254780470

254780470

translation initiation factor IF-1

GeneID in NCBI database:8209459Locus tag:CLIBASIA_01775
Protein GI in NCBI database:254780470Protein Accession:YP_003064883.1
Gene range:-(392922, 393254)Protein Length:110aa
Gene description:translation initiation factor IF-1
COG prediction:[J] Translation initiation factor 1 (IF-1)
KEGG prediction:infA; translation initiation factor IF-1; K02518 translation initiation factor IF-1
SEED prediction:Translation initiation factor 1
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Translation initiation factors bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110
MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
cccccEEEEccEEEEEccccEEEEEEEcccccccccccccccccccccccccccccccccEEEcccccEEEEEEccEEEEEEEEEEcccEEEEEEccccccccEEEEEEc
cccccEEEEccEEEEccccccEEEEEcccccccccccEEEEEEEcccccccccccccccEHEEcccccEEEEEEccHHHccEEEEccccEEEEEEccccccccEEEEEcc
MPKEETLEFSGIVSELLPNANFRVKLitndddssadckldskvksnfsesgsesgndgvdpisylDNAVVIAYTAGRMRKHRIRISLGdkvkvamnpydmtrarityrfk
mpkeetlefsgIVSELLPNANFRVKLItndddssadcKLDSKVKSnfsesgsesgndgvdpisYLDNAVVIAYTagrmrkhririslgdkvkvamnpydmtrarityrfk
MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKsnfsesgsesgnDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
****ETLEFSGIVSELLPNANFRVKLITNDDDSSAD***************SESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR**
********FSGIVSELLPNANFRVKLITNDDDSSADCKLDSK**************DGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
***EETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
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MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK
MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target110 translation initiation factor IF-1 [Candidatus Liberiba
315122074119 translation initiation factor IF-1 [Candidatus Liberiba 1 8e-27
327191623114 translation initiation factor IF-1 [Rhizobium etli CNPA 1 2e-17
8635623672 translation initiation factor IF-1 [Rhizobium etli CFN 1 2e-17
11063254972 translation initiation factor IF-1 [Mesorhizobium sp. B 1 3e-17
22208723572 translation initiation factor IF-1 [Agrobacterium radio 1 4e-17
1347539772 translation initiation factor IF-1 [Mesorhizobium loti 1 6e-17
22782080987 translation initiation factor IF-1 [Sinorhizobium fredi 1 8e-17
31211307072 translation initiation factor IF-1 [Rhodomicrobium vann 1 1e-16
4947463072 translation initiation factor IF-1 [Bartonella quintana 1 1e-16
11859315372 translation initiation factor IF-1 [Stappia aggregata I 1 2e-16
>gi|315122074|ref|YP_004062563.1| translation initiation factor IF-1 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 119 Back     alignment and organism information
 Score =  123 bits (309), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 69/120 (57%), Positives = 85/120 (70%), Gaps = 11/120 (9%)

Query: 1   MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSN----------FSES 50
           M KEE LEFS +VSELLPNANFRV+LI  +D+SS  CK DS   S+             S
Sbjct: 1   MAKEEILEFSAVVSELLPNANFRVQLIALEDNSSY-CKSDSDSDSDSDSDSDSDSDLKSS 59

Query: 51  GSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
           GS+  +  +D IS +  + VIAYT+GRMRKHRIRIS+GD+VK+ ++P DMTRARITYRFK
Sbjct: 60  GSKLNSKDIDFISLIGKSKVIAYTSGRMRKHRIRISVGDRVKLEISPCDMTRARITYRFK 119


