RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2533
(684 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases.
Length = 82
Score = 66.1 bits (162), Expect = 1e-13
Identities = 24/57 (42%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIA 176
GI++ V GG A+ G L+ GD++L+V+G S+ G+T E+A E L +G VTL +
Sbjct: 27 GIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 82
Score = 47.9 bits (115), Expect = 3e-07
Identities = 18/41 (43%), Positives = 28/41 (68%)
Query: 288 GRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIA 328
G L+ GD++L+V+G S+ G+T E+A E L +G VTL +
Sbjct: 42 GGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 82
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 65.1 bits (159), Expect = 4e-13
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQG 179
G+ + SVV G A G L+ GD +L+V+G S+ G+T +A + L + G VTL + + G
Sbjct: 27 GVVVSSVVPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
Score = 44.7 bits (106), Expect = 5e-06
Identities = 16/42 (38%), Positives = 27/42 (64%)
Query: 290 LQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQG 331
L+ GD +L+V+G S+ G+T +A + L + G VTL + + G
Sbjct: 44 LRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 63.0 bits (154), Expect = 2e-12
Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 112 EGAGQDRLGIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIV 171
G+ D GI++ V+ GGAA+A G LQ GD++L ++GQ L ++ ++A L +G V
Sbjct: 18 GGSDGDP-GIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLALKGSGGEV 75
Query: 172 TLEIA 176
TL I
Sbjct: 76 TLTIL 80
Score = 43.0 bits (102), Expect = 2e-05
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 286 QNGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIA 328
+ G LQ GD++L ++GQ L ++ ++A L +G VTL I
Sbjct: 38 EAGGLQEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTIL 80
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 52.3 bits (126), Expect = 6e-09
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVR-TGPIVTLEI 175
G+ + SV G A+ G LQAGD +L V+G + +T E AE L + G VTL +
Sbjct: 14 GVVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTV 69
Score = 40.0 bits (94), Expect = 2e-04
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 286 QNGRLQAGDQLLKVDGQSLVGITQEKAAEYLVR-TGPIVTLEI 327
+ LQAGD +L V+G + +T E AE L + G VTL +
Sbjct: 27 ERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTV 69
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 45.7 bits (109), Expect = 2e-06
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLV-RTGPIVTLEI 175
G+ I SV+ G A G ++AGD ++ +DG+ + G++ E + L + G V L +
Sbjct: 14 GLVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTL 69
Score = 36.0 bits (84), Expect = 0.006
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 290 LQAGDQLLKVDGQSLVGITQEKAAEYLV-RTGPIVTLEI 327
++AGD ++ +DG+ + G++ E + L + G V L +
Sbjct: 31 IKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTL 69
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 45.0 bits (107), Expect = 1e-04
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 116 QDRLGIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRT-GPIVTLE 174
+D G+ + S + G A G ++ GD ++K+DG+S+ G++ ++A + + G VTL
Sbjct: 109 EDIGGVKVVSPIDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLT 167
Query: 175 IAKQGA 180
I + G
Sbjct: 168 ILRAGG 173
Score = 34.6 bits (80), Expect = 0.16
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 290 LQAGDQLLKVDGQSLVGITQEKAAEYLVRT-GPIVTLEIAKQGAIYHGLATLLSQPSPVM 348
++ GD ++K+DG+S+ G++ ++A + + G VTL I + G TL + +
Sbjct: 130 IKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAGGGKPFTVTLTREEIELE 189
Query: 349 TRAYK 353
A K
Sbjct: 190 DVAAK 194
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 90
Score = 40.3 bits (95), Expect = 2e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQG 179
G+ + SV G A G L+ GD +L V+G+ + + + A ++ G VTL + + G
Sbjct: 25 GVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLTVLRGG 83
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 42.0 bits (99), Expect = 8e-04
