Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
ID Alignment Graph Length
Definition
E-value Query 66
pfam01476 43
pfam01476, LysM, LysM domain
9e-08 PRK13914 481
PRK13914, PRK13914, invasion associated secreted e
1e-07 cd00118 45
cd00118, LysM, Lysine Motif is a small domain invo
4e-06 COG1388 124
COG1388, LytE, FOG: LysM repeat [Cell envelope bio
4e-05 PRK13914 481
PRK13914, PRK13914, invasion associated secreted e
2e-04 PRK06347 592
PRK06347, PRK06347, autolysin; Reviewed
4e-04 PRK06347 592
PRK06347, PRK06347, autolysin; Reviewed
5e-04 smart00257 44
smart00257, LysM, Lysin motif
0.001 PRK06347 592
PRK06347, PRK06347, autolysin; Reviewed
0.004 PRK06347 592
PRK06347, PRK06347, autolysin; Reviewed
0.004
>gnl|CDD|144899 pfam01476, LysM, LysM domain
Back Hide alignment and domain information
Score = 42.8 bits (102), Expect = 9e-08
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 23 RGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
+GDTL + + G++++ + E NGLS +Y
Sbjct: 5 KGDTLSSIAKRYGITVEELAELNGLSSPNLY 35
The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known. Length = 43
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase; Provisional
Back Show alignment and domain information
Score = 46.3 bits (109), Expect = 1e-07
Identities = 20/42 (47%), Positives = 26/42 (61%)
Query: 11 PEPASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTI 52
P AS V + GDTLWG + G ++DAIK+AN L+ D I
Sbjct: 22 PTIASASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKI 63
>gnl|CDD|212030 cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan
Back Show alignment and domain information
Score = 38.6 bits (91), Expect = 4e-06
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 23 RGDTLWGFSMKCGVSIDAIKEANGL-SGDTIY 53
GDTLW + K GV+++ + AN L + D IY
Sbjct: 7 PGDTLWSIAKKYGVTVEELAAANPLINPDCIY 38
LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes. Length = 45
>gnl|CDD|224306 COG1388, LytE, FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Back Show alignment and domain information
Score = 38.0 bits (88), Expect = 4e-05
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 7 DKSEPEPASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
S + + +GDTL + K GV++ +K+ N LS D I
Sbjct: 57 SSSASKAPPVVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSDKIK 103
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase; Provisional
Back Show alignment and domain information
Score = 37.1 bits (85), Expect = 2e-04
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 24 GDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
GDT+W S+K GVS+ I N LS +IY
Sbjct: 207 GDTIWALSVKYGVSVQDIMSWNNLSSSSIY 236
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed
Back Show alignment and domain information
Score = 36.2 bits (83), Expect = 4e-04
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 1 KPNIFMDKSEPEPAS---CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
KP+ S+P + ++ +++GD+LW + V+I +K N L D IY
Sbjct: 387 KPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKSDFIY 442
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed
Back Show alignment and domain information
Score = 35.8 bits (82), Expect = 5e-04
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 9 SEPEPASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
++P ++ + + +GD+LW S + ++D IK N L+ + I+
Sbjct: 540 NKPSNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIH 584
>gnl|CDD|197609 smart00257, LysM, Lysin motif
Back Show alignment and domain information
Score = 32.4 bits (75), Expect = 0.001
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 23 RGDTLWGFSMKCGVSIDAIKEANG-LSGDTIY-YSIICI 59
+GDTL + + G+S+ + E N L D + + I
Sbjct: 6 KGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed
Back Show alignment and domain information
Score = 33.1 bits (75), Expect = 0.004
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 14 ASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
++ +I +++GD+LW + V++ +K N L D IY
Sbjct: 328 SNAKIYTVVKGDSLWRIANNHKVTVANLKAWNNLKSDFIY 367
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed
Back Show alignment and domain information
Score = 33.1 bits (75), Expect = 0.004
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 1 KPNIFMDKSEPEPA---SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
KP+ + S+P + ++ + +GD+LW + V+I +K N L D IY
Sbjct: 461 KPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIY 516
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
ID Alignment Graph Length
Definition
Probability Query
66
PF01476 44
LysM: LysM domain; InterPro: IPR018392 This domain
99.64 PRK14125 103
cell division suppressor protein YneA; Provisional
99.54 TIGR02899 44
spore_safA spore coat assembly protein SafA. in wh
99.4 cd00118 46
LysM Lysin domain, found in a variety of enzymes i
99.37 PRK06347 592
autolysin; Reviewed
99.36 PRK13914 481
invasion associated secreted endopeptidase; Provis
99.33 PRK10871 319
nlpD lipoprotein NlpD; Provisional
99.32 TIGR02907 338
spore_VI_D stage VI sporulation protein D. SpoVID,
99.32 PRK10783 456
mltD membrane-bound lytic murein transglycosylase
99.27 PRK06347 592
autolysin; Reviewed
99.24 smart00257 44
LysM Lysin motif.