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|327191623|gb|EGE58635.1| translation initiation factor IF-1 [Rhizobium etli CNPAF512] Length = 114 Back     alignment and organism information
>gi|86356236|ref|YP_468128.1| translation initiation factor IF-1 [Rhizobium etli CFN 42] Length = 72 Back     alignment and organism information
>gi|110632549|ref|YP_672757.1| translation initiation factor IF-1 [Mesorhizobium sp. BNC1] Length = 72 Back     alignment and organism information
>gi|222087235|ref|YP_002545770.1| translation initiation factor IF-1 [Agrobacterium radiobacter K84] Length = 72 Back     alignment and organism information
>gi|13475397|ref|NP_106961.1| translation initiation factor IF-1 [Mesorhizobium loti MAFF303099] Length = 72 Back     alignment and organism information
>gi|227820809|ref|YP_002824779.1| translation initiation factor IF-1 [Sinorhizobium fredii NGR234] Length = 87 Back     alignment and organism information
>gi|312113070|ref|YP_004010666.1| translation initiation factor IF-1 [Rhodomicrobium vannielii ATCC 17100] Length = 72 Back     alignment and organism information
>gi|49474630|ref|YP_032672.1| translation initiation factor IF-1 [Bartonella quintana str. Toulouse] Length = 72 Back     alignment and organism information
>gi|118593153|ref|ZP_01550539.1| translation initiation factor IF-1 [Stappia aggregata IAM 12614] Length = 72 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target110 translation initiation factor IF-1 [Candidatus Liberiba
PRK0027672 PRK00276, infA, translation initiation factor IF-1; Val 3e-24
PRK1244287 PRK12442, PRK12442, translation initiation factor IF-1; 3e-17
TIGR0000868 TIGR00008, infA, translation initiation factor IF-1 8e-15
CHL0001078 CHL00010, infA, translation initiation factor 1 2e-14
COG036175 COG0361, InfA, Translation initiation factor 1 (IF-1) [ 2e-14
pfam0117665 pfam01176, eIF-1a, Translation initiation factor 1A / I 4e-09
cd0445164 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor 1e-14
>gnl|CDD|178954 PRK00276, infA, translation initiation factor IF-1; Validated Back     alignment and domain information
>gnl|CDD|183529 PRK12442, PRK12442, translation initiation factor IF-1; Reviewed Back     alignment and domain information
>gnl|CDD|129120 TIGR00008, infA, translation initiation factor IF-1 Back     alignment and domain information
>gnl|CDD|176953 CHL00010, infA, translation initiation factor 1 Back     alignment and domain information
>gnl|CDD|30710 COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|110196 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1 Back     alignment and domain information
>gnl|CDD|88417 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 110 translation initiation factor IF-1 [Candidatus Liberiba
PRK1244287 translation initiation factor IF-1; Reviewed 100.0
CHL0001078 infA translation initiation factor 1 100.0
PRK0027672 infA translation initiation factor IF-1; Validated 100.0
TIGR0000869 infA translation initiation factor IF-1; InterPro: IPR0 99.97
cd0445164 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-li 99.97
COG036175 InfA Translation initiation factor 1 (IF-1) [Translatio 99.94
pfam0117665 eIF-1a Translation initiation factor 1A / IF-1. This fa 99.72
cd0579377 S1_IF1A S1_IF1A: Translation initiation factor IF1A, al 98.73
smart0065283 eIF1a eukaryotic translation initiation factor 1A. 98.62
PRK0401299 translation initiation factor IF-1A; Provisional 98.33
PTZ00329155 translation initiation factor eIF-1A; Provisional 97.9
cd0445678 S1_IF1A_like S1_IF1A_like: Translation initiation facto 97.5
PRK00098 298 ribosome-associated GTPase; Reviewed 96.72
PRK12289 351 ribosome-associated GTPase; Reviewed 96.71
cd0446668 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also 96.51
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 94.51
PRK05054644 exoribonuclease II; Provisional 92.71
TIGR02063755 RNase_R ribonuclease R; InterPro: IPR011805 This family 92.04
PRK11642813 exoribonuclease R; Provisional 91.9
KOG3403145 consensus 94.62
cd01854 287 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) r 93.85
>PRK12442 translation initiation factor IF-1; Reviewed Back     alignment and domain information
>CHL00010 infA translation initiation factor 1 Back     alignment and domain information
>PRK00276 infA translation initiation factor IF-1; Validated Back     alignment and domain information
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts Back     alignment and domain information
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain Back     alignment and domain information
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam01176 eIF-1a Translation initiation factor 1A / IF-1 Back     alignment and domain information
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain Back     alignment and domain information
>smart00652 eIF1a eukaryotic translation initiation factor 1A Back     alignment and domain information
>PRK04012 translation initiation factor IF-1A; Provisional Back     alignment and domain information
>PTZ00329 translation initiation factor eIF-1A; Provisional Back     alignment and domain information
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain Back     alignment and domain information
>PRK00098 ribosome-associated GTPase; Reviewed Back     alignment and domain information
>PRK12289 ribosome-associated GTPase; Reviewed Back     alignment and domain information
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>KOG3403 consensus Back     alignment and domain information
>cd01854 YjeQ_engC YjeQ/EngC Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target110 translation initiation factor IF-1 [Candidatus Liberiba
1ah9_A71 The Structure Of The Translational Initiation Facto 5e-23
3i4o_A79 Crystal Structure Of Translation Initiation Factor 4e-22
1hr0_W71 Crystal Structure Of Initiation Factor If1 Bound To 1e-18
>gi|253722723|pdb|1AH9|A Chain A, The Structure Of The Translational Initiation Factor If1 From Escherichia Coli, Nmr, 19 Structures Length = 71 Back     alignment and structure
 Score =  110 bits (276), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 34/109 (31%), Positives = 48/109 (44%), Gaps = 38/109 (34%)