Identities = 26/58 (44%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 126 VVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTL--EIAKQGAI 181
V AA G LQAGD+++KVDGQ L TQ + LVR P L EI +QG+
Sbjct: 228 VQPNSAASKAG-LQAGDRIVKVDGQPL---TQWQTFVTLVRDNPGKPLALEIERQGSP 281
Score = 37.7 bits (88), Expect = 0.017
Identities = 22/46 (47%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 290 LQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTL--EIAKQGAI 333
LQAGD+++KVDGQ L TQ + LVR P L EI +QG+
Sbjct: 239 LQAGDRIVKVDGQPL---TQWQTFVTLVRDNPGKPLALEIERQGSP 281
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 36.4 bits (85), Expect = 0.004
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 122 YIKSVVKGGAADANGRLQAGDQLLKVDGQ 150
I VV G A G L+AGD++L ++GQ
Sbjct: 15 VIGEVVPGSPAAKAG-LKAGDRILAINGQ 42
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 39.5 bits (92), Expect = 0.005
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQG 179
G + V+ G A G ++AGD + V+G+ + ++ AA R G V L++ + G
Sbjct: 271 GAVVLGVLPGSPAAKAG-IKAGDIITAVNGKPVASLSDLVAAVASNRPGDEVALKLLRGG 329
Query: 180 AIYHGLATLLSQPSP 194
LA L SP
Sbjct: 330 KE-RELAVTLGDRSP 343
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal beta-strand
is thought to form the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 34.0 bits (78), Expect = 0.025
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 6/62 (9%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYL--VRTGPIVTLEIAK 177
G+Y+ SVV+G A G+L+AGD ++ VDG+ E+ +Y+ + G V L++ +
Sbjct: 9 GVYVTSVVEG--MPAAGKLKAGDHIIAVDGKPF--KEAEELIDYIQSKKEGDTVKLKVKR 64
Query: 178 QG 179
+
Sbjct: 65 EE 66
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 35.7 bits (83), Expect = 0.085
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 120 GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQG 179
G + V+ G A+ G L+AGD + V+G+ + + A ++ G VTL I ++G
Sbjct: 258 GALVAQVLPGSPAEKAG-LKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKG 316
Query: 180 AI 181
Sbjct: 317 KE 318
Score = 31.4 bits (72), Expect = 1.5
Identities = 28/102 (27%), Positives = 41/102 (40%), Gaps = 10/102 (9%)
Query: 86 RLDSSMKSHSVRDMLRQEAKLSEMSEEGAGQDRL-----GIYIKSVVKGGAADANGRLQA 140
L +S + + ++ +S E + RL G+ + VV G A G LQ
Sbjct: 324 TLGASPEEQASSSNPFLGLTVANLSPEIRKELRLKGDVKGVVVTKVVSGSPAARAG-LQP 382
Query: 141 GDQLLKVDGQSLVGITQE--KAAEYLVRTGPIVTLEIAKQGA 180
GD +L V+ Q V E K + G V L I + GA
Sbjct: 383 GDVILSVNQQP-VSSVAELRKVLARAKKGG-RVALLILRGGA 422
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 34.6 bits (80), Expect = 0.16
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 6/62 (9%)
Query: 121 IYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPI---VTLEIAK 177
I I S +G A+ G ++ GD+++K++G+S+ G++ + A L+R G V+LEI +
Sbjct: 64 IVIVSPFEGSPAEKAG-IKPGDKIIKINGKSVAGMSLDDAVA-LIR-GKKGTKVSLEILR 120
Query: 178 QG 179
G
Sbjct: 121 AG 122
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 34.4 bits (79), Expect = 0.18
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 106 LSEMSEEGAGQDRL-GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGI--TQEKAAE 162
++ + +G G L GI I V G A A + D +LK DG+ ++G ++ AE
Sbjct: 264 INSVVAQGLGLPDLRGIVITGVDPNGPA-ARAGILVRDVILKYDGKDVIGAEELMDRIAE 322
Query: 163 YLVRTGPIVTLEIAKQGAI 181
R G V + + +QG
Sbjct: 323 --TRPGSKVMVTVLRQGKQ 339
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 31.5 bits (72), Expect = 0.21
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 115 GQDRLGIYIKSVVKGGAADANGRLQAGDQLLKVDGQ 150
+ G+ + SV +G A G L+ GD +L +DG+
Sbjct: 9 QNEGTGVTVVSVKEGSPAAKAG-LKPGDIILSIDGK 43
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 33.8 bits (78), Expect = 0.31
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 109 MSEEGAGQDRL-GIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGI--TQEKAAEYLV 165
+ +G G D+L GI + V G A G +Q D ++ V+ + + T ++ AE +
Sbjct: 268 LHAQGGGIDQLQGIVVNEVSPDGPAAKAG-IQVNDLIISVNNKPAISALETMDQVAE--I 324
Query: 166 RTGPIVTLEIAKQG 179
R G ++ + + +
Sbjct: 325 RPGSVIPVVVMRDD 338
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 33.5 bits (77), Expect = 0.35
Identities = 17/50 (34%), Positives = 17/50 (34%), Gaps = 17/50 (34%)
Query: 228 VGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADPERFY 277
V G P PGP TP P P P P PA ERF
Sbjct: 1 VDGEPGPKPGP-------------TPTPPPPA----PTPEPTPAKHERFI 33
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 33.3 bits (76), Expect = 0.51
Identities = 21/83 (25%), Positives = 28/83 (33%), Gaps = 5/83 (6%)
Query: 191 QPSPVMTRGQVKT----YESTISVQQRKERSSQNLHDMNNGVGGSHHPAPGPGSGMNHHP 246
+ R + Y+ R R + + G G H PGP + P
Sbjct: 194 REPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPEPPPGAGHVHRGGPGP-PERDDAP 252
Query: 247 VVSRQASTPSLPQASPYPAPAPA 269
VV + S P A P PAP P
Sbjct: 253 VVPIRPSAPGPLAAQPAPAPGPG 275
Score = 30.2 bits (68), Expect = 4.9
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 9/49 (18%)
Query: 234 PAPGPGSGMNHH--PVVSRQASTPSLPQASPYP-------APAPAPADP 273
P P PG+G H P + P +P P APAP P +P
Sbjct: 229 PEPPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQPAPAPGPGEP 277
>gnl|CDD|238491 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal zinc
metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 29.6 bits (67), Expect = 0.96
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 119 LGIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEI 175
G+ I V+ G A+ L GD + ++G + + A + G ++T+ +
Sbjct: 10 AGVVIVGVIVGSPAENAV-LHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTV 65
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 30.1 bits (68), Expect = 1.1
Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 7/77 (9%)
Query: 232 HHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADPERFYQNLSVYRNQNGRL- 290
P + P +Q PQ PYP +P P +F LS ++N +G
Sbjct: 22 QQPYHQQMPPPPYSPPQQQQGHFMP-PQPQPYPKQSPQQQQPPQFSSFLSQFKNSDGTFD 80
Query: 291 -----QAGDQLLKVDGQ 302
Q++ Q
Sbjct: 81 FNKMMNTVGQMVNTVNQ 97
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 31.6 bits (72), Expect = 1.5
Identities = 18/90 (20%), Positives = 25/90 (27%), Gaps = 15/90 (16%)
Query: 199 GQVKTYESTISVQQRKERSSQNLHDMNNGV-----GGSHHPAPG-----PGSGMNHHPVV 248
G ++++T SV + S + V S G P N
Sbjct: 236 GTAPSFDATPSVSPSGQPLSPAAPPGTSSVAGTALSASPAALFGDMVYVPLDAYNQLLAG 295
Query: 249 SRQASTPSLPQASPY-----PAPAPAPADP 273
P +P PAPAP P
Sbjct: 296 QAFNQPPDPQGPAPPAELAPPAPAPPPPAN 325
>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional.
Length = 141
Score = 30.2 bits (68), Expect = 1.6
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 2/40 (5%)
Query: 234 PAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
+P P P+ P PA AP P+DP
Sbjct: 97 QSPAPAVPTPPPTSTPAVPPAPAAA--VPAPAAAPPPSDP 134
>gnl|CDD|152960 pfam12526, DUF3729, Protein of unknown function (DUF3729). This
family of proteins is found in viruses. Proteins in this
family are typically between 145 and 1707 amino acids in
length. The family is found in association with
pfam01443, pfam01661, pfam05417, pfam01660, pfam00978.
There is a single completely conserved residue L that
may be functionally important.
Length = 115
Score = 29.6 bits (67), Expect = 2.1
Identities = 14/48 (29%), Positives = 15/48 (31%), Gaps = 7/48 (14%)
Query: 233 HPAPGPGSGMNHHPVVS-------RQASTPSLPQASPYPAPAPAPADP 273
HP P G PVV P A+P P P P P
Sbjct: 36 HPDDPPPVGDPRPPVVDTPPPVSAVWVLPPPSEPAAPPPDPEPPVPGP 83
>gnl|CDD|177328 PHA01929, PHA01929, putative scaffolding protein.
Length = 306
Score = 30.8 bits (69), Expect = 2.1
Identities = 24/92 (26%), Positives = 29/92 (31%), Gaps = 24/92 (26%)
Query: 191 QPSPVMTRGQVKTYESTISVQQRKERSSQNLHDMNNGVGGSHHPAPGPGSGMNHHPVVSR 250
QP+PV+ + QQ + Q P P P S M H V
Sbjct: 28 QPNPVIQPQAPVQPGQPGAPQQLAIPTQQ--------------PQPVPTSAMTPHVV--- 70
Query: 251 QASTPSLPQASPYPAPAPAPADPERFYQNLSV 282
QA PAPA PA + L V
Sbjct: 71 -------QQAPAQPAPAAPPAAGAALPEALEV 95
>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP). This family
contains bacterial fibronectin-attachment proteins
(FAP). Family members are rich in alanine and proline,
are approximately 300 long, and seem to be restricted to
mycobacteria. These proteins contain a
fibronectin-binding motif that allows mycobacteria to
bind to fibronectin in the extracellular matrix.
