 0.7 18 60-77 1-19 (36)
45 PF05194 UreE_C: UreE urease a 25.1 1.1E+02 0.0025 20.4 3.4 29 40-73 23-51 (87)
46 PF02641 DUF190: Uncharacteriz 24.9 91 0.002 21.6 2.9 30 43-78 5-34 (101)
47 cd06398 PB1_Joka2 The PB1 doma 24.9 1.4E+02 0.0031 20.7 3.9 52 47-98 7-72 (91)
48 cd01310 TatD_DNAse TatD like p 23.9 88 0.0019 23.5 2.9 38 61-103 105-142 (251)
49 PF12926 MOZART2: Mitotic-spin 23.7 1.6E+02 0.0036 20.8 4.0 51 61-119 22-72 (88)
50 TIGR03198 pucE xanthine dehydr 23.5 2.1E+02 0.0045 21.8 4.9 62 52-123 69-136 (151)
51 COG2899 Uncharacterized protei 23.2 43 0.00093 28.8 1.1 16 2-17 56-71 (346)
52 PF11490 DNA_pol3_a_NII: DNA p 23.0 74 0.0016 21.3 2.1 36 44-79 25-64 (117)
53 PRK09908 xanthine dehydrogenas 22.6 2.2E+02 0.0048 21.9 4.9 60 52-123 73-143 (159)
54 cd04404 RhoGAP-p50rhoGAP RhoGA 22.5 2.3E+02 0.005 21.4 5.0 40 67-106 28-67 (195)
55 PF07582 AP_endonuc_2_N: AP en 22.2 2.2E+02 0.0048 18.1 4.3 22 66-89 2-23 (55)
56 COG5431 Uncharacterized metal- 22.1 1E+02 0.0022 22.8 2.8 62 41-102 32-103 (117)
57 PF10087 DUF2325: Uncharacteri 20.9 2.7E+02 0.0059 18.6 5.7 48 48-98 46-94 (97)
58 PF14974 DUF4511: Domain of un 20.5 2.6E+02 0.0056 20.3 4.6 37 64-105 47-84 (105)
59 PF09475 Dot_icm_IcmQ: Dot/Icm 20.3 34 0.00074 27.1 0.0 55 11-65 78-146 (179)
60 PRK10308 3-methyl-adenine DNA 20.3 3.8E+02 0.0082 22.0 6.2 60 41-100 45-121 (283)
61 COG1852 Uncharacterized conser 20.3 1.4E+02 0.003 24.3 3.5 21 80-100 154-174 (209)
62 PF00191 Annexin: Annexin; In 20.1 1.8E+02 0.0039 17.7 3.4 35 64-114 30-65 (66)
No 1
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=4.7e-38 Score=224.07 Aligned_cols=98 Identities=41% Similarity=0.657 Sum_probs=87.1
Q ss_pred CCChHHHHHHHHHHHhhhhccccccccccccCCCCccccccCeEEEEEec-ceeeEEeecccCcHHHHHHHHHHH-HcCC
Q 048122 1 MISTKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKCYVKGHFIVYTVD-HKRFVLPLVYLNNNVVQALLELAE-EFGL 78 (125)
Q Consensus 1 m~~~~kL~~~~rKWq~~a~~~~~r~s~~~~~~~~~~~~vpkG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~ae-EfG~ 78 (125)
|++.+|..+.++||++.+...+++.+..... ...++|+||||||||+ ++||+||++|||||+|++||++|| ||||
T Consensus 1 M~~~~k~~~~~~k~~~~~~~~~~~~~~~~~~---~~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~ 77 (100)
T PF02519_consen 1 MASRLKSLASAKKWQSRARSKSSSSSSSRSS---SESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGF 77 (100)
T ss_pred CccHHHHHHHHHhhhhhhhhccccccccccc---ccCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCc
Confidence 9999999999999999887666544433222 2367999999999997 999999999999999999999999 9999
Q ss_pred CCCCCeEecCcHHHHHHHHHHHh
Q 048122 79 PTNGPLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 79 ~~~G~L~iPC~~~~Fe~vl~~i~ 101 (125)
+++|+|+||||+++||+++|+|+
T Consensus 78 ~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 78 DQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred CCCCcEEeeCCHHHHHHHHHHhC
Confidence 99999999999999999999985
No 2
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.1e-36 Score=219.02 Aligned_cols=90 Identities=28% Similarity=0.498 Sum_probs=79.3
Q ss_pred hHHHHHHHHHHHhhhhccccccccccccCCCCccccccCeEEEEEec-ceeeEEeecccCcHHHHHHHHHHH-HcCCCCC
Q 048122 4 TKKLIKLARKWQKLAAIRQKRIMSTIFKGDDAEKCYVKGHFIVYTVD-HKRFVLPLVYLNNNVVQALLELAE-EFGLPTN 81 (125)
Q Consensus 4 ~~kL~~~~rKWq~~a~~~~~r~s~~~~~~~~~~~~vpkG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~~~ 81 (125)
+++|++|.|||++++..+. . ..+..+.+||+||||||||+ ++||+||++|||||+|++||++|| ||||+++
T Consensus 12 ~~~~kq~l~r~~s~~~~~~----~---~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~ 84 (104)
T PLN03090 12 TAMLKQILKRCSSLGKKQG----Y---DEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFDHD 84 (104)
T ss_pred HHHHHHHHHHHHHhcccCC----c---ccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCC
Confidence 6899999999998855321 1 11235678999999999997 689999999999999999999999 9999999
Q ss_pred CCeEecCcHHHHHHHHHHH
Q 048122 82 GPLTVLCDTAFMEYVVTLI 100 (125)
Q Consensus 82 G~L~iPC~~~~Fe~vl~~i 100 (125)
|+|+||||+++|++++|+|
T Consensus 85 G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 85 MGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CcEEEeCCHHHHHHHHHHh
Confidence 9999999999999999998
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=99.97 E-value=9.6e-32 Score=193.54 Aligned_cols=64 Identities=34% Similarity=0.615 Sum_probs=60.2
Q ss_pred CccccccCeEEEEEec-----ceeeEEeecccCcHHHHHHHHHHH-HcCCCC-CCCeEecCcHHHHHHHHH
Q 048122 35 AEKCYVKGHFIVYTVD-----HKRFVLPLVYLNNNVVQALLELAE-EFGLPT-NGPLTVLCDTAFMEYVVT 98 (125)
Q Consensus 35 ~~~~vpkG~~~VyVGe-----~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~~-~G~L~iPC~~~~Fe~vl~ 98 (125)
.+.+|||||||||||+ ++||+||++|||||+|++||++|| ||||++ +|+|+||||++.|++++.
T Consensus 31 ~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~ 101 (105)
T PLN03220 31 SSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIA 101 (105)
T ss_pred ccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHH
Confidence 4668999999999996 699999999999999999999999 999997 699999999999999985
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=8.8e-32 Score=194.56 Aligned_cols=87 Identities=28% Similarity=0.429 Sum_probs=69.7
Q ss_pred HHHHhhhhccccccccccccCCCCccccccCeEEEEEec---ceeeEEeecccCcHHHHHHHHHHH-HcCCCC-CCCeEe
Q 048122 12 RKWQKLAAIRQKRIMSTIFKGDDAEKCYVKGHFIVYTVD---HKRFVLPLVYLNNNVVQALLELAE-EFGLPT-NGPLTV 86 (125)
Q Consensus 12 rKWq~~a~~~~~r~s~~~~~~~~~~~~vpkG~~~VyVGe---~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~~-~G~L~i 86 (125)
+-|+..+..+++-.+.++ ...+.+.++||||||||||+ ++||+||++|||||+|++||++|| ||||++ +|+|+|
T Consensus 13 ~~~~~~~~~~~~~~~~~~-~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~I 91 (108)
T PLN03219 13 QIFKSQSMRNKNGSSSPS-SSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTI 91 (108)
T ss_pred HHHHHHHHhcccCCCCCc-cCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEE
Confidence 456655444433222222 22344678999999999996 799999999999999999999999 999996 699999
Q ss_pred cCcHHHHHHHHHH
Q 048122 87 LCDTAFMEYVVTL 99 (125)
Q Consensus 87 PC~~~~Fe~vl~~ 99 (125)
|||++.|++++..