Query: 2   PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDP 61
            KE+ +E  G V E LPN  FRV+L                                   
Sbjct: 1   AKEDNIEMQGTVLETLPNTMFRVEL----------------------------------- 25

Query: 62  ISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
               +  VV A+ +G+MRK+ IRI  GDKV V + PYD+++ RI +R +
Sbjct: 26  ---ENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR 71


>gi|289526630|pdb|3I4O|A Chain A, Crystal Structure Of Translation Initiation Factor 1 From Mycobacterium Tuberculosis Length = 79 Back     alignment and structure
>gi|13096415|pdb|1HR0|W Chain W, Crystal Structure Of Initiation Factor If1 Bound To The 30s Ribosomal Subunit Length = 71 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target110 translation initiation factor IF-1 [Candidatus Liberiba
3i4o_A79 Translation initiation factor IF-1; cytoplasm, protein 3e-18
1hr0_W71 Translation initiation factor; ribosomal subunit, ribos 2e-16
1ah9_A71 IF1, initiation factor 1; ribosome binding, protein-RNA 2e-16
1jt8_A102 EIF-1A, probable translation initiation factor 1A; beta 2e-09
2oqk_A117 Putative translation initiation factor EIF-1A; malaria, 3e-07
1d7q_A143 Translation initiation factor 1A; OB-fold, beta-barrel, 6e-07
>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} Length = 79 Back     alignment and structure
 Score = 85.1 bits (211), Expect = 3e-18
 Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 39/111 (35%)

Query: 1   MPKEE-TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGV 59
           M K++  +E  G V E LPNA FR++L                                 
Sbjct: 7   MAKKDGAIEVEGRVVEPLPNAMFRIEL--------------------------------- 33

Query: 60  DPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
                 +   V+A+ +G+MR+H IRI   D+V V ++PYD++R RI YR+K
Sbjct: 34  -----ENGHKVLAHISGKMRQHYIRILPEDRVVVELSPYDLSRGRIVYRYK 79