Length = 297
Score = 30.6 bits (69), Expect = 2.2
Identities = 13/40 (32%), Positives = 14/40 (35%), Gaps = 5/40 (12%)
Query: 234 PAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
P P P S + A P P PAP P DP
Sbjct: 43 PPPPPPS-----TAAAAPAPAAPPPPPPPAAPPAPQPDDP 77
Score = 29.5 bits (66), Expect = 5.3
Identities = 14/40 (35%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 234 PAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
P P P P + P P A P AP P P DP
Sbjct: 60 PPPPPPPAAPPAPQPDDPNAAPPPPPADP-NAPPPPPVDP 98
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 31.1 bits (71), Expect = 2.3
Identities = 30/134 (22%), Positives = 58/134 (43%), Gaps = 26/134 (19%)
Query: 500 RNKDFKKSRFLSS-MLELNFSEMK---IDDKDDNKFNNNNMDPDNRELNNNISNNESEEP 555
N+++ R L + ++ L +E+ D + + N + E+ N +SN
Sbjct: 489 NNENYLLLRKLRTLLVGLGLNEVITYSFVDPEKAEKFNFPKLENLVEIKNPLSN------ 542
Query: 556 AEFTVGKVNLGLNSIL--------RQSTVVKL-DL-RMFKKDP----RQRRLAQQQQEKM 601
E +V + +L L S+L R++ VK+ ++ ++F KD Q RLA +
Sbjct: 543 -ERSVLRTSL-LPSLLEVLAYNQNRKNKDVKIFEIGKVFAKDGEAVKEQLRLAILISGEK 600
Query: 602 LSNKTSQVPEKLSF 615
+ + EK+ F
Sbjct: 601 NPSSWNHKEEKVDF 614
>gnl|CDD|225455 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 31.2 bits (71), Expect = 2.3
Identities = 22/119 (18%), Positives = 42/119 (35%), Gaps = 19/119 (15%)
Query: 427 SDNTTSTQSSDNNSEPKQEVHQSTSVDVVETNKDKLTLEEREKALKELDEIINSIKITRN 486
DN+ SD+ EV+ +++ KLT ER L + + + S+ + N
Sbjct: 1146 IDNSAGVDCSDH------EVNIKIALNSAVF-AGKLTRGERNALLASMTDEVASLVLRNN 1198
Query: 487 IREFGSLDLSTSDRNKDFK-KSRFLSSMLELNFSEMKIDDKDDNKFNNNNMDPDNRELN 544
+ ++ L SRF+S++ ++ P + EL
Sbjct: 1199 YLQTEAISLLERLNLSLITELSRFISTL---------EAKGLLDREVEF--LPSDAELA 1246
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 31.1 bits (71), Expect = 2.5
Identities = 9/54 (16%), Positives = 15/54 (27%), Gaps = 1/54 (1%)
Query: 227 GVGGSHHPAPGPGSGMNH-HPVVSRQASTPSLPQASPYPAPAPAPADPERFYQN 279
+ AP P + + A+ P +P PAP +
Sbjct: 401 AAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAP 454
Score = 29.2 bits (66), Expect = 9.2
Identities = 14/46 (30%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 231 SHHPAPGPG---SGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
PAP P + S P S PAPAPA A
Sbjct: 430 QPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPE 475
>gnl|CDD|216421 pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).