99.2 PRK13914 481
invasion associated secreted endopeptidase; Provis
99.19 COG1388 124
LytE FOG: LysM repeat [Cell envelope biogenesis, o
99.16 PRK11198 147
LysM domain/BON superfamily protein; Provisional
99.14 PRK10783 456
mltD membrane-bound lytic murein transglycosylase
99.04 PF04225 85
OapA: Opacity-associated protein A LysM-like domai
98.23 COG1652 269
XkdP Uncharacterized protein containing LysM domai
98.13 TIGR03505 74
FimV_core FimV N-terminal domain. This region is f
97.96 PRK10190 310
L,D-transpeptidase; Provisional
97.87 PRK10260 306
L,D-transpeptidase; Provisional
97.85 COG3858 423
Predicted glycosyl hydrolase [General function pre
97.61 PRK11649 439
putative peptidase; Provisional
97.4 COG3170 755
FimV Tfp pilus assembly protein FimV [Cell motilit
96.95 COG3061 242
OapA Cell envelope opacity-associated protein A [C
96.8 PF05489 60
Phage_tail_X: Phage Tail Protein X; InterPro: IPR0
95.89 COG3858 423
Predicted glycosyl hydrolase [General function pre
95.78 COG4784 479
Putative Zn-dependent protease [General function p
95.72 COG1388 124
LytE FOG: LysM repeat [Cell envelope biogenesis, o
95.32 COG0739 277
NlpD Membrane proteins related to metalloendopepti
93.82 PF13518 52
HTH_28: Helix-turn-helix domain
92.75 KOG2850 186
consensus Predicted peptidoglycan-binding protein,
92.11 PF01527 76
HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp
91.2 PF02796 45
HTH_7: Helix-turn-helix domain of resolvase; Inter
90.28 PRK09413 121
IS2 repressor TnpA; Reviewed
87.38 PF13384 50
HTH_23: Homeodomain-like domain; PDB: 2X48_C.
87.15 COG4254 339
Uncharacterized protein conserved in bacteria [Fun
84.71 PF05225 45
HTH_psq: helix-turn-helix, Psq domain; InterPro: I
84.5 PF04545 50
Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763
84.04 COG2963 116
Transposase and inactivated derivatives [DNA repli
83.62 PF04218 53
CENP-B_N: CENP-B N-terminal DNA-binding domain; In
83.2 cd00569 42
HTH_Hin_like Helix-turn-helix domain of Hin and re
81.58 PF13936 44
HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
81.08 PHA00675 78
hypothetical protein
80.89 PF13542 52
HTH_Tnp_ISL3: Helix-turn-helix domain of transposa
80.08
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []
Back Hide alignment and domain information
Probab=99.64 E-value=2.6e-16 Score=76.21 Aligned_cols=43 Identities=26% Similarity=0.480 Sum_probs=36.3
Q ss_pred EEEccCCcHHHHHHHhCCCHHHHHHhh-CCCCCCcCCCCEEEEc
Q 037180 19 VEILRGDTLWGFSMKCGVSIDAIKEAN-GLSGDTIYYSIICIFL 61 (66)
Q Consensus 19 y~V~~GdTl~~Ia~~~~~~~~~l~~~N-~l~~~~l~~G~~l~i~ 61 (66)
|+|++|||||+||++|++++++|+++| ++....+.+||.|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 899999999999999999999999999 7777559999999986
This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
>PRK14125 cell division suppressor protein YneA; Provisional
Back Show alignment and domain information
Probab=99.54 E-value=3.6e-14 Score=80.38 Aligned_cols=53 Identities=21% Similarity=0.314 Sum_probs=44.9
Q ss_pred CCCccEEEEccCCcHHHHHHHhCCC--------HHHHHHhhCCCCCCcCCCCEEEEcccCC
Q 037180 13 PASCRIVEILRGDTLWGFSMKCGVS--------IDAIKEANGLSGDTIYYSIICIFLCLSS 65 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~~~~--------~~~l~~~N~l~~~~l~~G~~l~i~~~~~ 65 (66)
...-..|+|++|||||+||++|+.+ ++.|++.|+++++.+++||.|.||...+
T Consensus 33 ~~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~~ 93 (103)
T PRK14125 33 KNQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLKS 93 (103)
T ss_pred CCCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCCC
Confidence 3455689999999999999999765 5677888999888899999999997643
>TIGR02899 spore_safA spore coat assembly protein SafA
Back Show alignment and domain information
Probab=99.40 E-value=8.8e-13 Score=62.99 Aligned_cols=41 Identities=37% Similarity=0.604 Sum_probs=36.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhhC-CCC-CCcCCCCEEEEc
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEANG-LSG-DTIYYSIICIFL 61 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N~-l~~-~~l~~G~~l~i~ 61 (66)
|++|||||+||++|++++++|.++|+ +.. ..+.+|+.|.|+
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip 43 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIP 43 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence 57899999999999999999999997 444 679999999987
in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation
Back Show alignment and domain information
Probab=99.37 E-value=3e-12 Score=60.21 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=40.5
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCC-CCCcCCCCEEEEc
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLS-GDTIYYSIICIFL 61 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~-~~~l~~G~~l~i~ 61 (66)
+|+|++|||+|+||++|+++..++.++|+.. ...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 6899999999999999999999999999984 4789999999875
This domain may have a general peptidoglycan binding function.
