254780430

254780430

nitrogen fixation protein

GeneID in NCBI database:8209416Locus tag:CLIBASIA_01575
Protein GI in NCBI database:254780430Protein Accession:YP_003064843.1
Gene range:-(337204, 337773)Protein Length:189aa
Gene description:nitrogen fixation protein
COG prediction:[O] Thioredoxin-like proteins and domains
KEGG prediction:nitrogen fixation protein
SEED prediction:NifU protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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
TOPPRED1 TM-Helix
HMMTOP1 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-------120-------130-------140-------150-------160-------170-------180-------19
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
ccEEEcccccccEEEEEcccEEccccccccccHHHccccHHHHHHHccccEEEEEEEccEEEEEcccccHHHHHHHHHHHHHHHHHHcHHHcccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHcccccEEEEEEEccEEEEEEcccccccHHHHHHHHHHHHHHHHHHcccccEEEEc
ccEEEcccccccHHccccccEcccccccccccHHHHHccHHHHHHHcccccEEEEEcccEEEEEcccccHHHccHHHHHHHHHHHHccccccccccHHHHcccccccccccccHHHHHHHHHHHHHccccccEccccccEEEEcccccEEEEEEccccccccccHHHHHHHHHHHHHHccccccEEEEc
mfiqtedtpnpatlkfipgqVVLVEGAihfsnakeaeisplasrifsipgiasvyfgydfitvgkdqydwehlrppvLGMIMEHfisgdpiihngglgdmklddmgsgdfiesDSAVVQRIKEVLdnrvrpavardggdivfkGYRDGIVFLSmrgacsgcpsasetLKYGVANILnhfvpevkdirtv
mfiqtedtpnpatlkfipGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKevldnrvrpavardggdivfKGYRDGIVFLSMRGACSGCPSASETLKYGVANilnhfvpevkdirtv
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNgglgdmklddmgsgdFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHN*********************AVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
********PNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGG***********GDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV
MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV

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
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
315122122190 nitrogen fixation protein [Candidatus Liberibacter sola 1 8e-87
325291785187 scaffold protein Nfu/NifU [Agrobacterium sp. H13-3] Len 1 4e-63
222084688188 nitrogen fixation protein [Agrobacterium radiobacter K8 1 1e-62
15887702187 hypothetical protein Atu0351 [Agrobacterium tumefaciens 1 8e-62
227820624188 putative scaffold protein Nfu/NifU [Sinorhizobium fredi 1 9e-62
150395264188 scaffold protein Nfu/NifU [Sinorhizobium medicae WSM419 1 9e-62
86356038188 nitrogen fixation protein [Rhizobium etli CFN 42] Lengt 1 1e-61
15964154188 hypothetical protein SMc01119 [Sinorhizobium meliloti 1 1 1e-61
190890051188 nitrogen fixation protein [Rhizobium etli CIAT 652] Len 1 2e-61
209547636188 Scaffold protein Nfu/NifU [Rhizobium leguminosarum bv. 1 2e-61
>gi|315122122|ref|YP_004062611.1| nitrogen fixation protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 190 Back     alignment and organism information
 Score =  323 bits (828), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 156/190 (82%), Positives = 171/190 (90%), Gaps = 1/190 (0%)

Query: 1   MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDF 60
           MFIQTE TPNPATLKFIPGQVVLV G++HFSNAKEA ISPLASRIFSI GI SVY GYDF
Sbjct: 1   MFIQTEYTPNPATLKFIPGQVVLVRGSVHFSNAKEAGISPLASRIFSISGIVSVYLGYDF 60

Query: 61  ITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKL-DDMGSGDFIESDSAVVQ 119
           ITV KD+YDWE L+P +LG+IMEHF+SGDPII NGGL  + + DD+G GDF ESDS +VQ
Sbjct: 61  ITVAKDKYDWEQLKPLILGVIMEHFMSGDPIISNGGLDAVNVNDDLGEGDFSESDSVIVQ 120

