RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10269
(108 letters)
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 104 bits (262), Expect = 9e-31
Identities = 57/88 (64%), Positives = 67/88 (76%), Gaps = 4/88 (4%)
Query: 20 GEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAP 79
+ I +LKAAGV VEPYWPGLFAKALEG ++K+L+SNVG G G AAPAAA AAA
Sbjct: 20 ADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSNVGGGGG----GAAPAAAAAAAA 75
Query: 80 AAAEAKEDKKKKEESDEGSDDDMGFGLF 107
AAA + ++KKEE +E SDDDMGFGLF
Sbjct: 76 AAAAEAKKEEKKEEEEEESDDDMGFGLF 103
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 75.0 bits (185), Expect = 3e-19
Identities = 49/87 (56%), Positives = 57/87 (65%), Gaps = 3/87 (3%)
Query: 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPA 80
I+ VLKAAG EVE L K LEG N+KELI+N + A AAAA A AAA A
Sbjct: 5 ADIKHVLKAAGKEVEAERLELLVKFLEGKNIKELIANGSAKLSAAAAAAAAA---AAAAA 61
Query: 81 AAEAKEDKKKKEESDEGSDDDMGFGLF 107
AA A E++KK+EE +E DDDMGFGLF
Sbjct: 62 AAAAAEEEKKEEEEEEEEDDDMGFGLF 88
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 66.3 bits (162), Expect = 1e-15
Identities = 45/92 (48%), Positives = 59/92 (64%), Gaps = 2/92 (2%)
Query: 19 DGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAA 78
+ +++VL+AAGVEVE ALEGV++ E+I N A AA A AAA A A
Sbjct: 18 TEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGA 77
Query: 79 PAAAEA--KEDKKKKEESDEGSDDDMGFGLFD 108
AAAEA E+++K+EE++E SDDDM FGLF
Sbjct: 78 EAAAEADEAEEEEKEEEAEEESDDDMLFGLFG 109
>gnl|CDD|100111 cd05833, Ribosomal_P2, Ribosomal protein P2. This subfamily
represents the eukaryotic large ribosomal protein P2.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P2 is located in the L12 stalk, with proteins
P1, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers). Bacteria may have four or six copies
of L7/L12 (two or three homodimers) depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plants have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site in the C-terminal region
of P2. TCS inactivates the ribosome by depurinating a
specific adenine in the sarcin-ricin loop of 28S rRNA.
Length = 109
Score = 64.2 bits (157), Expect = 8e-15
Identities = 45/89 (50%), Positives = 55/89 (61%), Gaps = 5/89 (5%)
Query: 23 IQTVLKAAGVEVEPYWPGLFAKALEGVNVKELI---SNVGSGAGAGPAAAAPAAAQAAAP 79
++ +L + GVEV+ LEG +V+ELI + AG AAPAAA AAA
Sbjct: 23 VKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAAAAAA 82
Query: 80 AAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
AAA KE +KKEES+E SDDDMGFGLFD
Sbjct: 83 AAAAKKE--EKKEESEEESDDDMGFGLFD 109
>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and L12p.
Ribosomal proteins P1 and P2 are the eukaryotic proteins
that are functionally equivalent to bacterial L7/L12.
L12p is the archaeal homolog. Unlike other ribosomal
proteins, the archaeal L12p and eukaryotic P1 and P2 do
not share sequence similarity with their bacterial
counterparts. They are part of the ribosomal stalk
(called the L7/L12 stalk in bacteria), along with 28S
rRNA and the proteins L11 and P0 in eukaryotes (23S
rRNA, L11, and L10e in archaea). In bacterial ribosomes,
L7/L12 homodimers bind the extended C-terminal helix of
L10 to anchor the L7/L12 molecules to the ribosome.
Eukaryotic P1/P2 heterodimers and archaeal L12p
homodimers are believed to bind the L10 equivalent
proteins, eukaryotic P0 and archaeal L10e, in a similar
fashion. P1 and P2 (L12p, L7/L12) are the only proteins
in the ribosome to occur as multimers, always appearing
as sets of dimers. Recent data indicate that most
archaeal species contain six copies of L12p (three
homodimers), while eukaryotes have two copies each of P1
and P2 (two heterodimers). Bacteria may have four or six
copies (two or three homodimers), depending on the
species. As in bacteria, the stalk is crucial for
binding of initiation, elongation, and release factors
in eukaryotes and archaea.
Length = 105
Score = 63.8 bits (155), Expect = 1e-14
Identities = 40/86 (46%), Positives = 51/86 (59%), Gaps = 1/86 (1%)
Query: 22 KIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAA 81
KI+ +L AAG E+EP LF AL G N+ E+IS + AAAA AA AAA A
Sbjct: 21 KIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPAATAAATAE 80
Query: 82 AEAKEDKKKKEESDEGSDDDMGFGLF 107
K ++ K+EE +E D+D GFGLF
Sbjct: 81 PAEKAEEAKEEEEEE-EDEDFGFGLF 105
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 53.0 bits (128), Expect = 2e-10
Identities = 38/86 (44%), Positives = 54/86 (62%), Gaps = 4/86 (4%)
Query: 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPA 80
+ ++ VL+AAGVEV+ ALE VN++E I A A P AAA AAA AAA A
Sbjct: 20 DNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKK----AAAAPVAAAAAAAAAAAAA 75
Query: 81 AAEAKEDKKKKEESDEGSDDDMGFGL 106
AAE K++++++EE E S+++ GL
Sbjct: 76 AAEEKKEEEEEEEEKEESEEEAAAGL 101
>gnl|CDD|165706 PLN00138, PLN00138, large subunit ribosomal protein LP2;
Provisional.
Length = 113
Score = 49.7 bits (118), Expect = 4e-09
Identities = 39/95 (41%), Positives = 53/95 (55%), Gaps = 9/95 (9%)
Query: 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELIS-------NVGSGAGAGPAAAAPAA 73
E ++ +L + G + + L ++G ++ ELI+ +V SG G AAAA A
Sbjct: 21 EDLKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPA 80
Query: 74 AQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
A AA AAEAK K++K E E SDDDMGF LFD
Sbjct: 81 AGGAAAPAAEAK--KEEKVEEKEESDDDMGFSLFD 113
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 49.1 bits (117), Expect = 6e-09
Identities = 39/95 (41%), Positives = 54/95 (56%), Gaps = 12/95 (12%)
Query: 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELIS-------NVGSGAGAGPAAAAPAA 73
++++ VL A +VE F K+LEG ELI+ N+G G A A PAA
Sbjct: 23 KEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAAA---PAA 79
Query: 74 AQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
A A A AEAK+++KK+EE +E +DD+GF LF
Sbjct: 80 GAATAGAKAEAKKEEKKEEEEEE--EDDLGFSLFG 112
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 47.7 bits (114), Expect = 2e-08
Identities = 36/85 (42%), Positives = 52/85 (61%), Gaps = 4/85 (4%)
Query: 19 DGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAA 78
+ E ++ VL+AAGVEV+ ALEGVN++E I A A P AAA AAA AAA
Sbjct: 18 NEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKK----AAAAPVAAAAAAAAAAA 73
Query: 79 PAAAEAKEDKKKKEESDEGSDDDMG 103
A E +E+++++EE +E ++ M
Sbjct: 74 AAEEEEEEEEEEEEEEEESEEEAMA 98
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 47.3 bits (113), Expect = 2e-07
Identities = 26/55 (47%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 54 LISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
L + AAAA AAA AA AAA A ++EE +E DDMGFGLFD
Sbjct: 261 LAEKIKEALANPSAAAAAAAA--AAAAAAAAAAAPAEEEEEEE---DDMGFGLFD 310
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 43.3 bits (102), Expect = 1e-06
Identities = 34/83 (40%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPA 80
E ++ VL+AAG+EV+ ALE VN+ E I A A AA A AAA AA
Sbjct: 20 ENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAAVAAAA--AAPAAAAAAAAEEK 77
Query: 81 AAEAKEDKKKKEESDEGSDDDMG 103
A E +E+KKK+EE +E ++ +
Sbjct: 78 AEEKEEEKKKEEEKEEEEEEALA 100
>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
Length = 323
Score = 39.6 bits (92), Expect = 8e-05
Identities = 21/47 (44%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFG 105
G G G AAA AAA AA +AA KEE +E +DD G G
Sbjct: 281 GLLGGGGSAAAEAAAAAPAAASAA-------AKEEEEESDEDDFGMG 320
>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase;
Validated.