T Consensus 92 PCd~~~F~~ll~~ 104 (108)
T PLN03219 92 PCREESFLHLITS 104 (108)
T ss_pred eCCHHHHHHHHHh
Confidence 9999999999975
No 5
>PRK02899 adaptor protein; Provisional
Probab=87.78 E-value=0.46 Score=37.41 Aligned_cols=24 Identities=25% Similarity=0.699 Sum_probs=20.7
Q ss_pred cHHHHHHHHHHH-HcCCCCCCCeEe
Q 048122 63 NNVVQALLELAE-EFGLPTNGPLTV 86 (125)
Q Consensus 63 hp~F~~LL~~ae-EfG~~~~G~L~i 86 (125)
+-+|.++|++|. |+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 357888899999 999999999875
No 6
>PRK02315 adaptor protein; Provisional
Probab=84.08 E-value=0.83 Score=36.67 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=21.6
Q ss_pred cHHHHHHHHHHH-HcCCCCCCCeEe
Q 048122 63 NNVVQALLELAE-EFGLPTNGPLTV 86 (125)
Q Consensus 63 hp~F~~LL~~ae-EfG~~~~G~L~i 86 (125)
+-+|.++|++|. |+||..+|||++
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 358999999999 999999999975
No 7
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=83.08 E-value=0.57 Score=31.45 Aligned_cols=53 Identities=13% Similarity=0.158 Sum_probs=41.1
Q ss_pred ceeeEEeecccC-c--HHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcC
Q 048122 51 HKRFVLPLVYLN-N--NVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHN 103 (125)
Q Consensus 51 ~~RfvVp~~yL~-h--p~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~ 103 (125)
+++|.++.+-|. + ..|..+++... ...-+.+|.+-|-++...|++|+..++.+
T Consensus 7 G~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~ 63 (94)
T PF02214_consen 7 GTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG 63 (94)
T ss_dssp TEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT
T ss_pred CEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHhhc
Confidence 678888888877 4 47888888653 33334679999999999999999999983
No 8
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=77.39 E-value=0.74 Score=36.09 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHH-HcCCCCCCCeEe
Q 048122 63 NNVVQALLELAE-EFGLPTNGPLTV 86 (125)
Q Consensus 63 hp~F~~LL~~ae-EfG~~~~G~L~i 86 (125)
+-+|.++|++|. |+||..+|||++
T Consensus 38 e~fF~~ileea~~e~~F~~~~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFENDGPLTF 62 (220)
T ss_dssp -------------------------
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 468999999999 999999999885
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=67.16 E-value=12 Score=23.93 Aligned_cols=52 Identities=23% Similarity=0.341 Sum_probs=36.7
Q ss_pred EEecceeeEEeecccCcHHHHHHHHHHH-HcCCC----------CCCC-eEecCcHHHHHHHHHHHhc
Q 048122 47 YTVDHKRFVLPLVYLNNNVVQALLELAE-EFGLP----------TNGP-LTVLCDTAFMEYVVTLISH 102 (125)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~----------~~G~-L~iPC~~~~Fe~vl~~i~~ 102 (125)
|-|+.+||.+|- .++-|.+|..+-. .||+. .+|- ++|.++ +.|+.++....+
T Consensus 7 ~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~~~ 70 (81)
T cd05992 7 YGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEARR 70 (81)
T ss_pred ecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHHhh
Confidence 446789999998 7888888888888 77774 3443 556665 566666666553
No 10
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=67.11 E-value=11 Score=24.44 Aligned_cols=50 Identities=20% Similarity=0.353 Sum_probs=35.7
Q ss_pred EEecceeeEEeecccCcHHHHHHHHHHH-HcCCC----------CCC-CeEecCcHHHHHHHHHHHh
Q 048122 47 YTVDHKRFVLPLVYLNNNVVQALLELAE-EFGLP----------TNG-PLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~----------~~G-~L~iPC~~~~Fe~vl~~i~ 101 (125)
|-|+.+||.+|- ..-|.+|..+.. .|++. .+| .++|.++. .++.++.+..
T Consensus 8 ~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~ 69 (81)
T smart00666 8 YGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYD 69 (81)
T ss_pred ECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHH
Confidence 445689999986 677999999988 88773 345 57788865 5555655554
No 11
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=63.78 E-value=21 Score=23.53 Aligned_cols=57 Identities=12% Similarity=0.138 Sum_probs=41.1
Q ss_pred EEEEEecceeeEEeeccc--CcHHHHHHHHHHHHcCCCCCC--CeEec-CcHHHHHHHHHHHhcC
Q 048122 44 FIVYTVDHKRFVLPLVYL--NNNVVQALLELAEEFGLPTNG--PLTVL-CDTAFMEYVVTLISHN 103 (125)
Q Consensus 44 ~~VyVGe~~RfvVp~~yL--~hp~F~~LL~~aeEfG~~~~G--~L~iP-C~~~~Fe~vl~~i~~~ 103 (125)
+.+.||++++|-+.-..| ..|.|+.+++.. +...++ .+.++ ++...|+.++..+-.+
T Consensus 13 ~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~---~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 13 VTIRVGDGKTFYVHKNILAARSPYFRNLFEGS---KFKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTT---TSTTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred EEEEECCCEEEeechhhhhccchhhhhccccc---ccccccccccccccccccccccccccccCC
Confidence 345566789999988887 569999999887 112233 35555 8899999999988655
No 12
>PF14317 YcxB: YcxB-like protein
Probab=57.70 E-value=20 Score=21.22 Aligned_cols=33 Identities=18% Similarity=0.332 Sum_probs=26.3
Q ss_pred cccCeEEEEEecceeeEEeecccCcHHHHHHHH
Q 048122 39 YVKGHFIVYTVDHKRFVLPLVYLNNNVVQALLE 71 (125)
Q Consensus 39 vpkG~~~VyVGe~~RfvVp~~yL~hp~F~~LL~ 71 (125)
.-+.++.+|+++..-++||-+.++.--..++.+
T Consensus 27 e~~~~~~l~~~~~~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 27 ETKDYFYLYLGKNQAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred EeCCEEEEEECCCeEEEEEHHHCCHhHHHHHHH
Confidence 347889999999999999999999655555544
No 13
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=44.69 E-value=46 Score=28.48 Aligned_cols=52 Identities=15% Similarity=0.296 Sum_probs=40.3
Q ss_pred ceeeEEeecccC--cHHHHHHHHH---HH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCc
Q 048122 51 HKRFVLPLVYLN--NNVVQALLEL---AE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVN 105 (125)
Q Consensus 51 ~~RfvVp~~yL~--hp~F~~LL~~---ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~ 105 (125)
.+=|..|.+.|- ...|++.|.. .. +. .+=.|.+-||+..|+.++.-+++..+
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~~p 70 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGEPP 70 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcCCC
Confidence 577999998885 5789999965 22 33 24568999999999999999988443
No 14
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=44.19 E-value=43 Score=22.76 Aligned_cols=47 Identities=23% Similarity=0.361 Sum_probs=31.7
Q ss_pred EEEEecceeeEEeecccCcHHHHHHHHHHH-HcCCCC-----------C-CCeEecCcHHHHHH
Q 048122 45 IVYTVDHKRFVLPLVYLNNNVVQALLELAE-EFGLPT-----------N-GPLTVLCDTAFMEY 95 (125)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~~-----------~-G~L~iPC~~~~Fe~ 95 (125)
+.|=||-.||-+|..- -|++|.++-. .|++.. + ..++|.|+.++=|-
T Consensus 5 ~~~~~d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~ea 64 (82)
T cd06407 5 ATYGEEKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEEC 64 (82)
T ss_pred EEeCCeEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHH
Confidence 3455678999988643 5777777777 666532 2 35788999876553
No 15
>PF08948 DUF1859: Domain of unknown function (DUF1859); InterPro: IPR015043 This entry is represented by Bacteriophage PRD1, P5. This protein has no known function though it is sometimes found in the N terminus of bacteriophage spike proteins []. ; PDB: 1W8X_N.