>PRK06347 autolysin; Reviewed
Back Show alignment and domain information
Probab=99.36 E-value=1.6e-12 Score=90.82 Aligned_cols=46 Identities=24% Similarity=0.394 Sum_probs=43.4
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFL 61 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~ 61 (66)
...|+|++|||||+||++||+++++|++||++..+.|++||.|.|+
T Consensus 547 ~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 547 VKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred ceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 4689999999999999999999999999999988889999999885
>PRK13914 invasion associated secreted endopeptidase; Provisional
Back Show alignment and domain information
Probab=99.33 E-value=4.5e-12 Score=86.74 Aligned_cols=50 Identities=36% Similarity=0.484 Sum_probs=46.0
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcccC
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCLS 64 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~~ 64 (66)
...+|.|++|||||+||++||+++++|+++|++..+.|++||.|+|+-.+
T Consensus 26 sa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVNEVA 75 (481)
T ss_pred cCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeCCCC
Confidence 44689999999999999999999999999999988899999999998654
>PRK10871 nlpD lipoprotein NlpD; Provisional
Back Show alignment and domain information
Probab=99.32 E-value=3.8e-12 Score=83.64 Aligned_cols=47 Identities=13% Similarity=0.140 Sum_probs=43.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
..+|+|++|||||.||.+||+++.+|.++|++.+ ..|++||.|+|+.
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~ 107 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGN 107 (319)
T ss_pred CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCC
Confidence 4589999999999999999999999999999966 8899999999964
>TIGR02907 spore_VI_D stage VI sporulation protein D
Back Show alignment and domain information
Probab=99.32 E-value=6.2e-12 Score=82.80 Aligned_cols=48 Identities=17% Similarity=0.195 Sum_probs=44.2
Q ss_pred CCccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEc
Q 037180 14 ASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFL 61 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~ 61 (66)
..-.+|+|++|||||.||++||+++..|+++|++....+++|+.|.||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 344689999999999999999999999999999988889999999986
SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Back Show alignment and domain information
Probab=99.27 E-value=1.5e-11 Score=83.88 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=44.0
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...+|+|++|||||+||++||+++++|++||++....|.+||+|.|...
T Consensus 401 ~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pGq~L~l~v~ 449 (456)
T PRK10783 401 DSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPGDKLTLFVK 449 (456)
T ss_pred cceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCCCEEEEecC
Confidence 3458999999999999999999999999999986668999999998753
>PRK06347 autolysin; Reviewed
Back Show alignment and domain information
Probab=99.24 E-value=2.4e-11 Score=84.98 Aligned_cols=48 Identities=25% Similarity=0.385 Sum_probs=44.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...|+|++|||||+||++||+++++|++||++..+.|++||.|.|+..
T Consensus 479 ~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~ 526 (592)
T PRK06347 479 AKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVSAG 526 (592)
T ss_pred ceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEecC
Confidence 357999999999999999999999999999998888999999999864
>smart00257 LysM Lysin motif
Back Show alignment and domain information
Probab=99.20 E-value=7.2e-11 Score=54.75 Aligned_cols=43 Identities=21% Similarity=0.332 Sum_probs=38.2
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCC-CCCCcCCCCEEEE
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGL-SGDTIYYSIICIF 60 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l-~~~~l~~G~~l~i 60 (66)
+|+|++|||+|+||++|+++..++.++|+. ....+.+|+.+.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 478999999999999999999999999995 4477899998864
>PRK13914 invasion associated secreted endopeptidase; Provisional
Back Show alignment and domain information
Probab=99.19 E-value=1e-10 Score=80.14 Aligned_cols=49 Identities=31% Similarity=0.457 Sum_probs=45.2
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...+|+|++|||||.||++|++++++|+++|++....+++||.|.|+..