Length = 407
Score = 38.3 bits (90), Expect = 2e-04
Identities = 21/50 (42%), Positives = 30/50 (60%)
Query: 49 VNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGS 98
V V +++ + GA AG AAAA AAA AAA A A+A+ ++ +D S
Sbjct: 67 VTVGQVLGRIDEGAAAGAAAAAAAAAAAAAAAPAQAQAAAAAEQSNDALS 116
Score = 27.5 bits (62), Expect = 1.2
Identities = 17/31 (54%), Positives = 19/31 (61%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
A AAAAPAA AAAPAAA A + +E
Sbjct: 149 AALAAAAAAPAAPAAAAPAAAPAPLGARPEE 179
Score = 27.1 bits (61), Expect = 1.9
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKK 91
A A AA AAA AAAPA A+ +++
Sbjct: 153 AAAAAPAAPAAAAPAAAPAPLGARPEERVP 182
Score = 26.7 bits (60), Expect = 2.5
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 63 GAGPAAAAPAAAQAAAPAAAEAKEDKKKKEE 93
A AAAA AA AAA AA + EE
Sbjct: 149 AALAAAAAAPAAPAAAAPAAAPAPLGARPEE 179
Score = 26.3 bits (59), Expect = 3.5
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 48 GVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
G KE + + A A PAA A AA AA E
Sbjct: 140 GRVTKEDVLAALAAAAAAPAAPAAAAPAAAPAPLGARPE 178
Score = 25.6 bits (57), Expect = 5.9
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEE 93
A A AAA A A AA AA + ++
Sbjct: 149 AALAAAAAAPAAPAAAAPAAAPAPLGARPEERV 181
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 33.7 bits (78), Expect = 0.009
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 30 AGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKK 89
AG+ + +KA+ L + + +AQA A AAAE +E+++
Sbjct: 252 AGIVTPETADDILSKAV--AQALALAAALADKDALDEELKEVLSAQAQA-AAAEEEEEEE 308
Query: 90 KKEESDEGSDDDMGFGL 106
++EE +E S+++ GL
Sbjct: 309 EEEEEEEPSEEEAAAGL 325
>gnl|CDD|234519 TIGR04244, nitrous_NosZ_RR, nitrous-oxide reductase,
TAT-dependent. Members of this family are the
nitrous-oxide reductase structural protein, NosZ, with
an N-terminal twin-arginine translocation (TAT) signal
sequence (see TIGR01409). The TAT system replaces the
Sec system for export of proteins with bound cofactor.
Length = 627
Score = 33.5 bits (77), Expect = 0.010
Identities = 17/31 (54%), Positives = 19/31 (61%)
Query: 56 SNVGSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
+ + AGAG A AA AAA AAA AAA A
Sbjct: 11 AALAGLAGAGAAGAAGAAAAAAAAAAAAAAG 41
Score = 29.3 bits (66), Expect = 0.34
Identities = 17/27 (62%), Positives = 18/27 (66%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAK 85
+GAGA AA A AAA AAA AAA K
Sbjct: 16 LAGAGAAGAAGAAAAAAAAAAAAAAGK 42
Score = 27.4 bits (61), Expect = 1.6
Identities = 19/44 (43%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 59 GSGAGAGPAAA-APAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
G+ A AG A A A AA AAA AAA A K G D+
Sbjct: 9 GTAALAGLAGAGAAGAAGAAAAAAAAAAAAAAGKYHVAPGELDE 52
>gnl|CDD|223582 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide acyltransferase (E2) component, and
related enzymes [Energy production and conversion].
Length = 404
Score = 33.5 bits (77), Expect = 0.012
Identities = 11/54 (20%), Positives = 18/54 (33%)
Query: 41 LFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
+ + + V V +I+ + PAAA AAA A+
Sbjct: 59 ILVEEGDTVPVGAVIARIEEEGADAPAAAEAPPEPAAAAPASAPATAASAAAGR 112
>gnl|CDD|234021 TIGR02811, formate_TAT, formate dehydrogenase region TAT target.
Members of this uncharacterized protein family are all
small, extending 70 or fewer residues from their
respective likely start codons. All have the
twin-arginine-dependent tranport (TAT) signal sequence
at the N-terminus and a conserved 20-residue C-terminal
region that includes the motif
Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal
sequence suggests a bound cofactor. All members are
encoded near genes for subunits of formate
dehydrogenase, and may themselves be a subunit or
accessory protein [Unknown function, General].
Length = 66
Score = 31.3 bits (71), Expect = 0.016
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 48 GVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKK 91
+ ++L+ +G GA AG AAA +A+ + ++ +KKKK
Sbjct: 8 DPSRRDLLKGLGVGAAAGAVAAATGRVASASVDSEPSEPEKKKK 51
Score = 26.7 bits (59), Expect = 0.99
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95
G G G AA A AAA +A+ E + +++
Sbjct: 17 GLGVGAAAGAVAAATGRVASASVDSEPSEPEKKKK 51
>gnl|CDD|236999 PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase;
Validated.
Length = 633
Score = 33.1 bits (76), Expect = 0.018
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGS 98
GA PAAA PA +AAAPA A AK + + +
Sbjct: 281 EGAAPAAA-PAKQEAAAPAPAAAKAEAPAAAPAAKAE 316
Score = 31.9 bits (73), Expect = 0.038
Identities = 17/30 (56%), Positives = 18/30 (60%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKED 87
V A A AAA AAA AAAPAAA +D
Sbjct: 179 VAGEAPAAAPAAAEAAAPAAAPAAAAGVKD 208
Score = 31.5 bits (72), Expect = 0.053
Identities = 21/43 (48%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 49 VNVKELISNVGSGAGAGPAAAAPA-----AAQAAAPAAAEAKE 86
V LI S GA AA A A AA AAAPAAA AK+
Sbjct: 65 VETGALIMIFESADGAADAAPAQAEEKKEAAPAAAPAAAAAKD 107
Score = 26.1 bits (58), Expect = 4.9
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
A PA AA A AA AA+A+ + E
Sbjct: 293 EAAAPAPAAAKAEAPAAAPAAKAEGKSEFAE 323
>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed.
Length = 547
Score = 32.9 bits (76), Expect = 0.019
Identities = 17/34 (50%), Positives = 18/34 (52%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
AGA AAAAPAAA A A AAA A +
Sbjct: 77 AAGAAAAAAAPAAAAAPAAAAAAAPAPAAAAPAA 110
Score = 29.8 bits (68), Expect = 0.23
Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 28 KAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
AGV E + K + V+V L+ + A A AAAAPAAA AA AAA
Sbjct: 167 PVAGVVKE-----IKVKVGDKVSVGSLLVVIEVAAAAPAAAAAPAAAAPAAAAAAAP 218
Score = 26.3 bits (59), Expect = 3.5
Identities = 19/43 (44%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 51 VKELISNVGSGAGAG-------PAAAAPAAAQAAAPAAAEAKE 86
VKE+ VG G AAAAPAAA A A AA A
Sbjct: 172 VKEIKVKVGDKVSVGSLLVVIEVAAAAPAAAAAPAAAAPAAAA 214
Score = 25.9 bits (58), Expect = 4.9
Identities = 15/43 (34%), Positives = 18/43 (41%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
G+ A A AAA A A AAA A A A + G +
Sbjct: 79 GAAAAAAAPAAAAAPAAAAAAAPAPAAAAPAAAAAAAGGGVVE 121
Score = 25.2 bits (56), Expect = 9.7
Identities = 15/25 (60%), Positives = 15/25 (60%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKE 86
A A AA APA A AAAPAAA
Sbjct: 211 AAAAAAAPAPAPAAAAAPAAAAPAA 235
>gnl|CDD|235915 PRK07042, PRK07042, amidase; Provisional.