Probab=41.76 E-value=12 Score=27.73 Aligned_cols=28 Identities=29% Similarity=0.602 Sum_probs=8.5
Q ss_pred ccCeEEEEEecceeeE----------EeecccCcHHHH
Q 048122 40 VKGHFIVYTVDHKRFV----------LPLVYLNNNVVQ 67 (125)
Q Consensus 40 pkG~~~VyVGe~~Rfv----------Vp~~yL~hp~F~ 67 (125)
.+||||+.|-.+..|+ +|+-|||.|+-+
T Consensus 86 ~QGYfPlL~~~~~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 86 KQGYFPLLVPGRAKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp --SS--EEE--SSSSEEEEEEEESS----S--------
T ss_pred CcccceeeccchhhhhhhhccCCCcceeeEEEeceeee
Confidence 4799999996655555 788899988754
No 16
>COG0826 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]
Probab=40.69 E-value=28 Score=29.69 Aligned_cols=63 Identities=17% Similarity=0.156 Sum_probs=42.8
Q ss_pred ccccCeEEEEEecceeeEEeecc--cCcHHHHHHHHHHHHcCCCCCCCeEecCcHHHHHHHHHHHh
Q 048122 38 CYVKGHFIVYTVDHKRFVLPLVY--LNNNVVQALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 38 ~vpkG~~~VyVGe~~RfvVp~~y--L~hp~F~~LL~~aeEfG~~~~G~L~iPC~~~~Fe~vl~~i~ 101 (125)
.+..|--+||+|++ +|-..... +++.-+++..+.|.++|=..-=.++..|.....+.+.+.++
T Consensus 22 ai~~GADaVY~G~~-~~~~R~~a~nfs~~~l~e~i~~ah~~gkk~~V~~N~~~~~~~~~~~~~~l~ 86 (347)
T COG0826 22 AIAAGADAVYIGEK-EFGLRRRALNFSVEDLAEAVELAHSAGKKVYVAVNTLLHNDELETLERYLD 86 (347)
T ss_pred HHHcCCCEEEeCCc-ccccccccccCCHHHHHHHHHHHHHcCCeEEEEeccccccchhhHHHHHHH
Confidence 35578889999987 66666555 88888999999888887543333455566666654444443
No 17
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=39.59 E-value=33 Score=21.52 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=36.8
Q ss_pred ccCeEEEEEecceeeEEeecccCcHHHHHHHHHHHHcCC-----CCCCCeEec-CcHHHHHHHHHHHh
Q 048122 40 VKGHFIVYTVDHKRFVLPLVYLNNNVVQALLELAEEFGL-----PTNGPLTVL-CDTAFMEYVVTLIS 101 (125)
Q Consensus 40 pkG~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeEfG~-----~~~G~L~iP-C~~~~Fe~vl~~i~ 101 (125)
+.|++.|. +-+|.--++-..++.|.+.|++||- +.+..|.|+ -+.+..+.+...|+
T Consensus 6 ~~g~~~v~------~~~~~G~i~~~~l~~la~ia~~yg~~~irlT~~Q~l~l~~v~~~~~~~i~~~L~ 67 (69)
T PF03460_consen 6 GDGFYMVR------IRIPGGRISAEQLRALAEIAEKYGDGEIRLTTRQNLQLRGVPEENLPAIFEELK 67 (69)
T ss_dssp STTEEEEE------EB-GGGEEEHHHHHHHHHHHHHHSTSEEEEETTSCEEEEEEEGGGHHHHHHHHH
T ss_pred CCeEEEEE------EeCCCEEECHHHHHHHHHHHHHhCCCeEEECCCCeEEEeCCCHHHHHHHHHHHH
Confidence 35666665 4566667788899999999999983 244456665 66666666665553
No 18
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=39.24 E-value=15 Score=32.00 Aligned_cols=75 Identities=20% Similarity=0.301 Sum_probs=43.2
Q ss_pred ccccccCeEEEEEe-c--ceeeEEee---------cccCcHHHHHHHHHHH-Hc--CCC----CCCCeE-----------
Q 048122 36 EKCYVKGHFIVYTV-D--HKRFVLPL---------VYLNNNVVQALLELAE-EF--GLP----TNGPLT----------- 85 (125)
Q Consensus 36 ~~~vpkG~~~VyVG-e--~~RfvVp~---------~yL~hp~F~~LL~~ae-Ef--G~~----~~G~L~----------- 85 (125)
..-+|.|-|++||| | -..|.||+ +- ..-.-..||++|- -+ =|+ .||++.
T Consensus 87 ~I~IP~gSfv~Y~G~d~ie~~~~vP~fGnR~lLrwE~-~~~~~~~lLekAgi~~P~~~~~PeeIdr~VIVK~pgAkggRG 165 (361)
T COG1759 87 AIFIPHGSFVAYVGYDGIENEFEVPMFGNRELLRWEE-DRKLEYKLLEKAGLRIPKKYKSPEEIDRPVIVKLPGAKGGRG 165 (361)
T ss_pred eEEecCCceEEEecchhhhhcccCcccccHhHhhhhc-chhhHHHHHHHcCCCCCcccCChHHcCCceEEecCCccCCce
Confidence 34589999999999 4 35677764 22 2334467888886 33 121 245432
Q ss_pred --ecCcHHHHH-HHHHHHhcCCc--hhhhhH
Q 048122 86 --VLCDTAFME-YVVTLISHNVN--EDAERP 111 (125)
Q Consensus 86 --iPC~~~~Fe-~vl~~i~~~~~--~~~e~~ 111 (125)
+.=+...|. .+-.+++++.- +|++.|
T Consensus 166 yFiA~s~eef~ek~e~l~~~gvi~~edlkna 196 (361)
T COG1759 166 YFIASSPEEFYEKAERLLKRGVITEEDLKNA 196 (361)
T ss_pred EEEEcCHHHHHHHHHHHHHcCCcchhhhhhc
Confidence 334455554 44456665533 555554
No 19
>COG4923 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=36.36 E-value=51 Score=27.05 Aligned_cols=15 Identities=20% Similarity=0.439 Sum_probs=11.6
Q ss_pred CCeEecCcHHHHHHH
Q 048122 82 GPLTVLCDTAFMEYV 96 (125)
Q Consensus 82 G~L~iPC~~~~Fe~v 96 (125)
...++||.+..+..+
T Consensus 87 SvF~vPcR~A~Y~~~ 101 (245)
T COG4923 87 SVFSVPCRAALYSDI 101 (245)
T ss_pred ceeccchHHHHHHHH
Confidence 346799999888766
No 20
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=34.99 E-value=1.1e+02 Score=21.10 Aligned_cols=56 Identities=14% Similarity=0.292 Sum_probs=38.0
Q ss_pred EEEEecceeeEEeecccCcHHHHHHHHHHH-HcCCC--------CC-CCeEecCcHHHHHHHHHHHhcC
Q 048122 45 IVYTVDHKRFVLPLVYLNNNVVQALLELAE-EFGLP--------TN-GPLTVLCDTAFMEYVVTLISHN 103 (125)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~--------~~-G~L~iPC~~~~Fe~vl~~i~~~ 103 (125)
|-|=||..||.+|- -.++-|.+|.++-+ -||++ .| -+++|.|++++ +..+.+.++.
T Consensus 5 aty~~d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eL-eE~~rl~~~~ 70 (81)
T cd06396 5 VTYNGESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEY-EEALKSAVRQ 70 (81)
T ss_pred EEECCeEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhH-HHHHHHHHhC
Confidence 44667889999875 12456888888888 88853 33 47899998765 4445555443
No 21
>PF06849 DUF1246: Protein of unknown function (DUF1246); InterPro: IPR010672 The last two steps of de novo purine biosynthesis are: i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR) ii) conversion of FAICAR to inosine5'-monophopsphate (IMP) In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH []. Archaea do not appear to posses PurH, however, and perform these reactions by a different mecahnism []. In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species [, ]. This entry represents the N-terminal domain of PurP. Its function is not known, though it is almost always found in association with IPR009720 from INTERPRO.; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0006188 IMP biosynthetic process; PDB: 2PBZ_C 2R85_B 2R87_E 2R84_A 2R86_A 2R7L_A 2R7N_A 2R7K_A 2R7M_A.
Probab=34.56 E-value=1.8 Score=32.45 Aligned_cols=23 Identities=26% Similarity=0.576 Sum_probs=13.4
Q ss_pred ccccccCeEEEEEe-c--ceeeEEee
Q 048122 36 EKCYVKGHFIVYTV-D--HKRFVLPL 58 (125)
Q Consensus 36 ~~~vpkG~~~VyVG-e--~~RfvVp~ 58 (125)
..-||.|-|++||| | .++|.||+
T Consensus 67 ~I~VPhgSfv~Y~G~d~ie~~~~vP~ 92 (124)
T PF06849_consen 67 AIFVPHGSFVAYVGYDRIENEFKVPI 92 (124)
T ss_dssp EEE--BTTHHHHH-HHHHHHT-SS-E
T ss_pred eEEecCCCeeEeecHHHHhhcCCCCe
Confidence 45689999999999 4 35577775
No 22
>PF12058 DUF3539: Protein of unknown function (DUF3539); InterPro: IPR021926 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved NHP sequence motif. ; PDB: 3N5B_B 2XKO_C 2XG8_F.