Length = 305
Score = 30.5 bits (69), Expect = 2.6
Identities = 25/109 (22%), Positives = 34/109 (31%), Gaps = 17/109 (15%)
Query: 202 KTYESTISVQQRKERSSQNLHDMNNGVGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQAS 261
TY S + LHD+ A + + A+
Sbjct: 41 TTYRCVSSTTVPMTNVTVTLHDV-------TLQAYLSNGTFSKTETRCEADTPSPTTVAT 93
Query: 262 PYPAPAPAPADPERFYQNLSVYRNQNG---RLQAGDQL----LKVDGQS 303
P P+P P P+ P N SV N NG G QL DG++
Sbjct: 94 PSPSPTPVPSSPAVG--NYSV-TNGNGTCLLASMGLQLNITYETKDGKT 139
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 30.9 bits (70), Expect = 2.6
Identities = 30/187 (16%), Positives = 64/187 (34%), Gaps = 21/187 (11%)
Query: 384 IDCDSEDAKAVSSYTNNTESEQVKENVDVDTASSSMSECCCNHSDNTTSTQSSDNNSEPK 443
D ++ + + + N E + E D T S+++SE N ++ S + D N
Sbjct: 479 FDLENNFSNSFNPENGNKIDENINETFDTSTISANLSE---NKTNFAQSFNNKDTNLINS 535
Query: 444 QEVHQSTSVDVVETNKDKLTLEEREKALKELDEIINSIKITRNI-----------REFGS 492
+ + N K + K ++E+IN I + + +
Sbjct: 536 EIPIDLIKDTITINNSQKNVKKNGNKDYLSVEEVINLIMLAIKFHSQNQVEYKKLVQNWN 595
Query: 493 LDLSTSDRNKDFKKSRFLSSMLELNFSEMKIDDKDDNKFNNNNMDPDNR--ELNNNISNN 550
+L + + +F + L++ S + F++ + D +LN N
Sbjct: 596 KNLPLFEYDVEFMEIAHFLKDLKILAS-----SDNFILFSSKRDEIDELIIKLNKNNYKV 650
Query: 551 ESEEPAE 557
+ E
Sbjct: 651 NFQNFLE 657
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 30.9 bits (70), Expect = 2.6
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 112 EGAGQDRLGIYIKSVVKGGAADANGRLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPI- 170
G+ G+ + + GG A G ++ GD +L +DG S G++ +AA+ L GP
Sbjct: 95 TGSDGPPAGLVVVAPAPGGPAARAG-IRPGDVILAIDGTSTEGLSLYEAADRL--QGPEG 151
Query: 171 --VTLEIAKQG 179
V L + +
Sbjct: 152 SSVELTLRRGP 162
>gnl|CDD|184866 PRK14864, PRK14864, putative biofilm stress and motility protein A;
Provisional.
Length = 104
Score = 28.9 bits (65), Expect = 3.4
Identities = 12/36 (33%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 256 SLPQASPYPAPAPAPADPERFYQNLSVYRNQNGRLQ 291
S Q +P PAP PA + R Q LQ
Sbjct: 21 SALQGTPQPAPPPAD-------HAQEIRRAQTQGLQ 49
>gnl|CDD|223029 PHA03264, PHA03264, envelope glycoprotein D; Provisional.
Length = 416
Score = 30.4 bits (68), Expect = 3.4
Identities = 16/49 (32%), Positives = 17/49 (34%), Gaps = 8/49 (16%)
Query: 225 NNGVGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
+ GG P PGP P R PSL P P PA P
Sbjct: 314 DGAAGG--EPKPGPPRP---APDADRPEGWPSLEAI---TFPPPTPATP 354
>gnl|CDD|236451 PRK09284, PRK09284, thiamine biosynthesis protein ThiC;
Provisional.
Length = 607
Score = 30.2 bits (69), Expect = 3.7
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 90 SMK-SHSVRDMLRQEAKLSEMSEE 112
SMK S VRD +EA ++E SEE
Sbjct: 572 SMKISQEVRDYAAEEAGMAEKSEE 595
Score = 29.4 bits (67), Expect = 7.0
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MK-SHSVRDMLRQEAKLSEMSEEEIHRNQEIHR 32
MK S VRD +EA ++E SEE E++
Sbjct: 573 MKISQEVRDYAAEEAGMAEKSEEFRASGGELYL 605
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 30.2 bits (69), Expect = 3.9
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 434 QSSDNNSEPKQEVHQSTSVD----VVETNKDKLTLEEREKALKELDEIINSIKITRNI 487
+ S + + K+E+ + S +++ +LT EE EK KE++E+ I I
Sbjct: 357 RGSIDLKKAKKELIEELSEIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKI 414
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.5 bits (69), Expect = 4.2
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 5/61 (8%)
Query: 216 RSSQNLHDMNNGVGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYP-APAPAPADPE 274
SS++ G S +P P P + +S P+ S P +PA + P
Sbjct: 331 SSSESSRGAAVSPGPSPSRSPSPSRP----PPPADPSSPRKRPRPSRAPSSPAASAGRPT 386
Query: 275 R 275
R
Sbjct: 387 R 387
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 30.2 bits (68), Expect = 4.3
Identities = 9/47 (19%), Positives = 11/47 (23%), Gaps = 4/47 (8%)
Query: 227 GVGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
G G P +G P + S P AD
Sbjct: 707 GGGLPPPPDLPAAAG----PAPCGSSLIASPTAPPEPEPPGAEQADG 749
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 30.2 bits (68), Expect = 4.3
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 362 KTPKDNELCLCEDIFQQHQAKLIDCDSEDAKAVSSYTNNTESEQVKENVDVD 413
K PK++EL D + + K + D E +K + N ++E+ EN +D
Sbjct: 448 KIPKNDEL---LDNLELAKQKFFNKDIELSKNMLQKFNKFKNEESAENSFID 496
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein which
is localized in the photoreceptor outer segment discs.
Mutation/s in its genetic loci is implicated in the
recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 30.4 bits (68), Expect = 4.3
Identities = 15/44 (34%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 230 GSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
HP GP P S +P P A P P P P DP
Sbjct: 1298 NLRHPCSGPTEKAGQTPQAS-HTCSPGQPAAHPEGQPPPEPEDP 1340
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 30.0 bits (68), Expect = 4.5
Identities = 21/98 (21%), Positives = 27/98 (27%), Gaps = 35/98 (35%)
Query: 213 RKERSS-------------------QNLHDMNNGVG-------------GSHHPAPGPGS 240
RKERSS + + GVG H A P
Sbjct: 29 RKERSSMFRDRPLKRMKSKRDDDSYDEDVEDDEGVGEVRVHRVNHAPANAQEHEAARPSP 88
Query: 241 GMNHHPVVSRQASTPSL---PQASPYPAPAPAPADPER 275
+ P + + P+A P AP PA P
Sbjct: 89 QHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAP 126
>gnl|CDD|177464 PHA02682, PHA02682, ORF080 virion core protein; Provisional.
Length = 280
Score = 29.8 bits (66), Expect = 5.0
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 253 STPSLPQASPYPAPAPAPADPERFYQN 279
ST P A P P P PAPA F N
Sbjct: 143 STRQCPPAPPLPTPKPAPAAKPIFLHN 169
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 30.1 bits (68), Expect = 5.0
Identities = 21/119 (17%), Positives = 36/119 (30%), Gaps = 4/119 (3%)
Query: 233 HPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPA----DPERFYQNLSVYRNQNG 288
P + + AS P+ P A+ PAP APA +V
Sbjct: 392 APVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAP 451
Query: 289 RLQAGDQLLKVDGQSLVGITQEKAAEYLVRTGPIVTLEIAKQGAIYHGLATLLSQPSPV 347
QA + + + + AA L ++G ++H L+ +
Sbjct: 452 PAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEEGDVWHATVQQLAAAEAI 510
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 29.9 bits (68), Expect = 5.4
Identities = 11/48 (22%), Positives = 14/48 (29%), Gaps = 1/48 (2%)
Query: 226 NGVGGSHHPAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADP 273
G GG P G G + A+ + P A A P
Sbjct: 394 PGGGGGGPPGGGGAPGAPA-AAAAPGAAAAAPAAGGPAAALAAVPDAA 440
>gnl|CDD|215443 PLN02829, PLN02829, Probable galacturonosyltransferase.
Length = 639
Score = 29.8 bits (67), Expect = 5.7
Identities = 33/190 (17%), Positives = 69/190 (36%), Gaps = 19/190 (10%)
Query: 436 SDNNSEPKQEVHQSTSVDVVETNKDKLTLEEREKALKELDEIINSIKITRNIREFGSLDL 495
SDN+S+ + Q +D +K ++ + + D+II + + +
Sbjct: 76 SDNSSKTIEPDSQDLLLDKRGEHKARVLSATDDDTHSQTDDIIKQVTQKAGQDDSDQQEK 135
Query: 496 STSDRNKDFKKSRFLSSMLELNFSEMKIDDKDDNKFNNNNMDPDNRELNNNISNNESEEP 555
++ ++ +S K+D+K+ + + +
Sbjct: 136 NSQSQSASQAESLEHVQQSAQT--SEKVDEKEPLLTKTDKQTDQTVMPDARVRQLRD--- 190
Query: 556 AEFTVGKVNLGLNSILRQSTVVKLDLRMFKKDPRQRRLAQQQQEKMLSNKTSQVPEKLSF 615
+ KV L L + + +LR+ K+ QR L ++K S +P+ +
Sbjct: 191 -QLIKAKVYLSLPATKANPHFTR-ELRLRIKEV-QRVLGD-------ASKDSDLPKNAN- 239
Query: 616 KEKMKMFAME 625
EK+K AME
Sbjct: 240 -EKLK--AME 246
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.9 bits (67), Expect = 5.7
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 235 APGPGSGMNHHPVVSRQASTPSLPQASPYPAPAP-APADP 273
A GPG P AS P+ P +P PA AP PA P
Sbjct: 396 ARGPGGDDQTRPAAPVPASVPT-PAPTPVPASAPPPPATP 434
>gnl|CDD|213914 TIGR04301, ODC_inducible, ornithine decarboxylase SpeF. Members of
this family are known or trusted examples of ornithine
decarboxylase, all encoded in the immediate vicinity of
an ornithine-putrescine antiporter. Decarboxylation of
ornithine to putrescine, followed by exchange of a
putrescine for a new ornithine, is a proton-motive cycle
that can be induced by low pH and protect a bacterium
against transient exposure to acidic conditions.