>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} SCOP: b.40.4.5 PDB: 1zo1_W Length = 71 Back     alignment and structure
>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} SCOP: b.40.4.5 Length = 71 Back     alignment and structure
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} SCOP: b.40.4.5 Length = 102 Back     alignment and structure
>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II} Length = 117 Back     alignment and structure
>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 143 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 translation initiation factor IF-1 [Candidatus Liberiba
1ah9_A71 IF1, initiation factor 1; ribosome binding, protein-RNA 99.94
3i4o_A79 Translation initiation factor IF-1; cytoplasm, protein 99.94
1hr0_W71 Translation initiation factor; ribosomal subunit, ribos 99.91
1jt8_A102 EIF-1A, probable translation initiation factor 1A; beta 99.3
2oqk_A117 Putative translation initiation factor EIF-1A; malaria, 99.15
1d7q_A143 Translation initiation factor 1A; OB-fold, beta-barrel, 99.1
2dgy_A111 MGC11102 protein; EIF-1A, structural genomics, NPPSFA, 97.63
1t9h_A 307 YLOQ, probable GTPase ENGC; N-terminal beta-barrel doma 96.23
2yv5_A 302 YJEQ protein; hydrolase, GTPase, permutation, structura 95.89
1u0l_A 301 Probable GTPase ENGC; permutation, OB-fold, zinc-finger 95.81
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA 94.4
>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} SCOP: b.40.4.5 Back     alignment and structure
Probab=99.94  E-value=2.6e-28  Score=184.49  Aligned_cols=71  Identities=48%  Similarity=0.793  Sum_probs=68.7

Q ss_pred             CCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEE
Q ss_conf             75645999789998158981799981667765333233544333445555444555554455568828999912511201
Q gi|254780470|r    2 PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKH   81 (110)
Q Consensus         2 ~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~   81 (110)
                      ||||.||++|+|+|+|||++|+|+|                                      +||+.++||+|||||++
T Consensus         1 aKed~ie~~G~V~e~lg~~~f~V~l--------------------------------------~dg~~~la~i~GkmRk~   42 (71)
T 1ah9_A            1 AKEDNIEMQGTVLETLPNTMFRVEL--------------------------------------ENGHVVTAHISGKMRKN   42 (71)
T ss_dssp             CCSCCEECCEEEEEECSSSEEEEEE--------------------------------------TTSCEEEEEECSSGGGT
T ss_pred             CCCCCEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCHHEEE
T ss_conf             9864489999999988996999998--------------------------------------89979999937345021


Q ss_pred             EEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             64770299699997467578435988429
Q gi|254780470|r   82 RIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +|+|++||+|.|||||||++||||+||||
T Consensus        43 ri~i~~GD~V~Vel~~yd~~kgrIi~R~k   71 (71)
T 1ah9_A           43 YIRILTGDKVTVELTPYDLSKGRIVFRSR   71 (71)
T ss_dssp             TCCCCTTCEECCEECSSCTTEEEECSCCC
T ss_pred             EEEECCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             49976999999997755699588999839



>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} Back     alignment and structure
>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} SCOP: b.40.4.5 PDB: 1zo1_W Back     alignment and structure
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} SCOP: b.40.4.5 Back     alignment and structure
>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II} Back     alignment and structure
>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein, gene regulation; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>2dgy_A MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8 Back     alignment and structure
>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus} Back     alignment and structure
>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8 Back     alignment and structure
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 110 translation initiation factor IF-1 [Candidatus Liberiba
d1hr0w_71 b.40.4.5 (W:) Translational initiation factor 1, IF1 {E 4e-17
d1ah9a_71 b.40.4.5 (A:) Translational initiation factor 1, IF1 {E 1e-16
d1jt8a_102 b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Arc 3e-10
d1d7qa_143 b.40.4.5 (A:) Translation initiation factor-1a, eIF1a { 1e-07
>d1hr0w_ b.40.4.5 (W:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} Length = 71 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Translational initiation factor 1, IF1
species: Escherichia coli [TaxId: 562]
 Score = 80.4 bits (199), Expect = 4e-17
 Identities = 35/106 (33%), Positives = 47/106 (44%), Gaps = 38/106 (35%)

Query: 3   KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62
           +++T+   G+V+E LPNA FRVKL                                    
Sbjct: 3   EKDTIRTEGVVTEALPNATFRVKL------------------------------------ 26

Query: 63  SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
                  ++AY +G+MR H IRI  GD+V V + PYD TR RI YR
Sbjct: 27  --DSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYR 70