Length = 464
Score = 31.9 bits (73), Expect = 0.048
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 49 VNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKED 87
V +KE I+ G G AA A A AP AA +E
Sbjct: 77 VTIKENIATRGVPVPLGTAATDLPPAAADAPPAARLREA 115
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 31.4 bits (72), Expect = 0.057
Identities = 13/41 (31%), Positives = 16/41 (39%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
A A A PAAA AAA A A + +D+
Sbjct: 76 AAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDE 116
Score = 31.0 bits (71), Expect = 0.081
Identities = 12/44 (27%), Positives = 16/44 (36%)
Query: 56 SNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSD 99
+ + A AA P A AAA AAA A + +
Sbjct: 69 APAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAA 112
Score = 28.7 bits (65), Expect = 0.54
Identities = 13/33 (39%), Positives = 15/33 (45%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
A AAAA A A A AAA A ++E
Sbjct: 85 KPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEV 117
Score = 28.3 bits (64), Expect = 0.73
Identities = 19/51 (37%), Positives = 22/51 (43%)
Query: 34 VEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
V+P W FA G + + A A AAAPAA AAPA A
Sbjct: 25 VDPSWREFFADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPP 75
Score = 28.3 bits (64), Expect = 0.76
Identities = 15/31 (48%), Positives = 15/31 (48%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKEDKK 89
S A PAA APAA A PAAA K
Sbjct: 55 ASAPAAAPAAKAPAAPAPAPPAAAAPAAPPK 85
Score = 26.8 bits (60), Expect = 2.7
Identities = 13/34 (38%), Positives = 14/34 (41%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95
A A PA A PAAA AAP A +
Sbjct: 66 APAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99
Score = 26.8 bits (60), Expect = 2.8
Identities = 8/35 (22%), Positives = 9/35 (25%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
A AP AA A A A +
Sbjct: 65 KAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99
Score = 26.4 bits (59), Expect = 4.0
Identities = 15/27 (55%), Positives = 16/27 (59%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+ A A AA PAAA AAAPAAA
Sbjct: 87 AAAAAAAAAPAAPPAAAAAAAPAAAAV 113
Score = 26.0 bits (58), Expect = 5.2
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 64 AGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
A AAAA AA AA AAA + E +
Sbjct: 88 AAAAAAAAPAAPPAAAAAAAPAAAAVEDEVT 118
Score = 26.0 bits (58), Expect = 5.5
Identities = 11/33 (33%), Positives = 11/33 (33%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
A A AA A A PAAA A
Sbjct: 67 PAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAP 99
Score = 25.6 bits (57), Expect = 6.1
Identities = 12/31 (38%), Positives = 13/31 (41%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
A A A AAPA A AA A A +
Sbjct: 61 APAAKAPAAPAPAPPAAAAPAAPPKPAAAAA 91
>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase;
Provisional.
Length = 418
Score = 30.0 bits (68), Expect = 0.19
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 28 KAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKED 87
A+GV + +FA+ + V V +S + +G GA PAAA AAA A A K
Sbjct: 93 PASGVITK-----IFAEEGDTVEVGAPLSEIDTG-GAPPAAAPAAAAAAKAEKTTPEKPK 146
Query: 88 KKKKEES 94
Sbjct: 147 AAAPTPE 153
>gnl|CDD|237001 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase
subunit E2; Reviewed.
Length = 411
Score = 29.8 bits (68), Expect = 0.21
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 28 KAAGVEVEPYWPG----LFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAE 83
KA VE+ G L + + V V +I+ + A AAAA AA +A AP A
Sbjct: 43 KAT-VEIPSPVAGTVAKLLVEEGDVVPVGSVIAVIEEEGEAEAAAAAEAAPEAPAPEPAP 101
Query: 84 AKEDKKKKEESDEGSDD 100
A + +
Sbjct: 102 AAAAAAAAAPAAAAAPA 118
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 29.9 bits (68), Expect = 0.24
Identities = 27/75 (36%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 30 AGVEVEPYWPGLFAKAL-----EGVNVKELISN-VGSGAGAGPAAAAPAAAQAAAPAAAE 83
A +EVE G K L EGV V I+ + G A A AAPAAA AA AA
Sbjct: 44 ATMEVEAVDEGTLGKILVPEGTEGVKVNTPIAVLLEEGESASDAGAAPAAAAEAAAAAPA 103
Query: 84 AKEDKKKKEESDEGS 98
A K+ + +
Sbjct: 104 AAAAAAAKKAAPAPA 118
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl
carrier protein subunit; Validated.
Length = 155
Score = 29.4 bits (67), Expect = 0.26
Identities = 16/32 (50%), Positives = 17/32 (53%)
Query: 64 AGPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95
A P AAAPAAA AAA A A A + E
Sbjct: 49 AAPVAAAPAAAAAAAAAPAAAPAAAAAEAEGH 80
Score = 25.9 bits (58), Expect = 3.3
Identities = 16/33 (48%), Positives = 17/33 (51%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
A PAAAA AAA AA AA A E + S
Sbjct: 52 VAAAPAAAAAAAAAPAAAPAAAAAEAEGHVVTS 84
Score = 24.8 bits (55), Expect = 9.9
Identities = 15/30 (50%), Positives = 16/30 (53%)
Query: 55 ISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
IS + A A A AA AAAPAAA A
Sbjct: 32 ISRAAAAPVAPVAQQAAAAPVAAAPAAAAA 61
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 29.1 bits (66), Expect = 0.34
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 69 AAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
AA AAA AAA + +ED + ++ DE D+D
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDED 66
>gnl|CDD|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein].
Length = 866
Score = 29.1 bits (65), Expect = 0.40
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKED 87
+ + PAAAAPA AAAPAAA + D
Sbjct: 22 AASAPAPAAAAPAPVAAAAPAAAGPRPD 49
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 28.8 bits (65), Expect = 0.51
Identities = 14/38 (36%), Positives = 16/38 (42%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSD 99
A AA A+AAA AAA +K DE D
Sbjct: 20 KQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETMD 57
Score = 26.1 bits (58), Expect = 4.7
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 64 AGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
A +A A AAA A + + +K + + D
Sbjct: 20 KQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETMD 57
Score = 25.0 bits (55), Expect = 9.6
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 67 AAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDM 102
A AA+ A AAA A K + +S D+ M
Sbjct: 21 QAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETM 56
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 28.8 bits (65), Expect = 0.54
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+ A AAAAPAAA A A AA A
Sbjct: 393 APAAAAPSAAAAAPAAAPAPAAAAPAA 419
Score = 28.4 bits (64), Expect = 0.66
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
+ A A AA APAAA APA A A
Sbjct: 413 AAAAPAAAAAPAPAAAPQPAPAPAPAPA 440
Score = 28.4 bits (64), Expect = 0.68
Identities = 16/27 (59%), Positives = 18/27 (66%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+G GAG AAA +A AAAPAAA A
Sbjct: 385 LGVAGGAGAPAAAAPSAAAAAPAAAPA 411
Score = 28.0 bits (63), Expect = 1.1
Identities = 16/23 (69%), Positives = 16/23 (69%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEA 84
A PAAAAPAAA A APAAA
Sbjct: 408 AAPAPAAAAPAAAAAPAPAAAPQ 430
Score = 27.6 bits (62), Expect = 1.4
Identities = 15/27 (55%), Positives = 15/27 (55%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
S A A PAAA AA A A AAA A
Sbjct: 398 APSAAAAAPAAAPAPAAAAPAAAAAPA 424
Score = 26.9 bits (60), Expect = 2.1
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+G PAAAAP+AA AA AA
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPAP 412
Score = 26.9 bits (60), Expect = 2.2
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEA 84
+ A AA A A A AAA AA A
Sbjct: 396 AAAPSAAAAAPAAAPAPAAAAPAAAA 421
Score = 26.9 bits (60), Expect = 2.7
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
+ A PA AA A A AAAPA A A +
Sbjct: 403 AAAPAAAPAPAAAAPAAAAAPAPAAAPQ 430
Score = 26.9 bits (60), Expect = 2.8
Identities = 12/26 (46%), Positives = 12/26 (46%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEA 84
A AAA A A AAAP A A
Sbjct: 409 APAPAAAAPAAAAAPAPAAAPQPAPA 434
Score = 26.5 bits (59), Expect = 3.1
Identities = 16/28 (57%), Positives = 16/28 (57%)
Query: 57 NVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
V GAGA AAA AAA A A A A A
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPAPA 413
Score = 26.5 bits (59), Expect = 3.4
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEA 84
+ A A A AAA AAA A A A
Sbjct: 401 AAAAAPAAAPAPAAAAPAAAAAPAPA 426
Score = 25.7 bits (57), Expect = 6.7
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
G+ A A P+AAA A A A APAAA
Sbjct: 391 AGAPAAAAPSAAAAAPAAAPAPAAAAP 417
>gnl|CDD|184543 PRK14157, PRK14157, heat shock protein GrpE; Provisional.