Length = 719
Score = 29.7 bits (67), Expect = 5.7
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 9 MLRQEAKLSEM------SEEEIHRNQEIHRNQQEMHNGYVDKSPTQLHK 51
+L ++A L+E+ + EE ++ I + QEMH+ YV ++ QL K
Sbjct: 565 LLEEDAPLAEVLPSVYKANEERYKGYTIRQLCQEMHDLYVSRNVKQLQK 613
>gnl|CDD|234609 PRK00068, PRK00068, hypothetical protein; Validated.
Length = 970
Score = 30.0 bits (68), Expect = 6.1
Identities = 16/92 (17%), Positives = 28/92 (30%), Gaps = 2/92 (2%)
Query: 391 AKAVSSYTNNTESEQVKENVDVDTASSSMSECCCNHSDNTTSTQSSDNNSEPKQEVHQST 450
+A++ + +T + T S + +E Q
Sbjct: 878 REALTQLFGDGAGATATGEAPGETKTPPDPPPTAAPPPPTGPVTLSPAKAAALKEA-QDA 936
Query: 451 SVDVVETNKDKLTLEEREKALKELDEIINSIK 482
+E K E +ALKELD+ +N
Sbjct: 937 YNKAIEAQKSG-DFAEYGEALKELDDALNKYN 967
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 28.6 bits (64), Expect = 7.1
Identities = 14/46 (30%), Positives = 15/46 (32%), Gaps = 4/46 (8%)
Query: 232 HHPAPGPGSGMNHHPVVSRQASTPSLPQ----ASPYPAPAPAPADP 273
P P P S +P Q P PQ A PY P P
Sbjct: 124 TTPLPQPPSTAPSYPGPQYQGYHPMPPQPGMPAPPYSLQYPPPGLL 169
>gnl|CDD|226003 COG3472, COG3472, Uncharacterized conserved protein [Function
unknown].
Length = 342
Score = 29.0 bits (65), Expect = 7.5
Identities = 16/54 (29%), Positives = 17/54 (31%), Gaps = 10/54 (18%)
Query: 51 KGYS----TQVLNRPPPGPER----GDRPASAYLPNY--PGTPPNRLDSSMKSH 94
G S VLNR P E GD S YL LD + H
Sbjct: 230 LGISNKEINSVLNRTPIPAETNVKIGDTSPSEYLGELENDVNEERILDEMLIPH 283
>gnl|CDD|234797 PRK00575, tatA, twin arginine translocase protein A; Provisional.
Length = 92
Score = 27.4 bits (61), Expect = 7.7
Identities = 6/29 (20%), Positives = 10/29 (34%)
Query: 251 QASTPSLPQASPYPAPAPAPADPERFYQN 279
+A + +PY P P +R
Sbjct: 51 KAEASAAAAQAPYQVATPTPVQSQRVDPA 79
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 29.4 bits (66), Expect = 7.8
Identities = 12/41 (29%), Positives = 13/41 (31%)
Query: 234 PAPGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPADPE 274
AP P SR + P A A APA P
Sbjct: 446 DAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPP 486
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 28.6 bits (64), Expect = 7.8
Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 11/93 (11%)
Query: 470 ALKELDEIINSIKITRNIR-------EFGSLDLSTSDRNKDFKKSRFLSSMLELNFSEMK 522
L E+DE I ++ ++I+ F D D ++D ++ + +
Sbjct: 83 PLDEIDEEIQAMTEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEE---EDDEVDSLDDEN 139
Query: 523 ID-DKDDNKFNNNNMDPDNRELNNNISNNESEE 554
D D+DD++ ++ D + + + +E +E
Sbjct: 140 DDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDE 172
>gnl|CDD|218806 pfam05911, DUF869, Plant protein of unknown function (DUF869).