>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} Length = 71 Back     information, alignment and structure
>d1jt8a_ b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 102 Back     information, alignment and structure
>d1d7qa_ b.40.4.5 (A:) Translation initiation factor-1a, eIF1a {Human (Homo sapiens) [TaxId: 9606]} Length = 143 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 translation initiation factor IF-1 [Candidatus Liberiba
d1ah9a_71 Translational initiation factor 1, IF1 {Escherichia col 99.94
d1hr0w_71 Translational initiation factor 1, IF1 {Escherichia col 99.91
d1jt8a_102 Archaeal initiation factor-1a, aIF1a {Archaeon Methanoc 99.22
d1d7qa_143 Translation initiation factor-1a, eIF1a {Human (Homo sa 98.88
d1u0la166 Probable GTPase EngC (YjeQ), N-terminal domain {Thermot 96.82
d1t9ha167 Probable GTPase EngC (YjeQ), N-terminal domain {Bacillu 96.77
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 94.8
>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Translational initiation factor 1, IF1
species: Escherichia coli [TaxId: 562]
Probab=99.94  E-value=3.8e-28  Score=182.14  Aligned_cols=71  Identities=48%  Similarity=0.793  Sum_probs=68.8

Q ss_pred             CCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEE
Q ss_conf             75645999789998158981799981667765333233544333445555444555554455568828999912511201
Q gi|254780470|r    2 PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKH   81 (110)
Q Consensus         2 ~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~   81 (110)
                      ||||.||++|+|+|+|||++|+|+|                                      +||+.++||+|||||++
T Consensus         1 aKed~ie~~G~V~e~lg~~~f~V~l--------------------------------------~ng~~~~a~i~Gkmrk~   42 (71)
T d1ah9a_           1 AKEDNIEMQGTVLETLPNTMFRVEL--------------------------------------ENGHVVTAHISGKMRKN   42 (71)
T ss_dssp             CCSCCEECCEEEEEECSSSEEEEEE--------------------------------------TTSCEEEEEECSSGGGT
T ss_pred             CCCCCEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEECCCHHHEE
T ss_conf             9863189999999986998899996--------------------------------------79979999846434302


Q ss_pred             EEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             64770299699997467578435988429
Q gi|254780470|r   82 RIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +|+|++||+|.|||||||++||||+||||
T Consensus        43 ri~i~~GD~V~Vel~pyd~~kgrIi~R~k   71 (71)
T d1ah9a_          43 YIRILTGDKVTVELTPYDLSKGRIVFRSR   71 (71)
T ss_dssp             TCCCCTTCEECCEECSSCTTEEEECSCCC
T ss_pred             EEEECCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             79964999999997766799388999749



>d1hr0w_ b.40.4.5 (W:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jt8a_ b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1d7qa_ b.40.4.5 (A:) Translation initiation factor-1a, eIF1a {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1u0la1 b.40.4.5 (A:3-68) Probable GTPase EngC (YjeQ), N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1t9ha1 b.40.4.5 (A:1-67) Probable GTPase EngC (YjeQ), N-terminal domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 110 translation initiation factor IF-1 [Candidatus Lib
1hr0_W_71 (W:) Translation initiation factor; ribosomal subu 8e-18
1ah9_A_71 (A:) IF1, initiation factor 1; ribosome binding, p 4e-17
3i4o_A_79 (A:) Translation initiation factor IF-1; cytoplasm 1e-16
1jt8_A_102 (A:) EIF-1A, probable translation initiation facto 1e-09
1d7q_A_143 (A:) Translation initiation factor 1A; OB-fold, be 1e-09
2oqk_A_117 (A:) Putative translation initiation factor EIF-1A 1e-09
>1hr0_W (W:) Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli}Length = 71 Back     alignment and structure
 Score = 83.9 bits (208), Expect = 8e-18
 Identities = 36/107 (33%), Positives = 49/107 (45%), Gaps = 40/107 (37%)

Query: 3   KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62
           +++T+   G+V+E LPNA FRVKL                                    
Sbjct: 3   EKDTIRTEGVVTEALPNATFRVKL------------------------------------ 26