Length = 227
Score = 28.4 bits (63), Expect = 0.56
Identities = 16/41 (39%), Positives = 18/41 (43%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDD 100
SG AA A A A A A AA E K E++ E D
Sbjct: 38 SGEQQDSAAQADANAGADAAPAAAEGEAKAAAEKTGEAQSD 78
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 28.5 bits (64), Expect = 0.61
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 52 KELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
+ELI++ A PAA A AA+ + KE ++ + +
Sbjct: 239 EELIADAKKAATGEPAANAAKAAKPEPMPDDQQKEAEQLQAAIAQ 283
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
Length = 155
Score = 28.1 bits (63), Expect = 0.61
Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 4/90 (4%)
Query: 15 VGSEDGEKIQTVLKAAG----VEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAA 70
VG++ E + +LK G + P G A + EL + + A GP A A
Sbjct: 62 VGAQPTEPVLALLKITGDWQKFKGLPGAEGTLKVAEPKPSKLELFNAALAEADGGPTAEA 121
Query: 71 PAAAQAAAPAAAEAKEDKKKKEESDEGSDD 100
+ A A A A E E+ +
Sbjct: 122 TTPKKKKAAAEAAAAEAAAPAAEAAAAAAA 151
Score = 28.1 bits (63), Expect = 0.73
Identities = 15/54 (27%), Positives = 22/54 (40%)
Query: 45 ALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGS 98
LE N ++ G A A AAA+AAA AA + ++E +
Sbjct: 102 KLELFNAALAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAAAAEEEA 155
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 28.4 bits (64), Expect = 0.65
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 2 GPKCAL---FLHMSYIVGSEDGEKIQTVLKAAGVEVEP 36
GP C L F M I ED E+++ +LK GVE E
Sbjct: 456 GPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPER 493
>gnl|CDD|235903 PRK06991, PRK06991, ferredoxin; Provisional.
Length = 270
Score = 28.2 bits (63), Expect = 0.78
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKK 89
A A AAAA A+ AAAPAA +A+ K+
Sbjct: 181 AAASAAAAAAEASAAAAPAADDAEAKKR 208
Score = 25.1 bits (55), Expect = 8.8
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEE 93
A A+AA AAA+A+A AA A + + KK
Sbjct: 178 AARAAASAAAAAAEASAAAAPAADDAEAKKRA 209
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of
the ribosome. The stalk base consists of a portion of
the 23S rRNA and ribosomal proteins L11 and L10. An
extended C-terminal helix of L10 provides the binding
site for L7/L12. L7/L12 consists of two domains joined
by a flexible hinge, with the helical N-terminal domain
(NTD) forming pairs of homodimers that bind to the
extended helix of L10. It is the only multimeric
ribosomal component, with either four or six copies per
ribosome that occur as two or three dimers bound to the
L10 helix. L7/L12 is the only ribosomal protein that
does not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They
are exposed to the cytoplasm and contain binding sites
for other molecules. Initiation factors, elongation
factors, and release factors are known to interact with
the L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of
L7/L12 has minimal effect on factor binding and it has
been proposed that L7/L12 induces the catalytically
active conformation of EF-Tu and EF-G, thereby
stimulating the GTPase activity of both factors. In
eukaryotes, the proteins that perform the equivalent
function to L7/L12 are called P1 and P2, which do not
share sequence similarity with L7/L12. However, a
bacterial L7/L12 homolog is found in some eukaryotes,
in mitochondria and chloroplasts. In archaea, the
protein equivalent to L7/L12 is called aL12 or L12p,
but it is closer in sequence to P1 and P2 than to
L7/L12.
Length = 127
Score = 27.5 bits (62), Expect = 0.92
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 66 PAAAAPAAAQAAAPAAAEAKEDKKKK 91
A+AA AAA AAAPAAA A + ++
Sbjct: 32 SASAAAAAAAAAAPAAAAAAAAEAEE 57
Score = 27.5 bits (62), Expect = 0.97
Identities = 17/27 (62%), Positives = 17/27 (62%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKE 86
S A A AAAAPAAA AAA A E E
Sbjct: 34 SAAAAAAAAAAPAAAAAAAAEAEEKTE 60
Score = 25.6 bits (57), Expect = 5.0
Identities = 15/27 (55%), Positives = 18/27 (66%)
Query: 64 AGPAAAAPAAAQAAAPAAAEAKEDKKK 90
+ AAAA AAA AAA AAA E+K +
Sbjct: 34 SAAAAAAAAAAPAAAAAAAAEAEEKTE 60
Score = 25.6 bits (57), Expect = 5.1
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 64 AGPAAAAPAAAQAAAPAAAEAKEDKKKK 91
A AAAA AAA AA AAA A+ ++K +
Sbjct: 33 ASAAAAAAAAAAPAAAAAAAAEAEEKTE 60
Score = 24.8 bits (55), Expect = 8.5
Identities = 17/25 (68%), Positives = 18/25 (72%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKE 86
A A AAAA AA AAA AAAEA+E
Sbjct: 33 ASAAAAAAAAAAPAAAAAAAAEAEE 57
Score = 24.8 bits (55), Expect = 9.5
Identities = 16/26 (61%), Positives = 18/26 (69%)
Query: 67 AAAAPAAAQAAAPAAAEAKEDKKKKE 92
AAAA AAA A A AAA A E ++K E
Sbjct: 35 AAAAAAAAAAPAAAAAAAAEAEEKTE 60
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 27.9 bits (62), Expect = 0.92
Identities = 20/59 (33%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 29 AAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAA-AQAAAPAAAEAKE 86
AA P + A E + S G G PA A AA A AA PAAA +
Sbjct: 413 AAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRP 471
>gnl|CDD|235082 PRK02888, PRK02888, nitrous-oxide reductase; Validated.
Length = 635
Score = 28.0 bits (63), Expect = 0.93
Identities = 18/39 (46%), Positives = 20/39 (51%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
GS G A AA AAA AAA AAA + + E DE
Sbjct: 27 AGSTGLLGGALAAGAAAAAAAAAAAAGGKYEVAPGELDE 65
Score = 27.2 bits (61), Expect = 1.6
Identities = 13/32 (40%), Positives = 14/32 (43%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKK 89
G+ G A AA AAA AAA A K
Sbjct: 24 AGAAGSTGLLGGALAAGAAAAAAAAAAAAGGK 55
Score = 25.3 bits (56), Expect = 7.2
Identities = 18/45 (40%), Positives = 20/45 (44%)
Query: 41 LFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAK 85
L AL G + + GA A AAAA AAA AAA E
Sbjct: 15 LGTAALAGAAGAAGSTGLLGGALAAGAAAAAAAAAAAAGGKYEVA 59
>gnl|CDD|182745 PRK10803, PRK10803, tol-pal system protein YbgF; Provisional.
Length = 263
Score = 27.8 bits (62), Expect = 0.93
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 55 ISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSD 99
+S+ G+ A + + AAA A A A + D +D
Sbjct: 101 LSSGGAAAQSTSGDQSGAAASATPAADAGTANAGAPVQSGDANTD 145
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 27.9 bits (63), Expect = 0.95
Identities = 13/42 (30%), Positives = 18/42 (42%)
Query: 55 ISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
I G A AA A A AA AA A ++ ++ + E
Sbjct: 55 IKEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAE 96
Score = 25.2 bits (56), Expect = 7.7
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 53 ELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSD 99
ELI+ + G G AAAA A AA A A+ ++ ++
Sbjct: 50 ELIAAIKEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAE 96
>gnl|CDD|227576 COG5251, TAF40, Transcription initiation factor TFIID, subunit
TAF11 [Transcription].
Length = 199
Score = 27.7 bits (61), Expect = 1.1
Identities = 8/46 (17%), Positives = 11/46 (23%), Gaps = 5/46 (10%)
Query: 65 GPAAAAPAAAQAAAPAAAEA-----KEDKKKKEESDEGSDDDMGFG 105
G + KE K E+D DD +
Sbjct: 24 GTSINNQLNKYPKYKYQKTRINQQEKESINKVPENDIEPDDILQQQ 69
>gnl|CDD|236712 PRK10547, PRK10547, chemotaxis protein CheA; Provisional.
Length = 670
Score = 27.8 bits (62), Expect = 1.2
Identities = 9/44 (20%), Positives = 13/44 (29%)
Query: 51 VKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
E + V + A APA +E + ES
Sbjct: 234 KAEETTEVVEVSPKISVPPVLKLAAEQAPAGRVEREKTARSSES 277
Score = 27.0 bits (60), Expect = 2.0
Identities = 9/52 (17%), Positives = 15/52 (28%)
Query: 43 AKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
A A +E V AA+ A E ++ + E +
Sbjct: 227 AVAAPQEKAEETTEVVEVSPKISVPPVLKLAAEQAPAGRVEREKTARSSEST 278
>gnl|CDD|234994 PRK01973, PRK01973, septum formation inhibitor; Reviewed.