This family consists of a number of sequences found in
Arabidopsis thaliana, Oryza sativa and Lycopersicon
esculentum (Tomato). The function of this family is
unknown.
Length = 767
Score = 29.5 bits (66), Expect = 8.1
Identities = 35/191 (18%), Positives = 72/191 (37%), Gaps = 12/191 (6%)
Query: 368 ELCLCEDIFQQHQAKLIDCDSEDAKAVSSYTNNTESEQVKENVDVDTASSSMSECCCNHS 427
E L + + L D E ++ ++ SE KE D ++
Sbjct: 539 EFSLTLEWVVNQEKSLQDVSVEASEIKKNFLGLKSSE--KEINSPDEVKGAVCIS----- 591
Query: 428 DNTTSTQSSDNNSEPKQEVHQSTSVDVVETNKDKLTLEEREKALKELDEIINSIKITRNI 487
T + + + + S D +E +K+KL +E EK L+EL +++ + + ++
Sbjct: 592 --TLEELETLKSEKENLDGELSKCKDDLEESKNKL--QETEKKLEELKSELDASQESNSL 647
Query: 488 REFGSLDLSTSDRNKDFKKSRFLSSMLELNFSEMKIDDK-DDNKFNNNNMDPDNRELNNN 546
E + S + + + + L ++D+ + + N+ + REL
Sbjct: 648 AETQLKCMVESYESLELRAKDLEAEHKSLQEKISSLEDELEKERQNHQELIAKCRELEEK 707
Query: 547 ISNNESEEPAE 557
I E EE +
Sbjct: 708 IERAEQEENMQ 718
>gnl|CDD|235219 PRK04098, PRK04098, sec-independent translocase; Provisional.
Length = 158
Score = 28.2 bits (63), Expect = 8.4
Identities = 16/97 (16%), Positives = 31/97 (31%), Gaps = 4/97 (4%)
Query: 465 EEREKALKELDEIINSIKITRNIREFGSLDLSTSDRNKDFKKS--RFLSSMLELNFSEMK 522
EE K KE + + S+K E L ++ + K + + S+ E
Sbjct: 61 EEALKYKKEFESAVESLKKKLKFEELDDLKITAENEIKSIQDLLQDYKKSLEEDTIPNHL 120
Query: 523 IDDKDDNKFNNNNMDPDN--RELNNNISNNESEEPAE 557
++ + D +E+ N + E
Sbjct: 121 NEEVSNETKLTQESSSDESPKEVKLATKNKTKKHDKE 157
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 28.8 bits (65), Expect = 8.5
Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)
Query: 464 LEEREKALKELDEIINSIKITRNIREFGSLDLSTSDRNKDFKKSRFLSSMLELN--FSEM 521
+E + ++L + +S++ + IR+ S L +LEL E+
Sbjct: 71 IERGRASPRDLLRLYDSLEGLKEIRQLLE---SLDGPLLGLLLKVILEPLLELLELLLEL 127
Query: 522 KIDD-----KDDNKFNNNNMDPDNRELNNNISNNESE 553
DD D + DP+ EL + E E
Sbjct: 128 LNDDDPLEVNDGGLIKDG-FDPELDELREKLEELEEE 163
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 28.2 bits (64), Expect = 8.9
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 10/47 (21%)
Query: 461 KLTLEEREKALKELDEIINSIKIT-RNIREFGSLDLSTSDRNKDFKK 506
LT E R++ +K+ ++ K+ RNIR D N KK
Sbjct: 86 PLTEERRKELVKQAKKLAEEAKVAIRNIR---------RDANDKLKK 123
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 29.1 bits (66), Expect = 9.8
Identities = 14/59 (23%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 235 APGPGSGMNHHPVVSRQASTPSLPQASPYPAPAPAPA-DPERFYQNLSVYRNQNGRLQA 292
AP + P + P AP APA L R Q R Q
Sbjct: 376 APAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQG 434
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.309 0.125 0.345
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,898,318
Number of extensions: 3151697
Number of successful extensions: 3782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3676
Number of HSP's successfully gapped: 125
Length of query: 684
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 581
Effective length of database: 6,369,140
Effective search space: 3700470340
Effective search space used: 3700470340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 62 (27.6 bits)