T Consensus 198 ~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIKQT 246 (481)
T ss_pred CCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEecCC
Confidence 4468999999999999999999999999999998888999999999854
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Back Show alignment and domain information
Probab=99.16 E-value=1.6e-10 Score=66.30 Aligned_cols=47 Identities=28% Similarity=0.328 Sum_probs=44.2
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
..+|+|+.||+|+.||++|+++..+|+++|++..+.+++||.|.++.
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPV 112 (124)
T ss_pred CceEEEecCCCHHHHHHHhCCCHHHHHHHhccCCCceecCcEEEEec
Confidence 35899999999999999999999999999999888999999999975
>PRK11198 LysM domain/BON superfamily protein; Provisional
Back Show alignment and domain information
Probab=99.14 E-value=1.7e-10 Score=68.64 Aligned_cols=47 Identities=28% Similarity=0.286 Sum_probs=40.6
Q ss_pred CccEEEEccCCcHHHHHHHhC---CCHHHHHHhhC--CCC-CCcCCCCEEEEc
Q 037180 15 SCRIVEILRGDTLWGFSMKCG---VSIDAIKEANG--LSG-DTIYYSIICIFL 61 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~---~~~~~l~~~N~--l~~-~~l~~G~~l~i~ 61 (66)
...+|+|++|||||+||++|. ..+.+|+++|+ +.. ..+++||.|.||
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 556899999999999999984 45789999997 655 789999999987
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Back Show alignment and domain information
Probab=99.04 E-value=6.3e-10 Score=76.01 Aligned_cols=49 Identities=24% Similarity=0.276 Sum_probs=45.1
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcccC
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCLS 64 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~~ 64 (66)
..+|+|++|||||+||++||++..+|.++|++....+.+||.|.|++.+
T Consensus 343 ~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~ 391 (456)
T PRK10783 343 SRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIGAGS 391 (456)
T ss_pred ceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEecCCc
Confidence 4579999999999999999999999999999977889999999999853
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein
Back Show alignment and domain information
Probab=98.23 E-value=2.9e-06 Score=46.46 Aligned_cols=47 Identities=15% Similarity=0.027 Sum_probs=28.2
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhC-----CCCCCcCCCCEEEEccc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANG-----LSGDTIYYSIICIFLCL 63 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~-----l~~~~l~~G~~l~i~~~ 63 (66)
..|+|++||||..|-+++|++..++.++=. ..-..|+|||.|.+..-
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 379999999999999999999988776542 22267999999987653
This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Back Show alignment and domain information
Probab=98.13 E-value=7.9e-07 Score=56.98 Aligned_cols=46 Identities=37% Similarity=0.436 Sum_probs=39.5
Q ss_pred EEEEccCCcHHHHHHHh---CCCHHHHHHhhC---CCC-CCcCCCCEEEEccc
Q 037180 18 IVEILRGDTLWGFSMKC---GVSIDAIKEANG---LSG-DTIYYSIICIFLCL 63 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~---~~~~~~l~~~N~---l~~-~~l~~G~~l~i~~~ 63 (66)
+|+|+.|||||.|++++ +..+..|..+|+ +.. +.|.+||.++||-.
T Consensus 212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 89999999999999986 455777999998 555 89999999999854
>TIGR03505 FimV_core FimV N-terminal domain
Back Show alignment and domain information
Probab=97.96 E-value=8.2e-06 Score=43.75 Aligned_cols=40 Identities=28% Similarity=0.417 Sum_probs=31.4
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHhhC---C-CC-CCcCCCCEEEEcccC
Q 037180 25 DTLWGFSMKC---G-VSID----AIKEANG---L-SG-DTIYYSIICIFLCLS 64 (66)
Q Consensus 25 dTl~~Ia~~~---~-~~~~----~l~~~N~---l-~~-~~l~~G~~l~i~~~~ 64 (66)
||||+||++| + +++. .|.+.|+ . .. +.|++|+.|.||..+
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~~ 53 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSEE 53 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCHH
Confidence 8999999999 4 6766 5667885 1 22 789999999999754
This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
>PRK10190 L,D-transpeptidase; Provisional
Back Show alignment and domain information
Probab=97.87 E-value=6.2e-05 Score=49.76 Aligned_cols=46 Identities=15% Similarity=0.012 Sum_probs=39.3
Q ss_pred cEEEEccCC--cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGD--TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~Gd--Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
.+|+|+++| +|.+||++|++...+|+++|+--+ ....+|++|.|+.