Length = 271
Score = 27.4 bits (61), Expect = 1.4
Identities = 16/40 (40%), Positives = 18/40 (45%)
Query: 45 ALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
A E + + A A AAAAPAAA A P A A
Sbjct: 114 ADEAAAAAAEAAAPAAAAAAEAAAAAPAAAAAPEPPPAPA 153
Score = 27.0 bits (60), Expect = 2.0
Identities = 17/31 (54%), Positives = 19/31 (61%)
Query: 56 SNVGSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
+ + A PAAAA A A AAAPAAA A E
Sbjct: 117 AAAAAAEAAAPAAAAAAEAAAAAPAAAAAPE 147
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 27.5 bits (61), Expect = 1.5
Identities = 10/48 (20%), Positives = 15/48 (31%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
A A + A AP K+ KK ES+ + +
Sbjct: 1184 RAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAMET 1231
Score = 26.4 bits (58), Expect = 3.6
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 45 ALEGVNVKELISNVGSGAGAG--PAAAAPAAAQAAAPAAAEAKEDK 88
A+E + L G A AA PAAA+ PA ++ +
Sbjct: 1321 AVEVSLAERLKKKGGRKPAAANKKAAKPPAAAKKRGPATVQSGQKL 1366
>gnl|CDD|236716 PRK10564, PRK10564, maltose regulon periplasmic protein;
Provisional.
Length = 303
Score = 27.3 bits (61), Expect = 1.6
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 54 LISNVGSGAGAGPAAAAPAAAQAAAPAAAEAK 85
LI + + P AA AAPA A AK
Sbjct: 216 LIGPLFGSSAPAPVTVGNTAAPVAAPAPAPAK 247
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 27.2 bits (61), Expect = 1.7
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 72 AAAQAAAPAAAEAKEDKKKKEESDE 96
AA + A E KE+KKK+E +
Sbjct: 275 AAEEERQEEAQEKKEEKKKEEREAK 299
>gnl|CDD|204676 pfam11574, DUF3235, Protein of unknown function (DUF3235). Some
members in this family of proteins with unknown
function are annotated as RpfA however this cannot be
confirmed.
Length = 90
Score = 26.2 bits (57), Expect = 1.9
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 57 NVGSGAGAGPAAAAPAAAQAAAPAAAEAKE 86
++ + PAAAAPA + AA A E
Sbjct: 9 DLVANPKPAPAAAAPAVQEYAAQAGLNTNE 38
>gnl|CDD|219009 pfam06404, PSK, Phytosulfokine precursor protein (PSK). This
family consists of several plant specific phytosulfokine
precursor proteins. Phytosulfokines, are active as
either a pentapeptide or a C-terminally truncated
tetrapeptide. These compounds were first isolated
because of their ability to stimulate cell division in
somatic embryo cultures of Asparagus officinalis.
Length = 74
Score = 25.8 bits (57), Expect = 2.0
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 54 LISNVGSGAGAG-PAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
L+ + S A A P + AA +K D+ + EG ++
Sbjct: 4 LVCSSSSLAAAARPLPTDTGHESSKIEAAESSKVDEDEVVSECEGEGEE 52
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 27.0 bits (60), Expect = 2.1
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAA 82
+ A A PA +AAAPAAA
Sbjct: 369 AAEAAAPAEKKTPARPEAAAPAAA 392
Score = 27.0 bits (60), Expect = 2.4
Identities = 14/21 (66%), Positives = 14/21 (66%)
Query: 64 AGPAAAAPAAAQAAAPAAAEA 84
A P AAAPAAA A AAA A
Sbjct: 382 ARPEAAAPAAAPVAQAAAAPA 402
Score = 25.4 bits (56), Expect = 7.3
Identities = 13/29 (44%), Positives = 13/29 (44%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDK 88
S A PAAA PA A A AA A
Sbjct: 412 SAPAAPPAAAPPAPVAAPAAAAPAAAPAA 440
Score = 25.4 bits (56), Expect = 7.6
Identities = 16/28 (57%), Positives = 16/28 (57%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKED 87
A PAAAAPAAA AAAPAA
Sbjct: 423 PAPVAAPAAAAPAAAPAAAPAAVALAPA 450
Score = 25.4 bits (56), Expect = 7.9
Identities = 13/23 (56%), Positives = 13/23 (56%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEA 84
A AAAP A AAAPA A A
Sbjct: 384 PEAAAPAAAPVAQAAAAPAPAAA 406
Score = 25.4 bits (56), Expect = 8.2
Identities = 12/23 (52%), Positives = 12/23 (52%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEA 84
A PAAA AAA A A A A
Sbjct: 399 AAPAPAAAPAAAASAPAAPPAAA 421
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 26.8 bits (60), Expect = 2.3
Identities = 15/34 (44%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 51 VKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
V N A PAAA PAA+ AAPAA
Sbjct: 285 VALSAQNEPVSALEAPAAA-PAASVPAAPAAEPR 317
>gnl|CDD|236786 PRK10882, PRK10882, hydrogenase 2 protein HybA; Provisional.
Length = 328
Score = 26.6 bits (59), Expect = 2.5
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPA 80
+ AGA A A P+ + AAA
Sbjct: 9 AASAGALLAGALPSVSHAAAEN 30
Score = 26.6 bits (59), Expect = 3.1
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 63 GAGPAAAAPAAAQAAAPAAAEAKE 86
A A A + + AAAE +
Sbjct: 9 AASAGALLAGALPSVSHAAAENRP 32
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 26.8 bits (59), Expect = 2.6
Identities = 11/46 (23%), Positives = 15/46 (32%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGL 106
G AA A +AAA A K ++ + GL
Sbjct: 871 FGGTVAVKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGL 916
Score = 25.7 bits (56), Expect = 6.4
Identities = 13/56 (23%), Positives = 15/56 (26%)
Query: 42 FAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEG 97
A + + A AAA A A A K KKK G
Sbjct: 860 AAAKAGAASAAFGGTVAVKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAG 915
Score = 25.7 bits (56), Expect = 7.5
Identities = 12/40 (30%), Positives = 17/40 (42%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGS 98
+ A PA A A AA AAA+ KK+ + +
Sbjct: 875 VAVKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAA 914
>gnl|CDD|181651 PRK09105, PRK09105, putative aminotransferase; Provisional.
Length = 370
Score = 26.5 bits (59), Expect = 2.7
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAA 82
+ A G AAA AAA+ AA A
Sbjct: 18 AAAAALGLLAAAAAAAKRAAAPPA 41
>gnl|CDD|177677 PLN00045, PLN00045, photosystem I reaction center subunit IV;
Provisional.
Length = 101
Score = 26.1 bits (57), Expect = 2.9
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 65 GPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGS 98
+++A + A AAAPAAA A + K GS
Sbjct: 11 ATSSSAASPAAAAAPAAAPAAKPKPPPIGPKRGS 44
>gnl|CDD|218932 pfam06191, DUF995, Protein of unknown function (DUF995). Family
of uncharacterized Proteobacteria proteins.
Length = 146
Score = 26.2 bits (58), Expect = 3.2
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEA 84
A A AAA+ AAA APA A
Sbjct: 6 AAALAAAASVAAAAVPAPANARP 28
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 26.4 bits (58), Expect = 3.2
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
G G G G +AP ++A + +E+ + ++ D + D
Sbjct: 229 GEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESD 271
>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 26.0 bits (58), Expect = 3.2
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 52 KELISNVGSGAG-AGPAAAAPAAAQAAAPAAAEAKEDK 88
+I G G G + P AAQ AA AA+ ++
Sbjct: 40 NVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEH 77
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 26.5 bits (58), Expect = 3.3
Identities = 11/48 (22%), Positives = 17/48 (35%)
Query: 47 EGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEES 94
+ V V +++ +G AG A A AAP E+
Sbjct: 65 DTVEVGGVLAIIGEPGEAGSEPAPAAPEPEAAPEPEAPAPAPTPAAEA 112
>gnl|CDD|233366 TIGR01348, PDHac_trf_long, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model describes a subset of pyruvate dehydrogenase
complex dihydrolipoamide acetyltransferase specifically
close by both phylogenetic and per cent identity (UPGMA)
trees. Members of this set include two or three copies
of the lipoyl-binding domain. E. coli AceF is a member
of this model, while mitochondrial and some other
bacterial forms belong to a separate model [Energy
metabolism, Pyruvate dehydrogenase].
Length = 546
Score = 26.4 bits (58), Expect = 3.5
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 49 VNVKELISNVGSGAGAGPAAAAPAAAQAAAPA-AAEAKE 86
V +LI + A APA+AQ AA + AA E
Sbjct: 180 VPTGDLILTLSVAGSTPATAPAPASAQPAAQSPAATQPE 218
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 26.4 bits (59), Expect = 3.6
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAK 85
G G G A A A AAAP AA A
Sbjct: 397 GGGGPPGGGGAPGAPAAAAAPGAAAAA 423
Score = 26.0 bits (58), Expect = 4.9
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 51 VKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
++E + G G G P A AAA A A
Sbjct: 387 LQEGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAA 420
>gnl|CDD|221459 pfam12200, DUF3597, Domain of unknown function (DUF3597). This
family of proteins is found in bacteria, eukaryotes and
viruses. Proteins in this family are typically between
126 and 281 amino acids in length. The function of this
domain is unknown. The structure of this domain has
been found to contain five helices with a long flexible
loop between helices one and two.
Length = 124
Score = 25.8 bits (57), Expect = 3.6
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+ A A AAA AAA AA P AA +
Sbjct: 19 APAAAPATAPAAAAAAAPAATPPAAAS 45
>gnl|CDD|218126 pfam04520, Senescence_reg, Senescence regulator. This protein
regulates the expression of proteins associated with
leaf senescence in plants.
Length = 146
Score = 25.8 bits (57), Expect = 3.6
Identities = 8/46 (17%), Positives = 15/46 (32%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMG 103
GA A++AP + + + + D+ D D
Sbjct: 54 RAGAGGAKAASSAPVNVPDWSKILRGRRRRSIEDSDDDDEEDGDGA 99
>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional.
Length = 331
Score = 26.1 bits (58), Expect = 3.7
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 56 SNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+NV + A PAA A A P
Sbjct: 215 ANVDTAATPAPAAPATPDGAAPLPTDQAG 243
>gnl|CDD|226198 COG3672, COG3672, Predicted transglutaminase-like cysteine
proteinase [General function prediction only].
Length = 191
Score = 26.2 bits (58), Expect = 3.9
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 64 AGPAAAAPAAAQAAAPAAAEA 84
+ AAAA A A AAAPA+A
Sbjct: 9 SLAAAAAGALAAAAAPASAAP 29
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 26.2 bits (58), Expect = 3.9
Identities = 14/35 (40%), Positives = 14/35 (40%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
V A A PAAA PA A A AAA
Sbjct: 408 VPPAAPARPAAARPAPAPAPPAAAAPPARSADPAA 442
>gnl|CDD|235745 PRK06214, PRK06214, sulfite reductase; Provisional.
Length = 530
Score = 26.2 bits (58), Expect = 4.0
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 51 VKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEA 84
+K+L G+ A AAA A A AA A
Sbjct: 128 LKKLAEEFGAAPAAAAPAAAAADAAPAAAALGPL 161
Score = 25.8 bits (57), Expect = 6.2
Identities = 16/24 (66%), Positives = 16/24 (66%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAK 85
GA PAAAAPAAA A A AA A
Sbjct: 135 FGAAPAAAAPAAAAADAAPAAAAL 158
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 26.2 bits (58), Expect = 4.0
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 66 PAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108
AA A A+ A A E KE K K+E+ ++G + D
Sbjct: 50 AKVAAKAKAKKALKAKIEEKE-KAKREKEEKGLRELEEDTPED 91
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 26.4 bits (58), Expect = 4.2
Identities = 14/19 (73%), Positives = 15/19 (78%)
Query: 67 AAAAPAAAQAAAPAAAEAK 85
A AA AAA+AAA A AEAK
Sbjct: 1439 AEAARAAAEAAAQAYAEAK 1457
Score = 25.2 bits (55), Expect = 9.3
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 67 AAAAPAAAQAAAPAAAEA 84
A AA AA+AAA AAA+A
Sbjct: 1435 AFAAAEAARAAAEAAAQA 1452
>gnl|CDD|236733 PRK10672, PRK10672, rare lipoprotein A; Provisional.
Length = 361
Score = 26.2 bits (58), Expect = 4.3
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 63 GAGPAAAAPAAAQAAAPAAA 82
G+ P AP++A A APAAA
Sbjct: 256 GSEPTPTAPSSAPATAPAAA 275
Score = 25.4 bits (56), Expect = 6.4
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEA 84
GS ++APA A AAA A A
Sbjct: 256 GSEPTPTAPSSAPATAPAAAAPQAAA 281
>gnl|CDD|150843 pfam10232, Med8, Mediator of RNA polymerase II transcription
complex subunit 8. Arc32, or Med8, is one of the
subunits of the Mediator complex of RNA polymerase II.
The region conserved contains two alpha helices
putatively necessary for binding to other subunits
within the core of the Mediator complex. The N-terminus
of Med8 binds to the essential core Head part of
Mediator and the C-terminus hinges to Med18 on the
non-essential part of the Head that also includes Med20.
Length = 226
Score = 26.0 bits (57), Expect = 4.4
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 45 ALEGVNVKELISNVGSGAGAGPA--AAAPAAAQAAAPAAAEAK 85
E + +L++ V G G PA A+P + + A K
Sbjct: 165 TSEEEDTNQLVAAVKDGKGLRPAIRQASPMGGKQMSQAGQPGK 207
>gnl|CDD|235867 PRK06819, PRK06819, flagellin; Validated.
Length = 376
Score = 25.9 bits (57), Expect = 4.6
Identities = 16/102 (15%), Positives = 29/102 (28%), Gaps = 8/102 (7%)
Query: 11 MSYIVGSEDGEKIQTVLKA--------AGVEVEPYWPGLFAKALEGVNVKELISNVGSGA 62
MS VG+ DGE I L+ V L + + ++ V +
Sbjct: 144 MSIQVGANDGETIDINLQKIDSKSLGLGSFSVSGVSGALTSLTFTDTALDTSVTGVTTTT 203
Query: 63 GAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGF 104
+ + A A + D + + D +
Sbjct: 204 ALDFSDISTFAKGATVHGIGDVGTDGAYADGYVIRTTDGKQY 245
>gnl|CDD|237381 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
Length = 342
Score = 25.9 bits (57), Expect = 4.8
Identities = 12/26 (46%), Positives = 12/26 (46%)
Query: 61 GAGAGPAAAAPAAAQAAAPAAAEAKE 86
A A PA AA A A A AE E
Sbjct: 38 AAAAAPAGEHGAAVHAEAAAHAEQAE 63
Score = 25.5 bits (56), Expect = 7.4
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDKKK 90
+ A AG AA A AA AE ++K
Sbjct: 40 AAAPAGEHGAAVHAEAAAHAEQAEGGHEEKA 70
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 25.9 bits (57), Expect = 4.9
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95
A A A A A A+ AA AA +A + KKK E++
Sbjct: 141 AAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAE 174
>gnl|CDD|178458 PLN02867, PLN02867, Probable galacturonosyltransferase.
Length = 535
Score = 26.0 bits (57), Expect = 5.0
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 55 ISNVGSGAGAGPAAAAPAAAQA 76
ISN GSG G+G AAA AAA A
Sbjct: 15 ISNPGSGKGSGGCAAAAAAAAA 36
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 26.0 bits (57), Expect = 5.1
Identities = 9/26 (34%), Positives = 9/26 (34%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEA 84
G G G A A A AA A
Sbjct: 365 GGAPGGGVPARVAGAVPAPGARAAAA 390
Score = 25.6 bits (56), Expect = 7.3
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 64 AGPAAAAPAAAQAAAPAAA 82
AAA PAAA AAAP A
Sbjct: 570 RAAAAAKPAAAPAAAPKPA 588
>gnl|CDD|227647 COG5342, COG5342, Invasion protein B, involved in pathogenesis
[General function prediction only].
Length = 181
Score = 25.5 bits (56), Expect = 5.1
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAA 82
+ A A A A +A Q A PA
Sbjct: 16 ALTLAFAALPAPAASAQQQAQPAGT 40
>gnl|CDD|236507 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
Length = 509
Score = 25.6 bits (57), Expect = 5.8
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 66 PAAAAPAAAQAAAPAAAEAKEDKKKK 91
AA A AAA AA + +K
Sbjct: 376 SAAPAAAAAAPAAKEEEKKPASPWRK 401
Score = 25.6 bits (57), Expect = 7.3
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 66 PAAAAPAAAQAAAPAAAEAKEDKKKK 91
P AA AAA A A +E+KK
Sbjct: 371 PPIQVSAAPAAAAAAPAAKEEEKKPA 396
>gnl|CDD|237002 PRK11857, PRK11857, dihydrolipoamide acetyltransferase; Reviewed.
Length = 306
Score = 25.5 bits (56), Expect = 5.8
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 50 NVKELISNVGSGAGAGPAAAAPAAAQAAA---PAAAEAKEDKKKK 91
+V+ I ++ S AA+ +A QAA PAAA K + K++
Sbjct: 35 DVENFIKSLKSAPTPAEAASVSSAQQAAKTAAPAAAPPKLEGKRE 79
>gnl|CDD|219207 pfam06864, PAP_PilO, Pilin accessory protein (PilO). This family
consists of several enterobacterial PilO proteins. The
function of PilO is unknown although it has been
suggested that it is a cytoplasmic protein in the
absence of other Pil proteins, but PilO protein is
translocated to the outer membrane in the presence of
other Pil proteins. Alternatively, PilO protein may form
a complex with other Pil protein(s). PilO has been
predicted to function as a component of the pilin
transport apparatus and thin-pilus basal body. This
family does not seem to be related to pfam04350.
Length = 414
Score = 25.9 bits (57), Expect = 5.8
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 66 PAAAAPAAAQAAAPAAAEAKE 86
AAAAPAAAQ AA + +
Sbjct: 192 EAAAAPAAAQLAARERLQFQA 212
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 25.5 bits (56), Expect = 6.0
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
A A AA AA A A EA ++ EES E
Sbjct: 152 AAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEESAE 186
>gnl|CDD|203911 pfam08328, ASL_C, Adenylosuccinate lyase C-terminal. This domain
is found at the C-terminus of adenylosuccinate
lyase(ASL; PurB in E. coli). It has been identified in
bacteria, eukaryotes and archaea and is found together
with the lyase domain pfam00206. ASL catalyzes the
cleavage of succinylaminoimidazole carboxamide ribotide
to aminoimidazole carboxamide ribotide and fumarate and
the cleavage of adenylosuccinate to adenylate and
fumarate.
Length = 115
Score = 25.1 bits (56), Expect = 6.1
Identities = 8/18 (44%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 20 GEKIQTVLKAAGVEVEPY 37
E IQTV++ G+ PY
Sbjct: 56 AEPIQTVMRRYGIP-NPY 72
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 25.7 bits (56), Expect = 6.1
Identities = 12/49 (24%), Positives = 19/49 (38%)
Query: 56 SNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGF 104
S GS A A A A A A+ + ++ +G++D F
Sbjct: 208 SRWGSAAAAAAPVPATNVADQAPYGEDSARPGNPPEGQAIKGNEDSEKF 256
>gnl|CDD|213312 cd05959, BCL_4HBCL, Benzoate CoA ligase (BCL) and
4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase).
Benzoate CoA ligase and 4-hydroxybenzoate-coenzyme A
ligase catalyze the first activating step for benzoate
and 4-hydroxybenzoate catabolic pathways, respectively.
Although these two enzymes share very high sequence
homology, they have their own substrate preference. The
reaction proceeds via a two-step process; the first
ATP-dependent step forms the substrate-AMP intermediate,
while the second step forms the acyl-CoA ester,
releasing the AMP. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Some bacteria can use benzoic acid
or benzenoid compounds as the sole source of carbon and
energy through degradation. Benzoate CoA ligase and
4-hydroxybenzoate-Coenzyme A ligase are key enzymes of
this process.
Length = 506
Score = 25.7 bits (57), Expect = 6.2
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 29 AAGVEVEPYWPGLFAKALEGV-NVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKED 87
A + + + AL+ +++ +I G+G GA A A A AAA + +D
Sbjct: 103 ARVLVISEELWEVLKPALQKDPHLRHVIVVGGAGPGALSYAQLIATAAEELEAAATSADD 162
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 25.7 bits (57), Expect = 6.2
Identities = 14/29 (48%), Positives = 14/29 (48%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKK 90
A A A A AAQ A A E ED KK
Sbjct: 649 AAAIARAKARKAAQQQANAEPEEAEDPKK 677
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 25.8 bits (57), Expect = 6.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 66 PAAAAPAAAQAAAPAAAEAK 85
PAA AAA AA A A+
Sbjct: 546 PAAPVVAAAPKAAAATPPAQ 565
>gnl|CDD|237034 PRK12278, PRK12278, 50S ribosomal protein L21/unknown domain fusion
protein; Provisional.
Length = 221
Score = 25.6 bits (56), Expect = 6.5
Identities = 15/30 (50%), Positives = 15/30 (50%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKK 91
A P AA AA AA PAAA A D K
Sbjct: 133 KEAAPKAAPAPAAAAAPPAAAAAGADDLTK 162
>gnl|CDD|213408 cd09758, Csn2, CRISPR/Cas system-associated protein Csn2. Csn2 is
a Nmeni subtype-specific Cas protein, which may function
in the adaptation process which mediates the
incorporation of foreign nucleic acids into the
microbial host genome. Csn 2 may interact directly with
double-stranded DNA. CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats) and associated
Cas proteins comprise a system for heritable host
defense by prokaryotic cells against phage and other
foreign DNA. Csn2 has been predicted to be a functional
analog of Cas4 based on anti-correlated phyletic
patterns; also known as SPy1049 family.
Length = 218
Score = 25.4 bits (56), Expect = 6.7
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 18 EDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNV------KELISNVGSGA 62
D IQ + KA G+++E +F K E + V K+L+ V GA
Sbjct: 121 YDEITIQELFKALGIKIETKSDTIFEKVFEILQVFKYLSKKKLLVFVNVGA 171
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 25.6 bits (57), Expect = 6.7
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
G GA A AAA A AAA A +
Sbjct: 296 AGGGAAAAGGAAAAARGGAAAAGGASS 322
Score = 25.6 bits (57), Expect = 7.0
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
V + AGAG AA AAA A AAA
Sbjct: 286 VAAAAGAGLAAGGGAAAAGGAAAAARG 312
Score = 25.3 bits (56), Expect = 7.9
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 59 GSGAGAGPAAAAPAAAQAAAPAAAEAK 85
+G GA A A AAA+ A AA A
Sbjct: 295 AAGGGAAAAGGAAAAARGGAAAAGGAS 321
Score = 25.3 bits (56), Expect = 8.0
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEA 84
VG+G AG AA A AA A A
Sbjct: 275 VGTGLAAGGAAVAAAAGAGLAAGGGAA 301
>gnl|CDD|220823 pfam10605, 3HBOH, 3HB-oligomer hydrolase (3HBOH).
D-(-)-3-hydroxybutyrate oligomer hydrolase (also known
as 3HB-oligomer hydrolase) functions in the degradation
of poly-3-hydroxybutyrate (PHB). It catalyzes the
hydrolysis of D(-)-3-hydroxybutyrate oligomers
(3HB-oligomers) into 3HB-monomers.
Length = 689
Score = 25.4 bits (56), Expect = 6.8
Identities = 13/26 (50%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 62 AGAGP----AAAAPAAAQAAAPAAAE 83
AG G +A APA A A P AAE
Sbjct: 42 AGLGKTGLASATAPAFANPANPTAAE 67
>gnl|CDD|211358 cd08352, Glo_EDI_BRP_like_1, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The proteins of this family share three
conserved metal binding amino acids with the type I
extradiol dioxygenases, which shows no domain swapping.
Length = 125
Score = 25.0 bits (55), Expect = 6.8
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 10 HMSYIVGSEDGEKIQTVLKAAGVEVEP 36
H+++ V ED E LKA GVEVEP
Sbjct: 75 HLAFAV--EDIEAAVAELKAHGVEVEP 99
>gnl|CDD|180753 PRK06924, PRK06924, short chain dehydrogenase; Provisional.
Length = 251
Score = 25.4 bits (56), Expect = 6.8
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 41 LFAKALEGVNVKELISNVGSGAGAGP 66
F K + V + + N+ SGA P
Sbjct: 122 TFMKHTKDWKVDKRVINISSGAAKNP 147
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 25.7 bits (56), Expect = 6.8
Identities = 10/42 (23%), Positives = 14/42 (33%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDD 101
A A PAA + A E + +K D D+
Sbjct: 390 DAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDE 431
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 25.6 bits (56), Expect = 7.0
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEA 84
GA A AA PA A+ AA A+
Sbjct: 370 PGASADAAARTPARARDAAAPDADT 394
>gnl|CDD|132411 TIGR03368, cellulose_yhjU, cellulose synthase operon protein YhjU.
This protein was identified by the partial phylogenetic
profiling algorithm (PMID:16930487) as part of the
system for cellulose biosynthesis in bacteria, and in
fact is found in cellulose biosynthesis gene regions.
The protein was designated YhjU in Salmonella
enteritidis, where disruption of its gene disrupts
cellulose biosynthesis and biofilm formation
(PMID:11929533) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 518
Score = 25.4 bits (56), Expect = 7.1
Identities = 17/91 (18%), Positives = 24/91 (26%), Gaps = 21/91 (23%)
Query: 25 TVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAE- 83
T A + W L + A A A + AA A P A
Sbjct: 118 TTFVVAALIALSLWQALSPTL------------AVTVANAQAQAQSAGAAATAPPTDANL 165
Query: 84 --------AKEDKKKKEESDEGSDDDMGFGL 106
A+E ++ +D F L
Sbjct: 166 NAALNAFFAQEAQRVVTFPALLADPAQQFDL 196
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 25.7 bits (56), Expect = 7.3
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 53 ELISNVGSGAGAGPAAAAPAAAQAAAPAAA 82
E++S + S AA A A A A A+A
Sbjct: 1374 EIVSYMQSKVPVASAAVAAIAPNATANASA 1403
>gnl|CDD|225599 COG3057, SeqA, Negative regulator of replication initiationR [DNA
replication, recombination, and repair].
Length = 181
Score = 25.2 bits (55), Expect = 7.3
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKE 92
A + AA A + A PA EAK K K+
Sbjct: 37 AASQTAAPATKEPRVAVPAKVEAKPTKTIKD 67
>gnl|CDD|236573 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 25.4 bits (56), Expect = 7.6
Identities = 17/61 (27%), Positives = 22/61 (36%), Gaps = 13/61 (21%)
Query: 46 LEGVNVKELISNVGSGAGAGPAAAAPAAAQA---AAPAAAE----------AKEDKKKKE 92
LEG + GA G AAPAA A A+ ++K K+E
Sbjct: 15 LEGFAAGADAARATRGAAGGQTPAAPAAEPTGPDAIHIKAQDRFLAAGKKLCDQEKWKRE 74
Query: 93 E 93
E
Sbjct: 75 E 75
>gnl|CDD|177447 PHA02664, PHA02664, hypothetical protein; Provisional.
Length = 534
Score = 25.3 bits (55), Expect = 7.7
Identities = 17/44 (38%), Positives = 22/44 (50%)
Query: 60 SGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMG 103
+GA P AA AAA AAA A D+ + E+ + D D G
Sbjct: 399 NGARGSPMAAPEEGRAAAAAAAANAPADQDVEAEAHDEFDQDPG 442
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 25.3 bits (56), Expect = 8.0
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEE 93
AAAA + A AAA + K + E
Sbjct: 130 RRLARAAAAAPRPRVPADAAAAVADAVKARIE 161
>gnl|CDD|235826 PRK06549, PRK06549, acetyl-CoA carboxylase biotin carboxyl
carrier protein subunit; Validated.
Length = 130
Score = 24.8 bits (54), Expect = 8.0
Identities = 7/22 (31%), Positives = 9/22 (40%)
Query: 65 GPAAAAPAAAQAAAPAAAEAKE 86
PA AA A A+ P +
Sbjct: 23 APAQAAAPAQPASTPVPVPTEA 44
>gnl|CDD|240577 cd12950, RRP7_Rrp7p, RRP7 domain ribosomal RNA-processing protein
7 (Rrp7p) and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C
gene from Saccharomyces cerevisiae. It is an essential
yeast protein involved in pre-rRNA processing and
ribosome assembly. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 128
Score = 24.9 bits (55), Expect = 8.1
Identities = 15/38 (39%), Positives = 17/38 (44%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95
V G GPAA A A + K+ KKKKE D
Sbjct: 56 VVRGGRKGPAAGEEAGKAAEEEKKEKEKKKKKKKELED 93
>gnl|CDD|187777 cd09646, Cas7_I-E, CRISPR/Cas system-associated RAMP superfamily
protein Cas7. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas7 is a RAMP superfamily protein; Subunit of the
Cascade complex; also known as Cse4/CasC family.
Length = 325
Score = 25.2 bits (55), Expect = 8.1
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 62 AGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMG 103
A A A AAA A A+ + DK KE+ G
Sbjct: 118 ARYAAELADEFDAAAAADAVADKELDKNFKEDLAAARLPQGG 159
>gnl|CDD|227159 COG4822, CbiK, Cobalamin biosynthesis protein CbiK, Co2+ chelatase
[Coenzyme metabolism].
Length = 265
Score = 25.1 bits (55), Expect = 8.3
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 17 SEDGEKIQTVLKAAGVEVEPYWPGL 41
S+D + + +L+ G +VE Y GL
Sbjct: 215 SDDEDSWKNILEKNGFKVEVYLHGL 239
>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
Length = 400
Score = 25.1 bits (55), Expect = 8.4
Identities = 14/43 (32%), Positives = 17/43 (39%)
Query: 58 VGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDD 100
V A A PA A A AAA A + + G+DD
Sbjct: 282 VSGTAAAEPAPKEAAKAAAAAAKPALEDKPRPLGIARPGGADD 324
>gnl|CDD|223351 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide
transport and metabolism].
Length = 228
Score = 24.9 bits (55), Expect = 8.9
Identities = 17/53 (32%), Positives = 24/53 (45%)
Query: 30 AGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAA 82
A V V P + L +AL+G V + + +G GA A A A+ A A
Sbjct: 39 AAVCVNPSYVPLAKEALKGSTVVRVCTVIGFPLGANTTAVKAAEAREAIENGA 91
>gnl|CDD|130065 TIGR00992, 3a0901s03IAP75, chloroplast envelope protein
translocase, IAP75 family. Two families of proteins are
involved in the chloroplast envelope import
appartus.They are the three proteins of the outer
membrane (TOC) and four proteins in the inner membrane
(TIC). This family is specific for the TOC IAP75 protein
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 718
Score = 25.3 bits (55), Expect = 9.1
Identities = 16/53 (30%), Positives = 20/53 (37%)
Query: 48 GVNVKELISNVGSGAGAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDD 100
G V +L G G G A AQ A+P AA A E+ +S
Sbjct: 4 GGGVGDLPPMGGGGGGELAGAHGNFWAQVASPVAAVADENLSADWDSHNLPAH 56
>gnl|CDD|131830 TIGR02783, TrbL_P, P-type conjugative transfer protein TrbL. The
TrbL protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbL
is a homolog of the F-type TraG protein (which is
believed to be a mating pair stabilization pore-forming
protein, pfam07916) as well as the vir system VirB6
protein [Cellular processes, Conjugation].
Length = 298
Score = 25.1 bits (55), Expect = 9.5
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 51 VKELISNVGSGA---GAGPAAAAPAAAQAAAPAAAEAK 85
+ + +++ SGA GAG A AA AA A A A
Sbjct: 246 IPPIAASLVSGASVMGAGGAVAAAAAVAGVAAAGGAAL 283
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 25.0 bits (54), Expect = 9.5
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 63 GAGPAAAAPAAAQAAAPAAAEAKEDKKKKEESDE 96
+ A AAA A E KKKK+E +
Sbjct: 438 EDQTSEDGKMLAIMGEAAAALALEPKKKKKEKEG 471
>gnl|CDD|204755 pfam11823, DUF3343, Protein of unknown function (DUF3343). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and archaea. Proteins
in this family are typically between 78 to 102 amino
acids in length.
Length = 73
Score = 24.1 bits (53), Expect = 9.7
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 17 SEDGEKIQTVLKAAGVEVEPYWP 39
ED E I+ +L+ G+E E +
Sbjct: 49 EEDLEAIKKILEENGIEPEGIYE 71
>gnl|CDD|235330 PRK05015, PRK05015, aminopeptidase B; Provisional.
Length = 424
Score = 24.8 bits (55), Expect = 9.8
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 17 SEDGEKIQTVLKAAGVEVEPYWP---GLFAKALEGVNVKELISNVGSGAGAGPAAAAPA 72
S D E Q +L +A E EP+W F ++ N +L +N GSGAG A+ A
Sbjct: 318 SFDDELAQRLLASAAQENEPFWRLPLAEFHRSQLPSNFADL-ANSGSGAGPAGASTAAG 375
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 0.129 0.368
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,532,764
Number of extensions: 490191
Number of successful extensions: 3843
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2853
Number of HSP's successfully gapped: 660
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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: 53 (24.1 bits)