Query: 63  SYLDN-AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
              D+   ++AY +G+MR H IRI  GD+V V + PYD TR RI YR
Sbjct: 27  ---DSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYR 70


>1ah9_A (A:) IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli}Length = 71 Back     alignment and structure
>3i4o_A (A:) Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis}Length = 79 Back     alignment and structure
>1jt8_A (A:) EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii}Length = 102 Back     alignment and structure
>1d7q_A (A:) Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein; NMR {Homo sapiens}Length = 143 Back     alignment and structure
>2oqk_A (A:) Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II}Length = 117 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target110 translation initiation factor IF-1 [Candidatus Liberiba
1hr0_W_71 Translation initiation factor; ribosomal subunit, 99.97
1ah9_A_71 IF1, initiation factor 1; ribosome binding, protei 99.93
3i4o_A_79 Translation initiation factor IF-1; cytoplasm, pro 99.93
1d7q_A_143 Translation initiation factor 1A; OB-fold, beta-ba 99.72
2oqk_A_117 Putative translation initiation factor EIF-1A; mal 99.64
1jt8_A_102 EIF-1A, probable translation initiation factor 1A; 99.63
2dgy_A_111 MGC11102 protein; EIF-1A, structural genomics, NPP 97.02
1t9h_A_1-7575 YLOQ, probable GTPase ENGC; N-terminal beta-barrel 96.74
1u0l_A_1-7373 Probable GTPase ENGC; permutation, OB-fold, zinc-f 96.42
2id0_A_559-64486 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 94.04
2wp8_J_888-97790 Exosome complex exonuclease DIS3; nucleus, hydrola 93.65
>1hr0_W (W:) Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} Back     alignment and structure
Probab=99.97  E-value=8.9e-33  Score=211.31  Aligned_cols=70  Identities=50%  Similarity=0.821  Sum_probs=66.8

Q ss_pred             CCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEE
Q ss_conf             75645999789998158981799981667765333233544333445555444555554455568828999912511201
Q gi|254780470|r    2 PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKH   81 (110)
Q Consensus         2 ~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~   81 (110)
                      .|||.|+++|+|+|+|||++|||+|                                      +||+.|+||+|||||+|
T Consensus         2 kke~~i~~eG~V~e~lpn~~F~V~L--------------------------------------eng~~vla~isGKmR~~   43 (71)
T 1hr0_W            2 KEKDTIRTEGVVTEALPNATFRVKL--------------------------------------DSGPEILAYISGKMRMH   43 (71)
T ss_dssp             CCSCCCCCEEECCCCCTTTBCCCEE--------------------------------------SSSCBCCCEECHHHHHT
T ss_pred             CCCCEEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCHHHHE
T ss_conf             8530589999999985997999998--------------------------------------99999999957755301


Q ss_pred             EEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             6477029969999746757843598842
Q gi|254780470|r   82 RIRISLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      +|||++||+|+|||||||||||||+||-
T Consensus        44 ~IrIl~GDrV~VE~spYDltkGRIv~R~   71 (71)
T 1hr0_W           44 YIRILPGDRVVVEITPYDPTRGRIVYRK   71 (71)
T ss_dssp             CCCCCTTCEEEEECCTTCTTCCEECSCC
T ss_pred             EEEECCCCEEEEEECCCCCCCEEEEECC
T ss_conf             5987599999999774569937799739



>1ah9_A (A:) IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} Back     alignment and structure
>3i4o_A (A:) Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} Back     alignment and structure
>1d7q_A (A:) Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein; NMR {Homo sapiens} Back     alignment and structure
>2oqk_A (A:) Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II} Back     alignment and structure
>1jt8_A (A:) EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>2dgy_A (A:) MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1t9h_A (A:1-75) YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} Back     alignment and structure
>1u0l_A (A:1-73) Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} Back     alignment and structure
>2id0_A (A:559-644) Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} Back     alignment and structure
>2wp8_J (J:888-977) Exosome complex exonuclease DIS3; nucleus, hydrolase, cytoplasm, RNA-binding, RNA binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure