Query         027730
Match_columns 219
No_of_seqs    140 out of 190
Neff          4.2 
Searched_HMMs 46136
Date          Fri Mar 29 14:19:29 2013
Command       hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027730hhsearch_cdd -cpu 12 -v 0 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF04640 PLATZ:  PLATZ transcri 100.0 4.4E-40 9.5E-45  244.2   5.9   72   66-137     1-72  (72)
  2 PF00643 zf-B_box:  B-box zinc   96.5 0.00078 1.7E-08   43.8   0.5   37   25-65      5-42  (42)
  3 cd00021 BBOX B-Box-type zinc f  95.0   0.016 3.5E-07   36.4   1.9   36   25-64      2-38  (39)
  4 smart00336 BBOX B-Box-type zin  94.2   0.041 8.9E-07   35.0   2.3   35   25-63      5-40  (42)
  5 PRK01343 zinc-binding protein;  87.5    0.25 5.5E-06   35.7   0.9   29  114-142     9-38  (57)
  6 PF12855 Ecl1:  Life-span regul  87.0    0.16 3.5E-06   34.6  -0.4   29  114-142     6-37  (43)
  7 PF03884 DUF329:  Domain of unk  86.3   0.095 2.1E-06   37.8  -1.8   29  114-142     2-35  (57)
  8 PRK00418 DNA gyrase inhibitor;  84.9    0.36 7.8E-06   35.4   0.6   29  114-142     6-39  (62)
  9 COG3024 Uncharacterized protei  83.3    0.44 9.5E-06   35.3   0.5   29  114-142     7-40  (65)
 10 PF10013 DUF2256:  Uncharacteri  77.2    0.82 1.8E-05   31.3   0.2   23  114-136     8-39  (42)
 11 PF09889 DUF2116:  Uncharacteri  68.5     1.8 3.9E-05   31.4   0.2   29  115-143     4-32  (59)
 12 PF13240 zinc_ribbon_2:  zinc-r  64.3     3.2   7E-05   24.5   0.7   16  117-132     2-17  (23)
 13 KOG4367 Predicted Zn-finger pr  60.8     2.8 6.1E-05   41.7   0.0   36   23-62    223-260 (699)
 14 COG4338 Uncharacterized protei  57.7       1 2.2E-05   32.1  -2.6   24  113-136    11-43  (54)
 15 PF13248 zf-ribbon_3:  zinc-rib  56.1     6.5 0.00014   23.5   1.1   19  114-132     2-20  (26)
 16 PF02207 zf-UBR:  Putative zinc  53.4     6.5 0.00014   28.5   0.9   34   35-68     10-48  (71)
 17 cd02340 ZZ_NBR1_like Zinc fing  52.1     8.8 0.00019   25.7   1.3   27   39-65     15-43  (43)
 18 PF06467 zf-FCS:  MYM-type Zinc  51.4     3.4 7.3E-05   26.6  -0.8   24  113-136     5-40  (43)
 19 KOG2177 Predicted E3 ubiquitin  44.0      12 0.00026   30.5   1.2   38   25-67     88-127 (386)
 20 PF04438 zf-HIT:  HIT zinc fing  36.6      11 0.00023   23.7  -0.2   21  116-136     4-29  (30)
 21 PF01412 ArfGap:  Putative GTPa  35.4     8.6 0.00019   30.3  -0.9   50   35-85     10-72  (116)
 22 COG4068 Uncharacterized protei  35.3      13 0.00028   27.4   0.1   23  114-136     8-30  (64)
 23 cd02341 ZZ_ZZZ3 Zinc finger, Z  32.7      26 0.00057   24.1   1.3   27   39-65     16-48  (48)
 24 smart00396 ZnF_UBR1 Putative z  28.7      57  0.0012   23.8   2.6   30   33-62      8-42  (71)
 25 PF04570 DUF581:  Protein of un  28.4      17 0.00036   26.3  -0.3   32  113-144    15-55  (58)
 26 TIGR00412 redox_disulf_2 small  26.9      95  0.0021   22.1   3.4   32   73-105    33-66  (76)
 27 smart00105 ArfGap Putative GTP  22.6      20 0.00044   28.0  -0.8   43   37-80      2-57  (112)
 28 smart00746 TRASH metallochaper  22.2      52  0.0011   18.2   1.1   11  127-137    23-33  (39)
 29 KOG4582 Uncharacterized conser  21.2      63  0.0014   29.5   1.9   56    9-67    132-199 (278)
 30 PF06906 DUF1272:  Protein of u  20.1      72  0.0016   23.2   1.6   23  115-137     6-31  (57)