Probab=34.25 E-value=6.3 Score=27.94 Aligned_cols=13 Identities=31% Similarity=0.467 Sum_probs=9.0
Q ss_pred cccCcHHHHHHHH
Q 048122 59 VYLNNNVVQALLE 71 (125)
Q Consensus 59 ~yL~hp~F~~LL~ 71 (125)
.|||||.|.-|-.
T Consensus 4 ~YLNHPtFGlLy~ 16 (88)
T PF12058_consen 4 TYLNHPTFGLLYR 16 (88)
T ss_dssp -EEEETTTEEEEE
T ss_pred ccccCCccchhee
Confidence 5889998876544
No 23
>TIGR02527 dot_icm_IcmQ Dot/Icm secretion system protein IcmQ. Members of this protein family are the IcmQ component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation (PubMed:15661013).
Probab=34.07 E-value=38 Score=26.91 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=33.8
Q ss_pred HHHHHh-hhhccccccccccccC--------CCCccccccCeEEEEEecc-----eeeEEeecccCcHH
Q 048122 11 ARKWQK-LAAIRQKRIMSTIFKG--------DDAEKCYVKGHFIVYTVDH-----KRFVLPLVYLNNNV 65 (125)
Q Consensus 11 ~rKWq~-~a~~~~~r~s~~~~~~--------~~~~~~vpkG~~~VyVGe~-----~RfvVp~~yL~hp~ 65 (125)
...|.+ +|++.+..++-|-=.+ -.+...+.+.|++|||-.. --=-+|++=|+.|+
T Consensus 78 lqsWerilanLprqmisRPIYanE~dvk~~IksKenk~NEAYVaiyI~q~dIl~~~~dk~p~Dk~GkpL 146 (182)
T TIGR02527 78 LKQWAKILASLERQMIGRPIYADEADAKAAIKQKENKLNEACVAIAIDQSDIIHLSADKAPKDKLGKLL 146 (182)
T ss_pred HHHHHHHHHhChhhhhCCCCcCCHHHHHHHHHhhhccccceEEEEEEchHhcccCCcccCcccccCCcc
Confidence 468987 6778887776543332 1235568899999999731 11124555555554
No 24
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=33.86 E-value=93 Score=21.80 Aligned_cols=46 Identities=22% Similarity=0.403 Sum_probs=34.2
Q ss_pred EEecceeeEEeecccCcHHHHHHHHHHH-HcCCC----------CCC-CeEecCcHHHHHHH
Q 048122 47 YTVDHKRFVLPLVYLNNNVVQALLELAE-EFGLP----------TNG-PLTVLCDTAFMEYV 96 (125)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~----------~~G-~L~iPC~~~~Fe~v 96 (125)
|-|+.|||..|. .|.+.+|-++-+ =|-++ .|| .|||.=+.++.+..
T Consensus 7 ~~g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~~ 64 (82)
T cd06397 7 FLGDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDFY 64 (82)
T ss_pred eCCceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHHH
Confidence 456789999998 799999988888 67665 343 57887766665544
No 25
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands [].; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 2E3T_A 1WYG_A 3AN1_B 2E1Q_C 2CKJ_A 3B9J_I 3NVY_J 1FO4_B 3NRZ_J 3AM9_A ....
Probab=32.82 E-value=99 Score=20.77 Aligned_cols=51 Identities=18% Similarity=0.363 Sum_probs=28.4
Q ss_pred cHHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCchhhhhHHHHhhh-ccccCC
Q 048122 63 NNVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVNEDAERPLLTLIA-GSHRAS 123 (125)
Q Consensus 63 hp~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~~~~-~~c~~~ 123 (125)
||+-+.+++.-. ..|| |..-+.-.+.++++++...+ +..+-..++ .-|||-
T Consensus 12 ~~iq~af~~~~a~QCGf---------CtpG~im~~~~ll~~~~~p~-~~ei~~al~gnlCRCT 64 (75)
T PF01799_consen 12 HPIQQAFVEHGAVQCGF---------CTPGMIMAAYALLRRNPDPT-EEEIREALSGNLCRCT 64 (75)
T ss_dssp -HHHHHHHHTT--SSSS---------SHHHHHHHHHHHHHHSSS-C-HHHHHHHTTTS--SSS
T ss_pred CHHHHHHHHhCCCcCCc---------chHHHHHHHHHHhhcccchh-hHHHHHHHHcCccCCC
Confidence 677777777666 6776 77777788888888654222 222222222 568884
No 26
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=30.79 E-value=82 Score=20.13 Aligned_cols=49 Identities=18% Similarity=0.266 Sum_probs=30.9
Q ss_pred ecceeeEEeecccCcHHHHHHHHHHH-HcCCC----------CCC-CeEecCcHHHHHHHHHHHh
Q 048122 49 VDHKRFVLPLVYLNNNVVQALLELAE-EFGLP----------TNG-PLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 49 Ge~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~----------~~G-~L~iPC~~~~Fe~vl~~i~ 101 (125)
|+.+| .+..-..+.|.+|.++.+ .||.. .+| .++|.++.+ |+..+...+
T Consensus 10 ~~~~~---~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~D-l~~a~~~~~ 70 (84)
T PF00564_consen 10 GDIRR---IISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDED-LQEAIEQAK 70 (84)
T ss_dssp TEEEE---EEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHH-HHHHHHHHH
T ss_pred CeeEE---EEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHH-HHHHHHHHH
Confidence 44555 333445679999999999 89883 455 466766655 444444443
No 27
>COG0623 FabI Enoyl-[acyl-carrier-protein]
Probab=30.03 E-value=80 Score=26.40 Aligned_cols=41 Identities=32% Similarity=0.477 Sum_probs=30.5
Q ss_pred EeecccCcHHHHHHHHHHHHcCCCCCCCeEecCcHHHHHHHHHHH
Q 048122 56 LPLVYLNNNVVQALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLI 100 (125)
Q Consensus 56 Vp~~yL~hp~F~~LL~~aeEfG~~~~G~L~iPC~~~~Fe~vl~~i 100 (125)
+-..|.+.-+.+.+-+.++|+|- .+.+|||+..=+++-.+.
T Consensus 35 L~fTy~~e~l~krv~~la~~~~s----~~v~~cDV~~d~~i~~~f 75 (259)
T COG0623 35 LAFTYQGERLEKRVEELAEELGS----DLVLPCDVTNDESIDALF 75 (259)
T ss_pred EEEEeccHHHHHHHHHHHhhccC----CeEEecCCCCHHHHHHHH
Confidence 33457888888888888888774 689999998766665544
No 28
>KOG1290 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=29.94 E-value=30 Score=31.88 Aligned_cols=19 Identities=21% Similarity=0.114 Sum_probs=15.8
Q ss_pred cccCeEEEEEec---ceeeEEe
Q 048122 39 YVKGHFIVYTVD---HKRFVLP 57 (125)
Q Consensus 39 vpkG~~~VyVGe---~~RfvVp 57 (125)
.+-||.||++|| ..||+|-
T Consensus 62 ~kGGYHpV~IGD~F~~gRY~v~ 83 (590)
T KOG1290|consen 62 RKGGYHPVRIGDVFNGGRYHVQ 83 (590)
T ss_pred hcCCCceeeccccccCceEEEE
Confidence 567999999998 4888874
No 29
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=29.58 E-value=1e+02 Score=21.44 Aligned_cols=43 Identities=16% Similarity=0.149 Sum_probs=27.0
Q ss_pred EEEEecceeeEEeecccCcHHHHHHHHHHH-HcCC-------------CCCCC-eEecCcH
Q 048122 45 IVYTVDHKRFVLPLVYLNNNVVQALLELAE-EFGL-------------PTNGP-LTVLCDT 90 (125)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~ae-EfG~-------------~~~G~-L~iPC~~ 90 (125)
+||-||-||+-+|..- =.|.+|.++.. .|.. +.||- +||.++.