T Consensus 38 ~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~ 86 (310)
T PRK10190 38 LTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQ 86 (310)
T ss_pred EEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecC
Confidence 468998866 699999999999999999998544 5568999999985
>PRK10260 L,D-transpeptidase; Provisional
Back Show alignment and domain information
Probab=97.85 E-value=7.1e-05 Score=49.38 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=39.3
Q ss_pred cEEEEccCC--cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGD--TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~Gd--Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
..|+|++|+ +|.+||++|++...+|+++|+--+ ....+|++|.|+.
T Consensus 41 ~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~ 89 (306)
T PRK10260 41 QVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQ 89 (306)
T ss_pred EEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCC
Confidence 479999966 599999999999999999998544 5567999999975
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Back Show alignment and domain information
Probab=97.61 E-value=0.00011 Score=50.25 Aligned_cols=52 Identities=21% Similarity=0.222 Sum_probs=43.3
Q ss_pred CCCccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcccC
Q 037180 13 PASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLCLS 64 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~~~ 64 (66)
++...+|.|++|||+++||++++++.+++..+|.+.. ..+.+|=.+.++...
T Consensus 46 ~~~~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 46 PPSGHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred CCcceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCCC
Confidence 4455789999999999999999999999999997655 667777777777553
>PRK11649 putative peptidase; Provisional
Back Show alignment and domain information
Probab=97.40 E-value=0.00084 Score=46.15 Aligned_cols=46 Identities=13% Similarity=0.107 Sum_probs=38.2
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCC-C-CCCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGL-S-GDTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l-~-~~~l~~G~~l~i~~ 62 (66)
..|+|++||||.+|-+++|++..++.++-.. . ...|++||.+.+..
T Consensus 96 ~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~ 143 (439)
T PRK11649 96 HEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTL 143 (439)
T ss_pred EEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEE
Confidence 3799999999999999999999998877432 2 26799999998753
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Back Show alignment and domain information
Probab=96.95 E-value=0.0016 Score=47.17 Aligned_cols=51 Identities=18% Similarity=0.317 Sum_probs=38.4
Q ss_pred CCCccEEEEccCCcHHHHHHHh----CCCHHH----HHHhhCC---CC--CCcCCCCEEEEccc
Q 037180 13 PASCRIVEILRGDTLWGFSMKC----GVSIDA----IKEANGL---SG--DTIYYSIICIFLCL 63 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~----~~~~~~----l~~~N~l---~~--~~l~~G~~l~i~~~ 63 (66)
.....+|++++|||||+||.+. +++.+. |.+.|+- +. +.++.|.+|+|+..
T Consensus 185 ~a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 185 AAPGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CCCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 4566799999999999999986 344444 6677852 22 57899999999864
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Back Show alignment and domain information
Probab=96.80 E-value=0.0062 Score=38.86 Aligned_cols=50 Identities=10% Similarity=0.082 Sum_probs=42.3
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-----CCcCCCCEEEEcccC
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-----DTIYYSIICIFLCLS 64 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-----~~l~~G~~l~i~~~~ 64 (66)
.-.+|+|+.|+||..+-+.+++++.++.++-.... ..|+.||.|.|+...
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 44689999999999999999999999988875422 578999999998754
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX
Back Show alignment and domain information
Probab=95.89 E-value=0.026 Score=28.99 Aligned_cols=46 Identities=24% Similarity=0.318 Sum_probs=34.4
Q ss_pred EEEEccCCcHHHHHHHh-CCC---HHHHHHhhC-CCC--CCcCCCCEEEEcccC
Q 037180 18 IVEILRGDTLWGFSMKC-GVS---IDAIKEANG-LSG--DTIYYSIICIFLCLS 64 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~-~~~---~~~l~~~N~-l~~--~~l~~G~~l~i~~~~ 64 (66)
.|+. .||||-.|+.|+ |.. .+.++++|+ +.. ..+..|..|.+|-..
T Consensus 3 v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 3 VYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred EEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 3444 899999999986 553 367899996 333 567889999998654
The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Back Show alignment and domain information
Probab=95.78 E-value=0.005 Score=42.29 Aligned_cols=46 Identities=13% Similarity=0.065 Sum_probs=40.9
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
..|.|++||++..|+++|+.+..+|...|.+..+.+-+||++.|+.
T Consensus 2 ~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~d~~~~~q~~~v~~ 47 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTNDDLVDGQTFVVPP 47 (423)
T ss_pred EEEEccCCceeeeehhhccccccccccccccccccccCceeEEECC
Confidence 3689999999999999999999999777777668899999999986
>COG4784 Putative Zn-dependent protease [General function prediction only]
Back Show alignment and domain information
Probab=95.72 E-value=0.024 Score=38.73 Aligned_cols=48 Identities=19% Similarity=0.276 Sum_probs=38.2
Q ss_pred CCccEEEEccCCcHHHHHHHh-CC--CHHHHHHhhCCCC-CCcCCCCEEEEc
Q 037180 14 ASCRIVEILRGDTLWGFSMKC-GV--SIDAIKEANGLSG-DTIYYSIICIFL 61 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~~Ia~~~-~~--~~~~l~~~N~l~~-~~l~~G~~l~i~ 61 (66)
-.....+|++|+|+.++|.+. |+ +++.+.-+|.+.. ..+.||+.+.|-
T Consensus 426 lrirvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 426 LRIRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred eEEEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 344568899999999999885 43 4666778899877 889999999773
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Back Show alignment and domain information
Probab=95.32 E-value=0.014 Score=33.18 Aligned_cols=33 Identities=33% Similarity=0.407 Sum_probs=29.9
Q ss_pred HHHHhCCCHHHHHHhhCCC--CCCcCCCCEEEEcc
Q 037180 30 FSMKCGVSIDAIKEANGLS--GDTIYYSIICIFLC 62 (66)
Q Consensus 30 Ia~~~~~~~~~l~~~N~l~--~~~l~~G~~l~i~~ 62 (66)
||.+|+++++++.++|.+. .+.+.+|+++.++.
T Consensus 1 ia~~~~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~ 35 (124)
T COG1388 1 IASKYGVSVKALKKANALTGKSDAIKPGQVLKIPG 35 (124)
T ss_pred CcccccccHHHHHHHhcccCCCCccccCceEEccC
Confidence 5788999999999999987 78999999999885
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Back Show alignment and domain information
Probab=93.82 E-value=0.22 Score=31.30 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=40.8
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCC-CcCCCCEEEEccc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGD-TIYYSIICIFLCL 63 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~-~l~~G~~l~i~~~ 63 (66)
..+.++.|+++..++++++.+...+...|..... .+..|+.+.++..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeeccc
Confidence 3588999999999999999999999999987664 7888998888764
>PF13518 HTH_28: Helix-turn-helix domain
Back Show alignment and domain information
Probab=92.75 E-value=0.14 Score=24.43 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=20.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|.++..+|++||++...+..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 468899999999999999988774
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Back Show alignment and domain information
Probab=92.11 E-value=0.14 Score=31.87 Aligned_cols=32 Identities=28% Similarity=0.343 Sum_probs=28.7
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLSG 49 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~ 49 (66)
..++++||||..||-+|.....++.+.|++..
T Consensus 11 ~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r 42 (186)
T KOG2850|consen 11 EVTIQEGDTLQAIALNYESDVADIKRVNNDDR 42 (186)
T ss_pred eeeeccCchhhhHHhhcccchhhheeeccchh
Confidence 56899999999999999999999999996543
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition
Back Show alignment and domain information
Probab=91.20 E-value=0.14 Score=26.42 Aligned_cols=25 Identities=12% Similarity=0.231 Sum_probs=21.1
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
...|.|+.++|++||+++..|..|=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 3679999999999999999998773
This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms
Back Show alignment and domain information
Probab=90.28 E-value=0.45 Score=22.59 Aligned_cols=24 Identities=17% Similarity=0.189 Sum_probs=17.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
...|-+..+||+.+|++...+.+.
T Consensus 18 ~~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 18 YAEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHTT--HHHHHHHTTS-HHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 357899999999999999988764
Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
>PRK09413 IS2 repressor TnpA; Reviewed
Back Show alignment and domain information
Probab=87.38 E-value=0.83 Score=26.04 Aligned_cols=25 Identities=16% Similarity=0.018 Sum_probs=22.5
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+..|.+..++|++||++...|..|=
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 5679999999999999999999883
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C
Back Show alignment and domain information
Probab=87.15 E-value=0.99 Score=21.39 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=17.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|.+...||+.+|++...+.+|
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w 37 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRW 37 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 34999999999999999998876
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Back Show alignment and domain information
Probab=84.71 E-value=1.1 Score=30.13 Aligned_cols=46 Identities=17% Similarity=-0.069 Sum_probs=36.7
Q ss_pred cEEEEccCCcHHHHHHHhCCCHH---HHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSID---AIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~---~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
-+|.|+.||||-.+...|-...+ .++..|...+ ..+.+|..|.|+.
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~ 55 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPL 55 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCC
Confidence 68999999999999999966544 4566787755 6788898888875
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []
Back Show alignment and domain information
Probab=84.50 E-value=1.1 Score=21.47 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=16.9
Q ss_pred EccC-CcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRG-DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~G-dTl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.| -++...|++||++...|.+.
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 3456 89999999999999988753
In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription
Back Show alignment and domain information
Probab=84.04 E-value=2.2 Score=20.29 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=18.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|+.+||+.+|++...+...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 46889999999999999887643
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=83.62 E-value=1.6 Score=24.38 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=20.2
Q ss_pred EccCCcHHHHHHHhCC-CHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGV-SIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~-~~~~l~~~ 44 (66)
.++|.|...||++||+ +...|..|
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHH
Confidence 4579999999999996 88887754
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere
Back Show alignment and domain information
Probab=83.20 E-value=0.63 Score=23.02 Aligned_cols=24 Identities=17% Similarity=0.302 Sum_probs=16.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|.+..+||++||++...+..+
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 467889999999999987776543
Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella
Back Show alignment and domain information
Probab=81.58 E-value=2.8 Score=17.10 Aligned_cols=22 Identities=18% Similarity=0.305 Sum_probs=18.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..|.+...+++.+|++...+..
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4678999999999999887764
The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A
Back Show alignment and domain information
Probab=81.08 E-value=2.7 Score=19.80 Aligned_cols=23 Identities=13% Similarity=0.263 Sum_probs=14.9
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+.|.+...||+++|.+...+.+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 35799999999999999887754
>PHA00675 hypothetical protein
Back Show alignment and domain information
Probab=80.89 E-value=2.6 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.091 Sum_probs=21.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+.|.+...||++||++...+...-
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 689999999999999999887654
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Back Show alignment and domain information
Probab=80.08 E-value=3 Score=19.80 Aligned_cols=21 Identities=14% Similarity=0.261 Sum_probs=17.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.-|+.+||+.+|+++..+.+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHH
Confidence 348999999999999988753
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
E-value Query 66
d1e0ga_ 48
d.7.1.1 (A:) Membrane-bound lytic murein transclyc
3e-08 d1y7ma2 48
d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term
2e-07
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Length = 48
Back Hide information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]
Score = 42.7 bits (101), Expect = 3e-08
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 23 RGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
+GD+L + + GV+I + N + +
Sbjct: 9 KGDSLSSIAKRHGVNIKDVMRWNSDT-ANLQ 38
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]} Length = 48
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Hypothetical protein YkuD, N-terminal domain
species: Bacillus subtilis [TaxId: 1423]
Score = 40.6 bits (95), Expect = 2e-07
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 23 RGDTLWGFSMKCGVSIDAIKEANGLSGDTIY 53
+GDTL + +S A+ +AN +
Sbjct: 8 QGDTLNSIAADFRISTAALLQANPSLQAGLT 38
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
Probability Query 66
d1e0ga_ 48
Membrane-bound lytic murein transclycosylase D, Ml
99.75 d1y7ma2 48
Hypothetical protein YkuD, N-terminal domain {Baci
99.73 d1ijwc_ 47
HIN recombinase (DNA-binding domain) {Synthetic}
93.6 d2jn6a1 89
Uncharacterized protein Cgl2762 {Corynebacterium g
87.78 d1d4ca3 146
Flavocytochrome c3 (respiratory fumarate reductase
86.84 d2croa_ 65
cro 434 {Bacteriophage 434 [TaxId: 10712]}
83.77 d1y0pa3 143
Flavocytochrome c3 (respiratory fumarate reductase
83.75 d1rr7a_ 94
Middle operon regulator, Mor {Bacteriophage Mu [Ta
83.42 d1k78a1 63
Pax-5 {Human (Homo sapiens) [TaxId: 9606]}
81.42
>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]}
Back Hide information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]
Probab=99.75 E-value=8.7e-19 Score=85.41 Aligned_cols=46 Identities=15% Similarity=0.195 Sum_probs=42.3
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
..+|+|++|||||.||++||+++++|+++|++.+ .+++||.|.|++
T Consensus 2 ~v~y~V~~GDTl~~IA~~y~vs~~~i~~~N~l~~-~l~~Gq~L~i~v 47 (48)
T d1e0ga_ 2 SITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTA-NLQPGDKLTLFV 47 (48)