No 1  
>PF04640 PLATZ:  PLATZ transcription factor;  InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=100.00  E-value=4.4e-40  Score=244.18  Aligned_cols=72  Identities=72%  Similarity=1.223  Sum_probs=71.1

Q ss_pred             EeccccceeeechhhhhhcccceeeEEECCeeEEEeeCCCCCCCCCCCCCcccccccccCCCCeeeeccccc
Q 027730           66 RRSSYHDVIRVSEIQKVLDISGVQTYVINSARVVFLNERPQPRPGKGVTNTCEVCDRSLLDSFRFCSLGCKI  137 (219)
Q Consensus        66 RRssY~dVVRv~dIqkl~D~S~IQtYvINsakVVfLn~RPq~r~~kg~~~~Ce~C~R~L~d~~rFCSL~CKv  137 (219)
                      |||||||||||+|||||||||+||||+|||+||||||+|||+++++++++.|++|+|+|+|+|+||||+|||
T Consensus         1 Rr~sY~dVVrv~di~kl~D~s~IQtY~iNs~kVVfLn~Rpq~~~~~~~~~~C~~C~R~L~d~~~fCSl~CKv   72 (72)
T PF04640_consen    1 RRYSYHDVVRVSDIQKLLDCSGIQTYVINSAKVVFLNPRPQSRPSKGSGNICETCHRSLQDPYRFCSLSCKV   72 (72)
T ss_pred             CcccccceEEHHHhHhhccccccEEEEeCCceEEEEccCCcCCCCCCCCCccCCCCCCCCCCCeEEeeeEEC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999997


No 2  
>PF00643 zf-B_box:  B-box zinc finger;  InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.  This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.53  E-value=0.00078  Score=43.77  Aligned_cols=37  Identities=35%  Similarity=0.859  Sum_probs=29.6

Q ss_pred             cCCCCCCCCCCCcceecccCCCCcCCccccc-CCCCCceeEE
Q 027730           25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD-YHKDHRAIQI   65 (219)
Q Consensus        25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hr~lQI   65 (219)
                      .|..|..   .+.++||.+|. ..+|..|.. .|++|.++.|
T Consensus         5 ~C~~H~~---~~~~~~C~~C~-~~~C~~C~~~~H~~H~~~~i   42 (42)
T PF00643_consen    5 KCPEHPE---EPLSLFCEDCN-EPLCSECTVSGHKGHKIVPI   42 (42)
T ss_dssp             B-SSTTT---SBEEEEETTTT-EEEEHHHHHTSTTTSEEEEC
T ss_pred             cCccCCc---cceEEEecCCC-CccCccCCCCCCCCCEEeEC
Confidence            5888874   34899999998 899999977 5999987754


No 3  
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=95.04  E-value=0.016  Score=36.42  Aligned_cols=36  Identities=22%  Similarity=0.509  Sum_probs=27.8

Q ss_pred             cCCCCCCCCCCCcceecccCCCCcCCccccc-CCCCCceeE
Q 027730           25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD-YHKDHRAIQ   64 (219)
Q Consensus        25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hr~lQ   64 (219)
                      .|..|..   +...+||.+|. ..+|..|.. .|++|.++-
T Consensus         2 ~C~~H~~---~~~~~fC~~~~-~~iC~~C~~~~H~~H~~~~   38 (39)
T cd00021           2 LCDEHGE---EPLSLFCETDR-ALLCVDCDLSVHSGHRRVP   38 (39)
T ss_pred             CCCccCC---cceEEEeCccC-hhhhhhcChhhcCCCCEee
Confidence            4777853   24589999997 899999965 688887654


No 4  
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.18  E-value=0.041  Score=34.96  Aligned_cols=35  Identities=26%  Similarity=0.803  Sum_probs=27.6

Q ss_pred             cCCCCCCCCCCCcceecccCCCCcCCccccc-CCCCCcee
Q 027730           25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD-YHKDHRAI   63 (219)
Q Consensus        25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hr~l   63 (219)
                      .|..|..   ....+||.+|. ..+|..|.. .|++|.++
T Consensus         5 ~C~~h~~---~~~~~~C~~c~-~~iC~~C~~~~H~~H~~~   40 (42)
T smart00336        5 KCDSHGD---EPAEFFCEECG-ALLCRTCDEAEHRGHTVV   40 (42)
T ss_pred             cCCCCCC---CceEEECCCCC-cccccccChhhcCCCcee
Confidence            4777763   24589999998 899999976 58888765


No 5  
>PRK01343 zinc-binding protein; Provisional
Probab=87.50  E-value=0.25  Score=35.68  Aligned_cols=29  Identities=24%  Similarity=0.607  Sum_probs=23.0

Q ss_pred             CCcccccccccCCCC-eeeeccccccccch
Q 027730          114 TNTCEVCDRSLLDSF-RFCSLGCKIVGTSK  142 (219)
Q Consensus       114 ~~~Ce~C~R~L~d~~-rFCSL~CKv~~~~~  142 (219)
                      ...|-+|++.....+ -|||-.||+.+..+
T Consensus         9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg~   38 (57)
T PRK01343          9 TRPCPECGKPSTREAYPFCSERCRDIDLNR   38 (57)
T ss_pred             CCcCCCCCCcCcCCCCcccCHHHhhhhHHH
Confidence            456999999887655 59999999866544


No 6  
>PF12855 Ecl1:  Life-span regulatory factor;  InterPro: IPR024368  The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=86.95  E-value=0.16  Score=34.63  Aligned_cols=29  Identities=31%  Similarity=0.747  Sum_probs=24.1

Q ss_pred             CCccccccccc---CCCCeeeeccccccccch
Q 027730          114 TNTCEVCDRSL---LDSFRFCSLGCKIVGTSK  142 (219)
Q Consensus       114 ~~~Ce~C~R~L---~d~~rFCSL~CKv~~~~~  142 (219)
                      .+.|.+|+|-+   .+...|||-.|++.+...
T Consensus         6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~~   37 (43)
T PF12855_consen    6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQEK   37 (43)
T ss_pred             hhHHHHhhccccCCCCCccccCHHHHhHhhhc
Confidence            46799999999   678999999999765443


No 7  
>PF03884 DUF329:  Domain of unknown function (DUF329);  InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=86.34  E-value=0.095  Score=37.76  Aligned_cols=29  Identities=34%  Similarity=0.856  Sum_probs=17.5

Q ss_pred             CCcccccccccCC----CCe-eeeccccccccch
Q 027730          114 TNTCEVCDRSLLD----SFR-FCSLGCKIVGTSK  142 (219)
Q Consensus       114 ~~~Ce~C~R~L~d----~~r-FCSL~CKv~~~~~  142 (219)
                      +..|-+|++...-    +|+ |||-.||+.+..+
T Consensus         2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg~   35 (57)
T PF03884_consen    2 TVKCPICGKPVEWSPENPFRPFCSERCKLIDLGR   35 (57)
T ss_dssp             EEE-TTT--EEE-SSSSS--SSSSHHHHHHHHS-
T ss_pred             cccCCCCCCeecccCCCCcCCcccHhhcccCHHH
Confidence            3469999998875    676 9999999865543


No 8  
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=84.89  E-value=0.36  Score=35.43  Aligned_cols=29  Identities=31%  Similarity=0.812  Sum_probs=22.4

Q ss_pred             CCcccccccccC---C-CCe-eeeccccccccch
Q 027730          114 TNTCEVCDRSLL---D-SFR-FCSLGCKIVGTSK  142 (219)
Q Consensus       114 ~~~Ce~C~R~L~---d-~~r-FCSL~CKv~~~~~  142 (219)
                      .-.|-+|++.+.   + +|+ |||-.||+....+
T Consensus         6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~   39 (62)
T PRK00418          6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGE   39 (62)
T ss_pred             cccCCCCCCcccccCCCCcCCcccHHHHhhhHHH
Confidence            457999999874   3 575 9999999876554


No 9  
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.35  E-value=0.44  Score=35.35  Aligned_cols=29  Identities=34%  Similarity=0.864  Sum_probs=22.8

Q ss_pred             CCcccccccccCC----CCe-eeeccccccccch
Q 027730          114 TNTCEVCDRSLLD----SFR-FCSLGCKIVGTSK  142 (219)
Q Consensus       114 ~~~Ce~C~R~L~d----~~r-FCSL~CKv~~~~~  142 (219)
                      +-.|-+|++...-    +|| |||-.||+-...+
T Consensus         7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~   40 (65)
T COG3024           7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGE   40 (65)
T ss_pred             cccCCCCCCcccccccCCcCcchhHhhhhcchhh
Confidence            3459999998864    666 9999999876554


No 10 
>PF10013 DUF2256:  Uncharacterized protein conserved in bacteria (DUF2256);  InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=77.18  E-value=0.82  Score=31.29  Aligned_cols=23  Identities=35%  Similarity=1.002  Sum_probs=19.8

Q ss_pred             CCcccccccccC---------CCCeeeecccc
Q 027730          114 TNTCEVCDRSLL---------DSFRFCSLGCK  136 (219)
Q Consensus       114 ~~~Ce~C~R~L~---------d~~rFCSL~CK  136 (219)
                      ..+|.+|+|.+.         |..+|||-.|.
T Consensus         8 ~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR   39 (42)
T PF10013_consen    8 SKICPVCGRPFTWRKKWARCWDEVKYCSDRCR   39 (42)
T ss_pred             CCcCcccCCcchHHHHHHHhchhhccHHHHhc
Confidence            457999999996         57899999996


No 11 
>PF09889 DUF2116:  Uncharacterized protein containing a Zn-ribbon (DUF2116);  InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=68.54  E-value=1.8  Score=31.37  Aligned_cols=29  Identities=24%  Similarity=0.598  Sum_probs=24.2

Q ss_pred             CcccccccccCCCCeeeeccccccccchh
Q 027730          115 NTCEVCDRSLLDSFRFCSLGCKIVGTSKN  143 (219)
Q Consensus       115 ~~Ce~C~R~L~d~~rFCSL~CKv~~~~~~  143 (219)
                      ..|..||..+..+-.|||-.|+-...+++
T Consensus         4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k~q   32 (59)
T PF09889_consen    4 KHCPVCGKPIPPDESFCSPKCREEYRKRQ   32 (59)
T ss_pred             CcCCcCCCcCCcchhhhCHHHHHHHHHHH
Confidence            47999999999999999999996555544


No 12 
>PF13240 zinc_ribbon_2:  zinc-ribbon domain
Probab=64.29  E-value=3.2  Score=24.53  Aligned_cols=16  Identities=31%  Similarity=0.926  Sum_probs=14.3

Q ss_pred             ccccccccCCCCeeee
Q 027730          117 CEVCDRSLLDSFRFCS  132 (219)
Q Consensus       117 Ce~C~R~L~d~~rFCS  132 (219)
                      |..|+..+.+...||+
T Consensus         2 Cp~CG~~~~~~~~fC~   17 (23)
T PF13240_consen    2 CPNCGAEIEDDAKFCP   17 (23)
T ss_pred             CcccCCCCCCcCcchh
Confidence            7889999999889986


No 13 
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=60.82  E-value=2.8  Score=41.65  Aligned_cols=36  Identities=31%  Similarity=0.738  Sum_probs=28.6

Q ss_pred             cccCCCCCCCCCCCcceecccCCCCcCCccccc--CCCCCce
Q 027730           23 FVQCKLHPDSHKSECNMYCLDCMNGAFCSLCLD--YHKDHRA   62 (219)
Q Consensus        23 F~~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~--~H~~Hr~   62 (219)
                      -..|..|....   ..|||+.|. .++|..|+.  .|..|.|
T Consensus       223 ~~~ct~h~~e~---~smyc~~ck-~pvc~~clee~khs~hev  260 (699)
T KOG4367|consen  223 VSTCTDHELEN---HSMYCVQCK-MPVCYQCLEEGKHSSHEV  260 (699)
T ss_pred             hhhccCCCCCC---ceEEEEecC-ChHHHHHHHhhcccchhh
Confidence            45799898632   579999998 899999998  6777763


No 14 
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.73  E-value=1  Score=32.08  Aligned_cols=24  Identities=33%  Similarity=0.931  Sum_probs=20.8

Q ss_pred             CCCcccccccccC---------CCCeeeecccc
Q 027730          113 VTNTCEVCDRSLL---------DSFRFCSLGCK  136 (219)
Q Consensus       113 ~~~~Ce~C~R~L~---------d~~rFCSL~CK  136 (219)
                      ...+|++|+|.+.         |...|||-.|+
T Consensus        11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr   43 (54)
T COG4338          11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR   43 (54)
T ss_pred             chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999985         57899999998


No 15 
>PF13248 zf-ribbon_3:  zinc-ribbon domain
Probab=56.09  E-value=6.5  Score=23.53  Aligned_cols=19  Identities=21%  Similarity=0.586  Sum_probs=15.8

Q ss_pred             CCcccccccccCCCCeeee
Q 027730          114 TNTCEVCDRSLLDSFRFCS  132 (219)
Q Consensus       114 ~~~Ce~C~R~L~d~~rFCS  132 (219)
                      ...|..|+..+.+..+||+
T Consensus         2 ~~~Cp~Cg~~~~~~~~fC~   20 (26)
T PF13248_consen    2 EMFCPNCGAEIDPDAKFCP   20 (26)
T ss_pred             cCCCcccCCcCCcccccCh
Confidence            3578999998888899996


No 16 
>PF02207 zf-UBR:  Putative zinc finger in N-recognin (UBR box);  InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.  The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=53.39  E-value=6.5  Score=28.52  Aligned_cols=34  Identities=29%  Similarity=0.655  Sum_probs=24.0

Q ss_pred             CCcceecccCCC---CcCCccc-cc-CCCCCceeEEEec
Q 027730           35 SECNMYCLDCMN---GAFCSLC-LD-YHKDHRAIQIRRS   68 (219)
Q Consensus        35 nE~N~FCldC~~---~~~C~~C-l~-~H~~Hr~lQIRRs   68 (219)
                      ++--..|++|..   .++|..| .. .|.+|+++.++-.
T Consensus        10 ~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~   48 (71)
T PF02207_consen   10 GQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS   48 (71)
T ss_dssp             T-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred             CCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence            366678999974   5789999 44 8999998877654


No 17 
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=52.07  E-value=8.8  Score=25.66  Aligned_cols=27  Identities=30%  Similarity=0.707  Sum_probs=20.4

Q ss_pred             eecccCCCCcCCccccc--CCCCCceeEE
Q 027730           39 MYCLDCMNGAFCSLCLD--YHKDHRAIQI   65 (219)
Q Consensus        39 ~FCldC~~~~~C~~Cl~--~H~~Hr~lQI   65 (219)
                      .-|+.|.+--||..|..  .|..|..++|
T Consensus        15 y~C~~C~d~dLC~~C~~~~~H~~H~f~~~   43 (43)
T cd02340          15 YKCLVCPDYDLCESCEAKGVHPEHAMLKI   43 (43)
T ss_pred             EECCCCCCccchHHhhCcCCCCCCCEEeC
Confidence            56888877889999955  5777776653


No 18 
>PF06467 zf-FCS:  MYM-type Zinc finger with FCS sequence motif;  InterPro: IPR010507 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.  MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=51.39  E-value=3.4  Score=26.60  Aligned_cols=24  Identities=29%  Similarity=0.758  Sum_probs=15.1

Q ss_pred             CCCcccccccccCC-C-----------Ceeeecccc
Q 027730          113 VTNTCEVCDRSLLD-S-----------FRFCSLGCK  136 (219)
Q Consensus       113 ~~~~Ce~C~R~L~d-~-----------~rFCSL~CK  136 (219)
                      ..+.|..|++.+.. +           ..|||..|.
T Consensus         5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~   40 (43)
T PF06467_consen    5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCL   40 (43)
T ss_dssp             SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHH
T ss_pred             cCCcCcccCCcccCCCccccccccCcccChhCHHHH
Confidence            46689999877743 2           379999985


No 19 
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.01  E-value=12  Score=30.48  Aligned_cols=38  Identities=21%  Similarity=0.625  Sum_probs=29.7

Q ss_pred             cCCCCCCCCCCCcceecccCCCCcCCcccc-c-CCCCCceeEEEe
Q 027730           25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCL-D-YHKDHRAIQIRR   67 (219)
Q Consensus        25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl-~-~H~~Hr~lQIRR   67 (219)
                      .|..|...    ..+||..|. ..+|..|. . .|.+|.++.+..
T Consensus        88 ~c~~~~~~----~~~~c~~~~-~~~c~~c~~~~~h~~h~~~~~~~  127 (386)
T KOG2177|consen   88 LCEKHGEE----LKLFCEEDE-KLLCVLCRESGEHRGHPVLPLEE  127 (386)
T ss_pred             hhhhcCCc----ceEEecccc-cccCCCCCCcccccCCccccHHH
Confidence            67777642    679999997 79999996 3 899998776654


No 20 
>PF04438 zf-HIT:  HIT zinc finger;  InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.  This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=36.55  E-value=11  Score=23.69  Aligned_cols=21  Identities=38%  Similarity=0.874  Sum_probs=12.6

Q ss_pred             cccccccccC-----CCCeeeecccc
Q 027730          116 TCEVCDRSLL-----DSFRFCSLGCK  136 (219)
Q Consensus       116 ~Ce~C~R~L~-----d~~rFCSL~CK  136 (219)
                      .|.+|+..-.     -..+||||.|.
T Consensus         4 ~C~vC~~~~kY~Cp~C~~~~CSl~C~   29 (30)
T PF04438_consen    4 LCSVCGNPAKYRCPRCGARYCSLACY   29 (30)
T ss_dssp             EETSSSSEESEE-TTT--EESSHHHH
T ss_pred             CCccCcCCCEEECCCcCCceeCcEeE
Confidence            4777776211     14689999984


No 21 
>PF01412 ArfGap:  Putative GTPase activating protein for Arf;  InterPro: IPR001164  This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins.  The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=35.36  E-value=8.6  Score=30.28  Aligned_cols=50  Identities=22%  Similarity=0.344  Sum_probs=29.4

Q ss_pred             CCcceecccCCC-----------CcCCcccccCCCC--CceeEEEeccccceeeechhhhhhcc
Q 027730           35 SECNMYCLDCMN-----------GAFCSLCLDYHKD--HRAIQIRRSSYHDVIRVSEIQKVLDI   85 (219)
Q Consensus        35 nE~N~FCldC~~-----------~~~C~~Cl~~H~~--Hr~lQIRRssY~dVVRv~dIqkl~D~   85 (219)
                      ..-|..|.||..           .-+|..|...|+.  .++-+| |+.-.|-...+||+.+...
T Consensus        10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~V-kSi~~d~w~~~ev~~~~~~   72 (116)
T PF01412_consen   10 KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRV-KSITMDNWSPEEVQRMREG   72 (116)
T ss_dssp             STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--E-EETTTS---HHHHHHHHHS
T ss_pred             CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhc-cccccCCCCHHHHHHHHHH
Confidence            356899999952           2389999887773  223344 6777888888888887654


No 22 
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=35.30  E-value=13  Score=27.44  Aligned_cols=23  Identities=26%  Similarity=0.676  Sum_probs=20.9

Q ss_pred             CCcccccccccCCCCeeeecccc
Q 027730          114 TNTCEVCDRSLLDSFRFCSLGCK  136 (219)
Q Consensus       114 ~~~Ce~C~R~L~d~~rFCSL~CK  136 (219)
                      ...|.+|+..+...-+|||-.|.
T Consensus         8 H~HC~VCg~aIp~de~~CSe~C~   30 (64)
T COG4068           8 HRHCVVCGKAIPPDEQVCSEECG   30 (64)
T ss_pred             CccccccCCcCCCccchHHHHHH
Confidence            35799999999998999999997


No 23 
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=32.70  E-value=26  Score=24.09  Aligned_cols=27  Identities=30%  Similarity=0.705  Sum_probs=19.1

Q ss_pred             eecccCC--CCcCCccccc---CCC-CCceeEE
Q 027730           39 MYCLDCM--NGAFCSLCLD---YHK-DHRAIQI   65 (219)
Q Consensus        39 ~FCldC~--~~~~C~~Cl~---~H~-~Hr~lQI   65 (219)
                      .-|++|.  +--||..|..   .|+ +|+.+.|
T Consensus        16 ~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i   48 (48)
T cd02341          16 YHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI   48 (48)
T ss_pred             EECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence            5688888  7789999954   343 6766654


No 24 
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=28.71  E-value=57  Score=23.82  Aligned_cols=30  Identities=30%  Similarity=0.528  Sum_probs=21.9

Q ss_pred             CCCCcceecccCCC---CcCCccccc--CCCCCce
Q 027730           33 HKSECNMYCLDCMN---GAFCSLCLD--YHKDHRA   62 (219)
Q Consensus        33 ~knE~N~FCldC~~---~~~C~~Cl~--~H~~Hr~   62 (219)
                      .++|.-..|++|..   ..+|..|..  .|.+|++
T Consensus         8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~   42 (71)
T smart00396        8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY   42 (71)
T ss_pred             CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence            34577788999973   358888844  7999983


No 25 
>PF04570 DUF581:  Protein of unknown function (DUF581);  InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=28.39  E-value=17  Score=26.30  Aligned_cols=32  Identities=28%  Similarity=0.592  Sum_probs=23.6

Q ss_pred             CCCcccccccccC---CC--Ce----eeeccccccccchhh
Q 027730          113 VTNTCEVCDRSLL---DS--FR----FCSLGCKIVGTSKNF  144 (219)
Q Consensus       113 ~~~~Ce~C~R~L~---d~--~r----FCSL~CKv~~~~~~~  144 (219)
                      .-..|-.|.|.|.   |-  |+    |||..|.-..|..++
T Consensus        15 FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~~de   55 (58)
T PF04570_consen   15 FLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQILMDE   55 (58)
T ss_pred             HHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHHHHH
Confidence            3468999999998   32  33    999999876665443


No 26 
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=26.95  E-value=95  Score=22.11  Aligned_cols=32  Identities=9%  Similarity=0.360  Sum_probs=22.5

Q ss_pred             eeeechhhhh--hcccceeeEEECCeeEEEeeCCC
Q 027730           73 VIRVSEIQKV--LDISGVQTYVINSARVVFLNERP  105 (219)
Q Consensus        73 VVRv~dIqkl--~D~S~IQtYvINsakVVfLn~RP  105 (219)
                      +++++|+...  +++.+|-|.++||..+ +....|
T Consensus        33 ~~~v~~~~~a~~~~v~~vPti~i~G~~~-~~G~~~   66 (76)
T TIGR00412        33 FEKVTDMNEILEAGVTATPGVAVDGELV-IMGKIP   66 (76)
T ss_pred             EEEeCCHHHHHHcCCCcCCEEEECCEEE-EEeccC
Confidence            5666655554  7999999999988766 554433


No 27 
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=22.55  E-value=20  Score=28.01  Aligned_cols=43  Identities=26%  Similarity=0.397  Sum_probs=26.5

Q ss_pred             cceecccCCC-----------CcCCcccccCCCCC--ceeEEEeccccceeeechhh
Q 027730           37 CNMYCLDCMN-----------GAFCSLCLDYHKDH--RAIQIRRSSYHDVIRVSEIQ   80 (219)
Q Consensus        37 ~N~FCldC~~-----------~~~C~~Cl~~H~~H--r~lQIRRssY~dVVRv~dIq   80 (219)
                      -|..|.||..           .-+|..|..-|+..  ++-. .|+.-.|...-++|+
T Consensus         2 ~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~-VkSl~md~w~~~~i~   57 (112)
T smart00105        2 GNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISK-VRSLTLDTWTEEELR   57 (112)
T ss_pred             CCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCe-eeecccCCCCHHHHH
Confidence            3889999962           13788888878764  2222 445555655555554


No 28 
>smart00746 TRASH metallochaperone-like domain.
Probab=22.24  E-value=52  Score=18.20  Aligned_cols=11  Identities=45%  Similarity=0.887  Sum_probs=8.2

Q ss_pred             CCeeeeccccc
Q 027730          127 SFRFCSLGCKI  137 (219)
Q Consensus       127 ~~rFCSL~CKv  137 (219)
                      .+.|||..|..
T Consensus        23 ~~~FCs~~c~~   33 (39)
T smart00746       23 VFYFCSSKCLS   33 (39)
T ss_pred             EEEEeCHHHHH
Confidence            36789988874


No 29 
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=21.24  E-value=63  Score=29.54  Aligned_cols=56  Identities=20%  Similarity=0.324  Sum_probs=35.1

Q ss_pred             CCCCcHHHHhhc-ccc-----c---cCCCCCCCCCCCcceecccCCCCcCCccccc---CCCCCceeEEEe
Q 027730            9 RWPPWLKPLLRE-SFF-----V---QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD---YHKDHRAIQIRR   67 (219)
Q Consensus         9 ~~P~WL~~LL~~-~FF-----~---~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~---~H~~Hr~lQIRR   67 (219)
                      ..+.||.+-+.+ -++     .   .|..|.-..   --.-|..|.+--||..|-.   .|..|..|||.+
T Consensus       132 ~~~~~~~~~~~~~H~~~~~~~v~CD~C~~~~IvG---~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t  199 (278)
T KOG4582|consen  132 SLVITLNPVVGEMHPNISKLSVPCDNCGKPGIVG---ARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT  199 (278)
T ss_pred             hhhhhcCCCccccCCCcccccccCCCccCCcccc---ceeeecCCCccchhHHhhcCCCCCcccceeeccc
Confidence            345566665542 233     2   444444322   2256999998889999944   456788899887


No 30 
>PF06906 DUF1272:  Protein of unknown function (DUF1272);  InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=20.06  E-value=72  Score=23.24  Aligned_cols=23  Identities=39%  Similarity=0.894  Sum_probs=19.1

Q ss_pred             CcccccccccCC-C--Ceeeeccccc
Q 027730          115 NTCEVCDRSLLD-S--FRFCSLGCKI  137 (219)
Q Consensus       115 ~~Ce~C~R~L~d-~--~rFCSL~CKv  137 (219)
                      ..||.|++.|.- +  .+-||..|-+
T Consensus         6 pnCE~C~~dLp~~s~~A~ICSfECTF   31 (57)
T PF06906_consen    6 PNCECCDKDLPPDSPEAYICSFECTF   31 (57)
T ss_pred             CCccccCCCCCCCCCcceEEeEeCcc
Confidence            359999999975 3  6899999976


Done!