T Consensus 5 ~~~g~DiR~~~~~~~~---~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~ 62 (81)
T cd06401 5 AQLGDDIRRIPIHNED---ITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSS 62 (81)
T ss_pred EEeCCeEEEEeccCcc---ccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHH
Confidence 4565677886666422 25778888886 6652 24565 6688763
No 30
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=29.23 E-value=22 Score=30.84 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=19.4
Q ss_pred ccccccCeEEEEEe-cc--eeeEEeecccCc
Q 048122 36 EKCYVKGHFIVYTV-DH--KRFVLPLVYLNN 63 (125)
Q Consensus 36 ~~~vpkG~~~VyVG-e~--~RfvVp~~yL~h 63 (125)
..-||.|-|++||| |+ ..|.|| ++++
T Consensus 87 ~i~iPh~sf~~y~g~~~ie~~~~vp--~fGn 115 (366)
T PRK13277 87 AIFVPNRSFAVYVGYDAIENEFKVP--IFGN 115 (366)
T ss_pred eEEecCCCeEEEecHHHHhhcCCCC--cccC
Confidence 34589999999999 42 478888 4444
No 31
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=29.23 E-value=1.5e+02 Score=22.55 Aligned_cols=62 Identities=19% Similarity=0.202 Sum_probs=39.4
Q ss_pred eeeEEeecccC-----cHHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCchhhhhHHHHhh-hccccCC
Q 048122 52 KRFVLPLVYLN-----NNVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVNEDAERPLLTLI-AGSHRAS 123 (125)
Q Consensus 52 ~RfvVp~~yL~-----hp~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~~~-~~~c~~~ 123 (125)
-+-++-++-|. ||+-+++++.-. ..||-..| +--.+..+++++... .+..+-..+ ..-|||-
T Consensus 67 G~~V~TiEgl~~~~~l~pvq~af~~~~a~QCGfCtPG---------~vms~~~ll~~~p~p-s~~ei~~al~GnLCRCT 135 (148)
T TIGR03193 67 GRKVETVEGLATNGRLSRLQQAFHERLGTQCGFCTPG---------MIMAAEALLRRNPSP-SRDEIRAALAGNLCRCT 135 (148)
T ss_pred CCcEEEeCCCCCCCCCCHHHHHHHHcCCCcCCCCCcc---------HHHHHHHHHHcCCCC-CHHHHHHHHcCCccCCC
Confidence 44577888886 999999998888 89995444 444556666665433 222233333 4557874
No 32
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=29.08 E-value=45 Score=23.10 Aligned_cols=29 Identities=14% Similarity=0.338 Sum_probs=21.7
Q ss_pred CCCeEecCcHHHHHHHHHHHhcCCchhhhh
Q 048122 81 NGPLTVLCDTAFMEYVVTLISHNVNEDAER 110 (125)
Q Consensus 81 ~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~ 110 (125)
.+++.+-|+++.|.+++.-|+ ++.+.+|+
T Consensus 64 ~~~i~f~c~~e~L~~Li~~Lk-~A~~~~e~ 92 (95)
T cd04751 64 KPDINFTCTLEQLQDLVNKLK-DAAKNIER 92 (95)
T ss_pred cceEEEEeCHHHHHHHHHHHH-HHHHHHHH
Confidence 358999999999999999884 33344443
No 33
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=28.72 E-value=1.6e+02 Score=22.89 Aligned_cols=45 Identities=7% Similarity=-0.263 Sum_probs=38.3
Q ss_pred eeeEEeecccCcHHHHHHHHHHHHcCCC----CCCCeEecCcHHHHHHH
Q 048122 52 KRFVLPLVYLNNNVVQALLELAEEFGLP----TNGPLTVLCDTAFMEYV 96 (125)
Q Consensus 52 ~RfvVp~~yL~hp~F~~LL~~aeEfG~~----~~G~L~iPC~~~~Fe~v 96 (125)
.-+++|.+-.+||..++=+++-+++|+. ..|.+.-|.+.+.+...
T Consensus 117 pvii~P~~M~~~p~~~~Nl~~L~~~G~~vi~P~~g~~a~p~~~~~~~~~ 165 (185)
T PRK06029 117 RLVLCVRETPLHLGHLRNMTKLAEMGAIIMPPVPAFYHRPQTLEDMVDQ 165 (185)
T ss_pred CEEEEeccccCCHHHHHHHHHHHHCcCEEECCCcccccCCCCHHHHHHH
Confidence 4588999999999999999999988983 57889999998877643
No 34
>PF04332 DUF475: Protein of unknown function (DUF475); InterPro: IPR007427 This entry contains proteins that are predicted to be an integral membrane proteins with multiple transmembrane domains.
Probab=28.27 E-value=39 Score=28.73 Aligned_cols=16 Identities=19% Similarity=0.515 Sum_probs=14.7
Q ss_pred CChHHHHHHHHHHHhh
Q 048122 2 ISTKKLIKLARKWQKL 17 (125)
Q Consensus 2 ~~~~kL~~~~rKWq~~ 17 (125)
+|++-|++|..+||+.
T Consensus 6 VNA~vLk~Ms~~Wq~~ 21 (294)
T PF04332_consen 6 VNATVLKRMSPFWQRR 21 (294)
T ss_pred hhHHHHHhhhHHHHHH
Confidence 6899999999999985
No 35
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=28.05 E-value=51 Score=20.26 Aligned_cols=18 Identities=39% Similarity=0.754 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCCCCCeEe
Q 048122 68 ALLELAEEFGLPTNGPLTV 86 (125)
Q Consensus 68 ~LL~~aeEfG~~~~G~L~i 86 (125)
||.++-.+||++. |||+=
T Consensus 10 eL~~~L~~~G~~~-gPIt~ 27 (44)
T smart00540 10 ELRAELKQYGLPP-GPITD 27 (44)
T ss_pred HHHHHHHHcCCCC-CCcCc
Confidence 4555555899964 99983
No 36
>TIGR03849 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679.
Probab=27.10 E-value=19 Score=29.42 Aligned_cols=53 Identities=13% Similarity=0.254 Sum_probs=35.7
Q ss_pred eEEEEEecceeeEEeecccCcHHHHHHHHHHHHcCCC----CCCCeEecCcHHHHHHHHHHHh
Q 048122 43 HFIVYTVDHKRFVLPLVYLNNNVVQALLELAEEFGLP----TNGPLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 43 ~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeEfG~~----~~G~L~iPC~~~~Fe~vl~~i~ 101 (125)
-+.||.|. --|.+ ++.+-.|.+.|+.++++||+ ++|.|.||.+.- .+++..++
T Consensus 54 ~V~v~~GG-tl~E~---~~~q~~~~~Yl~~~k~lGf~~IEiS~G~~~i~~~~~--~rlI~~~~ 110 (237)
T TIGR03849 54 GIKVYPGG-TLFEI---AHSKGKFDEYLNECDELGFEAVEISDGSMEISLEER--CNLIERAK 110 (237)
T ss_pred CCeEeCCc-cHHHH---HHHhhhHHHHHHHHHHcCCCEEEEcCCccCCCHHHH--HHHHHHHH
Confidence 46777773 22322 22447899999999999997 699999997643 34444444
No 37
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=26.99 E-value=46 Score=27.25 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=23.2
Q ss_pred CcHHHHHHHHHHH-HcCCCCCCCeEec
Q 048122 62 NNNVVQALLELAE-EFGLPTNGPLTVL 87 (125)
Q Consensus 62 ~hp~F~~LL~~ae-EfG~~~~G~L~iP 87 (125)
.|-+|.++++.+. |=+|..+|||.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 4789999999999 9999999999873
No 38
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=26.91 E-value=1.1e+02 Score=22.38 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=23.6
Q ss_pred HcCCCCCCCeEecCcHHHHHHHHHHHhc
Q 048122 75 EFGLPTNGPLTVLCDTAFMEYVVTLISH 102 (125)
Q Consensus 75 EfG~~~~G~L~iPC~~~~Fe~vl~~i~~ 102 (125)
-||-+..|.+.++++...-+++..+|++
T Consensus 90 ~YGQP~eGvV~v~v~~~~k~~~~~ll~~ 117 (121)
T PF04019_consen 90 LYGQPGEGVVLVKVTEEAKRRARELLKK 117 (121)
T ss_pred EECCCCCeEEEEEeCHHHHHHHHHHHHH
Confidence 3698889999999998888888888764
No 39
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=26.80 E-value=1.2e+02 Score=26.53 Aligned_cols=90 Identities=12% Similarity=0.176 Sum_probs=53.1
Q ss_pred HHHHHHHhhhhccccccccccccC----CCCccccccCeEEEEEec---------------------ceeeEEeecccC-
Q 048122 9 KLARKWQKLAAIRQKRIMSTIFKG----DDAEKCYVKGHFIVYTVD---------------------HKRFVLPLVYLN- 62 (125)
Q Consensus 9 ~~~rKWq~~a~~~~~r~s~~~~~~----~~~~~~vpkG~~~VyVGe---------------------~~RfvVp~~yL~- 62 (125)
...++|.... ++.-..+|++-. .......++|-..|.||. ..|++||+.|=.
T Consensus 149 ~~~~q~~~~~--~~~~lyfPt~m~~~~~~~~~~~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~ 226 (360)
T PF07429_consen 149 AYFQQRYPRV--PASLLYFPTRMDPALTLSEKNKKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGAN 226 (360)
T ss_pred HHHHHHcCCC--CceEEEcCCCCchhhhccccccCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCc
Confidence 3455565321 122455665532 111223457888899882 279999999974
Q ss_pred -cHHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcC
Q 048122 63 -NNVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHN 103 (125)
Q Consensus 63 -hp~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~ 103 (125)
.-...++.+.++ -||- +-+.+-=+---|+..+.+|++-
T Consensus 227 n~~Yi~~V~~~~~~lF~~---~~~~iL~e~mpf~eYl~lL~~c 266 (360)
T PF07429_consen 227 NQAYIQQVIQAGKELFGA---ENFQILTEFMPFDEYLALLSRC 266 (360)
T ss_pred hHHHHHHHHHHHHHhcCc---cceeEhhhhCCHHHHHHHHHhC
Confidence 567888888888 6773 3344433444566666666543
No 40
>PF11046 HycA_repressor: Transcriptional repressor of hyc and hyp operons; InterPro: IPR021285 This family is conserved in Proteobacteria. It is likely to be the transcriptional repressor molecule for the hyc and hyp operons, which express, amongst others, the protein HycA. This protein may be harnessed for the reduction of technetium oxide, an unwelcome product of radio-nucleotide bioaccumulation. HycA produces formate hydrogenlyase, one of the key proteins necessary for metal compound reduction [].
Probab=26.59 E-value=1.7e+02 Score=22.63 Aligned_cols=58 Identities=24% Similarity=0.375 Sum_probs=41.8
Q ss_pred ccCeEEEEEe--c-----ceeeEEeecccCcHHHHHHHHHHH--HcCCCCCCCeEecCcHHHHHHHHHHHh
Q 048122 40 VKGHFIVYTV--D-----HKRFVLPLVYLNNNVVQALLELAE--EFGLPTNGPLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 40 pkG~~~VyVG--e-----~~RfvVp~~yL~hp~F~~LL~~ae--EfG~~~~G~L~iPC~~~~Fe~vl~~i~ 101 (125)
==+||.|||- | .--|-|. ++.+-=+.|+-.|. |=|. -||.+..-=...+|||.|..|.
T Consensus 58 LF~HF~i~v~LadgF~sh~I~Y~~~---~~~g~d~~~ia~A~l~~dG~-iDg~v~nRDre~VLEHYL~KIa 124 (148)
T PF11046_consen 58 LFEHFMIYVTLADGFNSHTIEYYLE---LKDGEDKRLIAHATLDEDGL-IDGRVSNRDREQVLEHYLEKIA 124 (148)
T ss_pred EEcceEEEEEEcCCcccceEEEEEe---cCCCchhhhhhhhhcccCCc-cccccccccHHHHHHHHHHHHH
Confidence 3579999984 3 2334444 44555456788888 6665 6899999999999999998774
No 41
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=26.26 E-value=30 Score=20.45 Aligned_cols=18 Identities=22% Similarity=0.523 Sum_probs=13.8
Q ss_pred ccCcHHHHHHHHHHH-HcC
Q 048122 60 YLNNNVVQALLELAE-EFG 77 (125)
Q Consensus 60 yL~hp~F~~LL~~ae-EfG 77 (125)
||+.-.|++++.++. ||.
T Consensus 1 YLsd~dF~~vFgm~~~eF~ 19 (36)
T PF02209_consen 1 YLSDEDFEKVFGMSREEFY 19 (36)
T ss_dssp GS-HHHHHHHHSS-HHHHH
T ss_pred CcCHHHHHHHHCCCHHHHH
Confidence 788899999999998 873
No 42
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=26.01 E-value=1.1e+02 Score=23.13 Aligned_cols=22 Identities=14% Similarity=0.320 Sum_probs=16.5
Q ss_pred CCCCeEecCcHHHHHHHHHHHh
Q 048122 80 TNGPLTVLCDTAFMEYVVTLIS 101 (125)
Q Consensus 80 ~~G~L~iPC~~~~Fe~vl~~i~ 101 (125)
.+|.|-+.|+-++.+.+..+-.
T Consensus 107 p~~iigVAC~~dL~~g~~~~~~ 128 (158)
T PF01976_consen 107 PKAIIGVACERDLISGIQDLKP 128 (158)
T ss_pred CCEEEEEechHHHHHHHHHHhh
Confidence 4577888999888888776544
No 43
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=25.95 E-value=56 Score=21.79 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=14.3
Q ss_pred HHHHHHHHHHH-HcCCC
Q 048122 64 NVVQALLELAE-EFGLP 79 (125)
Q Consensus 64 p~F~~LL~~ae-EfG~~ 79 (125)
-.++|||+.|+ .||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 47999999999 99995
No 44
>smart00153 VHP Villin headpiece domain.
Probab=25.27 E-value=35 Score=20.10 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=15.5
Q ss_pred ccCcHHHHHHHHHHH-HcC
Q 048122 60 YLNNNVVQALLELAE-EFG 77 (125)
Q Consensus 60 yL~hp~F~~LL~~ae-EfG 77 (125)
||+.--|++++.++. ||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 788899999999988 873
No 45
>PF05194 UreE_C: UreE urease accessory protein, C-terminal domain; InterPro: IPR007864 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The C-terminal domain of this protein is the metal-binding region, which can bind up to six Ni molecules per dimer. Most members of this group contain a histidine-rich C-terminal motif that is involved in, but not solely responsible for, binding nickel ions in K. aerogenes UreE []. However, internal ligands, not the histidine residues at the C terminus, are necessary for UreE to assist in urease activation in K. aerogenes [], even though the truncated protein lacking the His-rich region binds two nickel ions instead of six. In H. pylori and some other organisms, the terminal histidine-rich binding sites are absent, but the internal histidine sites are present, and the latter probably function as nickel donors. Deletion analysis shows that this domain alone is sufficient for metal-binding and activation of urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B ....
Probab=25.10 E-value=1.1e+02 Score=20.45 Aligned_cols=29 Identities=17% Similarity=0.411 Sum_probs=18.2
Q ss_pred ccCeEEEEEecceeeEEeecccCcHHHHHHHHHH
Q 048122 40 VKGHFIVYTVDHKRFVLPLVYLNNNVVQALLELA 73 (125)
Q Consensus 40 pkG~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~a 73 (125)
-.=|+++++++. ++.|| ..+...+||++-
T Consensus 23 GNrH~p~~i~~~-~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 23 GNRHWPLFIEED-ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp HHTT--EEEETT-EEEEE------HHHHHHHHHT
T ss_pred cCCccceEEcCC-EEEec----CcHHHHHHHHHC
Confidence 346888999877 77777 666777777764
No 46
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=24.87 E-value=91 Score=21.58 Aligned_cols=30 Identities=27% Similarity=0.398 Sum_probs=22.5
Q ss_pred eEEEEEecceeeEEeecccCcHHHHHHHHHHHHcCC
Q 048122 43 HFIVYTVDHKRFVLPLVYLNNNVVQALLELAEEFGL 78 (125)
Q Consensus 43 ~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeEfG~ 78 (125)
.+-+|++|..| |=+.|+...|++.+.+.|.
T Consensus 5 ~Lriy~~e~~~------~~g~~l~~~ll~~~~~~gi 34 (101)
T PF02641_consen 5 LLRIYLSESDR------WGGKPLYEWLLERAREAGI 34 (101)
T ss_dssp EEEEEEETT-E------ETTEEHHHHHHHHHHHTT-
T ss_pred EEEEEEcCccc------cCceEHHHHHHHHHHHCCC
Confidence 35689998876 4678999999999985443
No 47
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=24.87 E-value=1.4e+02 Score=20.65 Aligned_cols=52 Identities=23% Similarity=0.349 Sum_probs=33.3
Q ss_pred EEecceeeEEeecc-cCcHHHHHHHHHHH-HcCCC-----------CCC-CeEecCcHHHHHHHHH
Q 048122 47 YTVDHKRFVLPLVY-LNNNVVQALLELAE-EFGLP-----------TNG-PLTVLCDTAFMEYVVT 98 (125)
Q Consensus 47 yVGe~~RfvVp~~y-L~hp~F~~LL~~ae-EfG~~-----------~~G-~L~iPC~~~~Fe~vl~ 98 (125)
|=|+-+||-+|..- -.+.-|..|.++-+ -|..+ .+| -++|.||.++-+-+-.
T Consensus 7 y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 7 YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 33568999999740 11346777777666 55553 345 4778999887665544
No 48
>cd01310 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
Probab=23.89 E-value=88 Score=23.49 Aligned_cols=38 Identities=32% Similarity=0.503 Sum_probs=26.4
Q ss_pred cCcHHHHHHHHHHHHcCCCCCCCeEecCcHHHHHHHHHHHhcC
Q 048122 61 LNNNVVQALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLISHN 103 (125)
Q Consensus 61 L~hp~F~~LL~~aeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~ 103 (125)
.+.++|+.+++.|+|+|. |+.|-|... .+.++.++++.
T Consensus 105 ~q~~~~~~~~~~a~e~~~----pv~iH~~~~-~~~~~~l~~~~ 142 (251)
T cd01310 105 VQKEVFRAQLELAKELNL----PVVIHSRDA-HEDVLEILKEY 142 (251)
T ss_pred HHHHHHHHHHHHHHHhCC----CeEEEeeCc-hHHHHHHHHhc
Confidence 567999999999999876 456655432 44556666544
No 49
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=23.72 E-value=1.6e+02 Score=20.78 Aligned_cols=51 Identities=25% Similarity=0.292 Sum_probs=39.3
Q ss_pred cCcHHHHHHHHHHHHcCCCCCCCeEecCcHHHHHHHHHHHhcCCchhhhhHHHHhhhcc
Q 048122 61 LNNNVVQALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLISHNVNEDAERPLLTLIAGS 119 (125)
Q Consensus 61 L~hp~F~~LL~~aeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~~~~~~ 119 (125)
+-.+-=+||.|.++--| ++=|.+.|..++.+++-+.+.+.--.+|.+|.+.
T Consensus 22 ~Ls~eE~EL~ELa~~AG--------v~~dp~VFriildLL~~nVsP~AI~qmLK~m~s~ 72 (88)
T PF12926_consen 22 VLSAEEVELYELAQLAG--------VPMDPEVFRIILDLLRLNVSPDAIFQMLKSMCSG 72 (88)
T ss_pred ccCHHHHHHHHHHHHhC--------CCcChHHHHHHHHHHHcCCCHHHHHHHHHHHHcc
Confidence 33455568888887333 2346789999999999999999999999988765
No 50
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=23.50 E-value=2.1e+02 Score=21.77 Aligned_cols=62 Identities=13% Similarity=0.153 Sum_probs=39.1
Q ss_pred eeeEEeecccC----cHHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCchhhhhHHHHhh-hccccCC
Q 048122 52 KRFVLPLVYLN----NNVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVNEDAERPLLTLI-AGSHRAS 123 (125)
Q Consensus 52 ~RfvVp~~yL~----hp~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~~~-~~~c~~~ 123 (125)
-+-++-++-|. ||+=+++++.-. ..||-..| +--.+..+++++... .+..+-..+ ..-|||-
T Consensus 69 G~~v~TiEgl~~~~l~pvQ~af~~~~a~QCGfCtpG---------~im~~~~ll~~~p~p-~~~ei~~al~gnlCRCt 136 (151)
T TIGR03198 69 GHEITTIEGIAENELDPCQTAFLEEGGFQCGYCTPG---------MVVALKALFRETPQP-SDEDMEEGLSGNLCRCT 136 (151)
T ss_pred CCEEEecCCcCCCCCCHHHHHHHHcCCCcCCCCCcc---------HHHHHHHHHHcCCCC-CHHHHHHHHcCCCcCCC
Confidence 66778888886 999999998888 99995554 333555666665332 222222223 3557774
No 51
>COG2899 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.16 E-value=43 Score=28.84 Aligned_cols=16 Identities=25% Similarity=0.461 Sum_probs=14.6
Q ss_pred CChHHHHHHHHHHHhh
Q 048122 2 ISTKKLIKLARKWQKL 17 (125)
Q Consensus 2 ~~~~kL~~~~rKWq~~ 17 (125)
+|+.+|+.|..+||++
T Consensus 56 vNA~iLk~MS~~Wqk~ 71 (346)
T COG2899 56 VNAAILKDMSPFWQKR 71 (346)
T ss_pred hhHHHHHhccHHHHHH
Confidence 6889999999999985
No 52
>PF11490 DNA_pol3_a_NII: DNA polymerase III polC-type N-terminus II; InterPro: IPR024754 This domain is found in the N-terminal region of DNA polymerase III polC subunit A. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria []. The domain is also found in chromosomal replication initiator protein DnaA.
Probab=23.03 E-value=74 Score=21.25 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=17.5
Q ss_pred EEEEEecceeeEEeecc----cCcHHHHHHHHHHHHcCCC
Q 048122 44 FIVYTVDHKRFVLPLVY----LNNNVVQALLELAEEFGLP 79 (125)
Q Consensus 44 ~~VyVGe~~RfvVp~~y----L~hp~F~~LL~~aeEfG~~ 79 (125)
-+.+-|+.=-+.||-.. |....+..+++....+||+
T Consensus 25 ~~~~~~~~l~i~v~~~~~~~~lk~~~~~~~~~~~~~~gF~ 64 (117)
T PF11490_consen 25 KPEFEGNKLIIKVPNEIEAEHLKKKKLDKIIEKYIKFGFG 64 (117)
T ss_pred CeEEECCEEEEEeCCHHHHHHHHHhhhHHHHHHHHHcCCC
Confidence 34444444334444433 3334455555555567774
No 53
>PRK09908 xanthine dehydrogenase subunit XdhC; Provisional
Probab=22.63 E-value=2.2e+02 Score=21.94 Aligned_cols=60 Identities=17% Similarity=0.182 Sum_probs=39.7
Q ss_pred eeeEEeecccC-----cHHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCC-----chhhhhHHHHhhhccc
Q 048122 52 KRFVLPLVYLN-----NNVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNV-----NEDAERPLLTLIAGSH 120 (125)
Q Consensus 52 ~RfvVp~~yL~-----hp~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~-----~~~~e~~~l~~~~~~c 120 (125)
-+-++-++-|. ||+-+++++.-. ..||-..| +--.+..++++.. .+|++.+| + ..-|
T Consensus 73 G~~V~TiEGl~~~~~l~pvQ~Af~~~~a~QCGyCtPG---------~ims~~aLl~~~~~~~~s~~eI~~al-~--GNlC 140 (159)
T PRK09908 73 GKEIRTLEGEAKGGKLSHVQQAYAKSGAVQCGFCTPG---------LIMATTAMLAKPREKPLTITEIRRGL-A--GNLC 140 (159)
T ss_pred CCEEEeecCCCCCCCCCHHHHHHHHcCCCcCCCCCcc---------HHHHHHHHHHcCCCCCCCHHHHHHHH-c--CCcc
Confidence 56777788885 999999998888 99995444 3445666777653 23344442 2 3557
Q ss_pred cCC
Q 048122 121 RAS 123 (125)
Q Consensus 121 ~~~ 123 (125)
||-
T Consensus 141 RCT 143 (159)
T PRK09908 141 RCT 143 (159)
T ss_pred CCC
Confidence 874
No 54
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.54 E-value=2.3e+02 Score=21.37 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=32.4
Q ss_pred HHHHHHHHHcCCCCCCCeEecCcHHHHHHHHHHHhcCCch
Q 048122 67 QALLELAEEFGLPTNGPLTVLCDTAFMEYVVTLISHNVNE 106 (125)
Q Consensus 67 ~~LL~~aeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~ 106 (125)
..+++.-++.|.+.+|.-++|-+....+.+...++++..-
T Consensus 28 ~~~i~~l~~~g~~~eGIFR~~g~~~~i~~l~~~~~~~~~~ 67 (195)
T cd04404 28 RETVEYLQAHALTTEGIFRRSANTQVVKEVQQKYNMGEPV 67 (195)
T ss_pred HHHHHHHHHcCCCCCCeeeCCCcHHHHHHHHHHHhCCCCC
Confidence 3455555578999999999999999999999999876543
No 55
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=22.23 E-value=2.2e+02 Score=18.13 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=12.8
Q ss_pred HHHHHHHHHHcCCCCCCCeEecCc
Q 048122 66 VQALLELAEEFGLPTNGPLTVLCD 89 (125)
Q Consensus 66 F~~LL~~aeEfG~~~~G~L~iPC~ 89 (125)
|.+++....+.|| ||+|.|=.+
T Consensus 2 w~~i~~~L~~~GY--dG~~siE~E 23 (55)
T PF07582_consen 2 WKRIFSALREIGY--DGWLSIEHE 23 (55)
T ss_dssp HHHHHHHHHHTT----SEEEE---
T ss_pred HHHHHHHHHHcCC--CceEEEEee
Confidence 4566666668898 699999875
No 56
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=22.05 E-value=1e+02 Score=22.84 Aligned_cols=62 Identities=15% Similarity=0.128 Sum_probs=42.0
Q ss_pred cCeEEEEEecceeeEEeecccCcHHHHHHHHH---H--H-HcCCC---CCCCeE-ecCcHHHHHHHHHHHhc
Q 048122 41 KGHFIVYTVDHKRFVLPLVYLNNNVVQALLEL---A--E-EFGLP---TNGPLT-VLCDTAFMEYVVTLISH 102 (125)
Q Consensus 41 kG~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~---a--e-EfG~~---~~G~L~-iPC~~~~Fe~vl~~i~~ 102 (125)
++-|.||||+.+-|++-.-|-+-|.|--=+-. + . --|.. ..|.++ |.=..+.|.+|+.-+-.
T Consensus 32 ~~~~fVyvG~~rdYIl~~gfCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~~d~~~Il~e~ys 103 (117)
T COG5431 32 KVKFFVYVGKERDYILEGGFCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYYVDYPDILREKYS 103 (117)
T ss_pred eEEEEEEEccccceEEEcCcccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEecccHHHHHHHHHh
Confidence 56689999999999999999999998732221 1 1 22332 345544 66777778888766543
No 57
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.93 E-value=2.7e+02 Score=18.64 Aligned_cols=48 Identities=13% Similarity=0.218 Sum_probs=33.3
Q ss_pred EecceeeEEeecccCcHHHHHHHHHHHHcCCCCCCCeEec-CcHHHHHHHHH
Q 048122 48 TVDHKRFVLPLVYLNNNVVQALLELAEEFGLPTNGPLTVL-CDTAFMEYVVT 98 (125)
Q Consensus 48 VGe~~RfvVp~~yL~hp~F~~LL~~aeEfG~~~~G~L~iP-C~~~~Fe~vl~ 98 (125)
+++-.=.+|+++|.+|-.....-+.|+.+|-+ .+... .....|+..+.
T Consensus 46 i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip---~~~~~~~~~~~l~~~l~ 94 (97)
T PF10087_consen 46 IKKADLVIVFTDYVSHNAMWKVKKAAKKYGIP---IIYSRSRGVSSLERALE 94 (97)
T ss_pred cCCCCEEEEEeCCcChHHHHHHHHHHHHcCCc---EEEECCCCHHHHHHHHH
Confidence 33345567899999999999999999888753 12233 55666666554
No 58
>PF14974 DUF4511: Domain of unknown function (DUF4511)
Probab=20.45 E-value=2.6e+02 Score=20.31 Aligned_cols=37 Identities=8% Similarity=0.170 Sum_probs=22.0
Q ss_pred HHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCc
Q 048122 64 NVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVN 105 (125)
Q Consensus 64 p~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~ 105 (125)
|+.-++--..= .|||+.+|. -+..|-+++..++++++
T Consensus 47 Pva~qiq~~VIk~yGF~~~~e-----G~~~f~~~i~~~e~~D~ 84 (105)
T PF14974_consen 47 PVATQIQMEVIKKYGFPESRE-----GVMQFAQLIRELEKDDP 84 (105)
T ss_pred HHHHHHHHHHHHHcCCCCCcc-----hHHHHHHHHHHHHccCH
Confidence 44444444444 799985321 13578888887766554
No 59
>PF09475 Dot_icm_IcmQ: Dot/Icm secretion system protein (dot_icm_IcmQ); InterPro: IPR013365 Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation ().; PDB: 3FXE_A 3FXD_C.
Probab=20.33 E-value=34 Score=27.12 Aligned_cols=55 Identities=16% Similarity=0.311 Sum_probs=0.0
Q ss_pred HHHHHh-hhhccccccccccccC--------CCCccccccCeEEEEEecce-----eeEEeecccCcHH
Q 048122 11 ARKWQK-LAAIRQKRIMSTIFKG--------DDAEKCYVKGHFIVYTVDHK-----RFVLPLVYLNNNV 65 (125)
Q Consensus 11 ~rKWq~-~a~~~~~r~s~~~~~~--------~~~~~~vpkG~~~VyVGe~~-----RfvVp~~yL~hp~ 65 (125)
..+|++ +|++.+..++-|-=.+ -.+...+.++|++|||-... -=-+|++=|+.|+
T Consensus 78 lqsWerilanLprqmisRPIY~nE~dvk~~IksKenk~NEAYVaiyInq~dIl~~~~dk~~~Dk~GkpL 146 (179)
T PF09475_consen 78 LQSWERILANLPRQMISRPIYANEEDVKAAIKSKENKLNEAYVAIYINQSDILSLSPDKIPTDKLGKPL 146 (179)
T ss_dssp ---------------------------------------------------------------------
T ss_pred HHHHHHHHHhCchhhhCCCCcCCHHHHHHHHHhhhcccceeEEEEEEchHhcccCCcccccccccCCcc
Confidence 467987 6778887776543322 12345688999999997421 1124555555554
No 60
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=20.30 E-value=3.8e+02 Score=22.02 Aligned_cols=60 Identities=20% Similarity=0.091 Sum_probs=41.3
Q ss_pred cCeEEEEEec-ceeeEEeecccCcHHHHHHHHHHH-HcCCCCC---------------CCeEecCcHHHHHHHHHHH
Q 048122 41 KGHFIVYTVD-HKRFVLPLVYLNNNVVQALLELAE-EFGLPTN---------------GPLTVLCDTAFMEYVVTLI 100 (125)
Q Consensus 41 kG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~ae-EfG~~~~---------------G~L~iPC~~~~Fe~vl~~i 100 (125)
.|++.|.-.. +.++.+-+..-.-+...+++.... -||++.| -+|++|...+.||-+++.|
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 4555555433 455666665543456667888888 7888755 3589999999999888876
No 61
>COG1852 Uncharacterized conserved protein [Function unknown]
Probab=20.29 E-value=1.4e+02 Score=24.26 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=16.7
Q ss_pred CCCCeEecCcHHHHHHHHHHH
Q 048122 80 TNGPLTVLCDTAFMEYVVTLI 100 (125)
Q Consensus 80 ~~G~L~iPC~~~~Fe~vl~~i 100 (125)
.|+.|-+.|.-+.++-+..+=
T Consensus 154 ~e~vlgVAC~~eL~~~m~~ls 174 (209)
T COG1852 154 PEAVLGVACYRELNEGMEALS 174 (209)
T ss_pred CceEEEEeehHHHHHHHHHhc
Confidence 567799999999998776553
No 62
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=20.05 E-value=1.8e+02 Score=17.72 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=23.0
Q ss_pred HHHHHHHHHHH-HcCCCCCCCeEecCcHHHHHHHHHHHhcCCchhhhhHHHH
Q 048122 64 NVVQALLELAE-EFGLPTNGPLTVLCDTAFMEYVVTLISHNVNEDAERPLLT 114 (125)
Q Consensus 64 p~F~~LL~~ae-EfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~ 114 (125)
+-.+++.+.-+ .||. .+...|+++.+.|.+++||+
T Consensus 30 ~ql~~i~~~Y~~~~g~----------------~L~~~i~~e~sGd~~~~Ll~ 65 (66)
T PF00191_consen 30 AQLRAIKQAYKKKYGK----------------DLEEDIKKETSGDFEKLLLA 65 (66)
T ss_dssp HHHHHHHHHHHHHHSS-----------------HHHHHHHHSTHHHHHHHHH
T ss_pred cccceeehhhhhhhHH----------------HHHHHHHHhCCHHHHHHHHh
Confidence 34555555555 6664 45667778888888888875
Done!