T ss_dssp CCEEEECTTCCHHHHHHHHTCCHHHHHHHCSCGG-GCCTTEEEECCC
T ss_pred cEEEEECCCCCHHHHHHHHCCCHHHHHHHcCCcc-cCcCCCEEEEEe
Confidence 3589999999999999999999999999999864 699999999975
>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Hypothetical protein YkuD, N-terminal domain
species: Bacillus subtilis [TaxId: 1423]
Probab=99.73 E-value=3.9e-19 Score=86.63 Aligned_cols=46 Identities=17% Similarity=0.120 Sum_probs=43.3
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
.+|+|++|||||+||++|++++++|+++|++..+.+++||.|.||-
T Consensus 2 i~y~V~~GDTL~~IA~~y~v~~~~i~~~N~~~~~~l~~Gq~L~IPg 47 (48)
T d1y7ma2 2 LTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPG 47 (48)
T ss_dssp EEEECCTTCCHHHHHHHTTSCCCCCCCTSCTTCSSCCTTCEEEETT
T ss_pred EEEEECCCCCHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCEEEeCC
Confidence 3799999999999999999999999999999887899999999985
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}
Back Show information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic
Probab=93.60 E-value=0.031 Score=25.53 Aligned_cols=24 Identities=8% Similarity=0.277 Sum_probs=21.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|.+..+||+.||++...|.++
T Consensus 18 ~~~G~s~~~iA~~~gVSr~TiYry 41 (47)
T d1ijwc_ 18 LEKGHPRQQLAIIFGIGVSTLYRY 41 (47)
T ss_dssp HHTTCCHHHHHHHHTCCHHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHhh
Confidence 467999999999999999999876
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}
Back Show information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]
Probab=87.78 E-value=0.23 Score=24.74 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
.|-+..+||++||++...|..|=
T Consensus 22 ~g~s~~~vA~~lGIs~~tl~~W~ 44 (89)
T d2jn6a1 22 DGASLQQIANDLGINRVTLKNWI 44 (89)
T ss_dssp GGSCHHHHHHHHTSCHHHHHHHH
T ss_pred CCCcHHHHHHHHCCCHHHHHHHH
Confidence 48899999999999999998883
>d1d4ca3 d.168.1.1 (A:360-505) Flavocytochrome c3 (respiratory fumarate reductase) {Shewanella putrefaciens [TaxId: 24]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
domain: Flavocytochrome c3 (respiratory fumarate reductase)
species: Shewanella putrefaciens [TaxId: 24]
Probab=86.84 E-value=0.19 Score=27.15 Aligned_cols=25 Identities=16% Similarity=0.243 Sum_probs=20.7
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N 45 (66)
+.++|||.++|++.|++.+.| .++|
T Consensus 81 ~~ka~TleeLA~~~gid~~~L~~Tv~~yN 109 (146)
T d1d4ca3 81 VKEGKTIEELAKQIDVPAAELAKTVTAYN 109 (146)
T ss_dssp CEEESSHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred eeEcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567899999999999997775 4566
>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}
Back Show information, alignment and structure
class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]
Probab=83.77 E-value=0.61 Score=21.56 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=18.2
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+.+++..||+.||++++.|..
T Consensus 43 ~~~~l~~ia~~l~v~~~~Ll~ 63 (65)
T d2croa_ 43 RPRFLFEIAMALNCDPVWLQY 63 (65)
T ss_dssp SCTTHHHHHHHTTSCHHHHHH
T ss_pred CHHHHHHHHHHhCCCHHHHhh
Confidence 458999999999999999863
>d1y0pa3 d.168.1.1 (A:362-504) Flavocytochrome c3 (respiratory fumarate reductase) {Shewanella frigidimarina [TaxId: 56812]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
domain: Flavocytochrome c3 (respiratory fumarate reductase)
species: Shewanella frigidimarina [TaxId: 56812]
Probab=83.75 E-value=0.33 Score=26.10 Aligned_cols=25 Identities=20% Similarity=0.179 Sum_probs=20.8
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N 45 (66)
+.++|||.++|++.|++.+.| .++|
T Consensus 80 ~~~adtleeLA~~~gid~~~L~~Tv~~yN 108 (143)
T d1y0pa3 80 APTADSLVKLGKMEGIDGKALTETVARYN 108 (143)
T ss_dssp CCEESSHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred eeecCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567899999999999998774 5566
>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}
Back Show information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]
Probab=83.42 E-value=0.63 Score=23.66 Aligned_cols=21 Identities=14% Similarity=0.436 Sum_probs=18.7
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|.+...+|++||++...+.+
T Consensus 65 ~G~n~~eLA~kY~lS~~~I~~ 85 (94)
T d1rr7a_ 65 NGRNVSELTTRYGVTFNTVYK 85 (94)
T ss_dssp CSSCHHHHHHHHTCCHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 599999999999999888764
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]
Probab=81.42 E-value=0.67 Score=22.06 Aligned_cols=24 Identities=17% Similarity=0.102 Sum_probs=20.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|.+..++|++|+++..-+.+|
T Consensus 27 ~~~G~s~r~aA~rf~VS~s~v~k~ 50 (63)
T d1k78a1 27 AHQGVRPCDISRQLRVSHGCVSKI 50 (63)
T ss_dssp HHTTCCHHHHHHHHTCCHHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 468999999999999998877665