Query: 120 RIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHF 179
           +IK+VLDNRVRPAVARDGGDIVFKGYRDGIVFLSM GACSGCPSA+ETLKYGV N+LNHF
Sbjct: 121 KIKDVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMMGACSGCPSATETLKYGVINLLNHF 180

Query: 180 VPEVKDIRTV 189
           VPEVKDIRTV
Sbjct: 181 VPEVKDIRTV 190


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325291785|ref|YP_004277649.1| scaffold protein Nfu/NifU [Agrobacterium sp. H13-3] Length = 187 Back     alignment and organism information
>gi|222084688|ref|YP_002543217.1| nitrogen fixation protein [Agrobacterium radiobacter K84] Length = 188 Back     alignment and organism information
>gi|15887702|ref|NP_353383.1| hypothetical protein Atu0351 [Agrobacterium tumefaciens str. C58] Length = 187 Back     alignment and organism information
>gi|227820624|ref|YP_002824594.1| putative scaffold protein Nfu/NifU [Sinorhizobium fredii NGR234] Length = 188 Back     alignment and organism information
>gi|150395264|ref|YP_001325731.1| scaffold protein Nfu/NifU [Sinorhizobium medicae WSM419] Length = 188 Back     alignment and organism information
>gi|86356038|ref|YP_467930.1| nitrogen fixation protein [Rhizobium etli CFN 42] Length = 188 Back     alignment and organism information
>gi|15964154|ref|NP_384507.1| hypothetical protein SMc01119 [Sinorhizobium meliloti 1021] Length = 188 Back     alignment and organism information
>gi|190890051|ref|YP_001976593.1| nitrogen fixation protein [Rhizobium etli CIAT 652] Length = 188 Back     alignment and organism information
>gi|209547636|ref|YP_002279553.1| Scaffold protein Nfu/NifU [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 188 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
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
pfam0871287 pfam08712, Nfu_N, Scaffold protein Nfu/NifU N terminal 6e-35
COG069493 COG0694, COG0694, Thioredoxin-like proteins and domains 2e-19
pfam0110668 pfam01106, NifU, NifU-like domain 1e-12
TIGR02000290 TIGR02000, NifU_proper, Fe-S cluster assembly protein N 5e-06
TIGR03341190 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI 9e-06
PRK11190192 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provi 0.001
KOG2358213 KOG2358, KOG2358, KOG2358, NifU-like domain-containing 2e-34
>gnl|CDD|149691 pfam08712, Nfu_N, Scaffold protein Nfu/NifU N terminal Back     alignment and domain information
>gnl|CDD|31038 COG0694, COG0694, Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>gnl|CDD|144628 pfam01106, NifU, NifU-like domain Back     alignment and domain information
>gnl|CDD|162652 TIGR02000, NifU_proper, Fe-S cluster assembly protein NifU Back     alignment and domain information
>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI Back     alignment and domain information
>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional Back     alignment and domain information
>gnl|CDD|37569 KOG2358, KOG2358, KOG2358, NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 189 nitrogen fixation protein [Candidatus Liberibacter asia
KOG2358213 consensus 100.0
pfam0871287 Nfu_N Scaffold protein Nfu/NifU N terminal. This domain 99.95
TIGR03341190 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) 99.92
COG069493 Thioredoxin-like proteins and domains [Posttranslationa 99.92
PRK11190192 putative DNA uptake protein; Provisional 99.91
pfam0110668 NifU NifU-like domain. This is an alignment of the carb 99.89
KOG2358213 consensus 98.16
>KOG2358 consensus Back     alignment and domain information
>pfam08712 Nfu_N Scaffold protein Nfu/NifU N terminal Back     alignment and domain information
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI Back     alignment and domain information
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK11190 putative DNA uptake protein; Provisional Back     alignment and domain information
>pfam01106 NifU NifU-like domain Back     alignment and domain information
>KOG2358 consensus 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
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
1veh_A92 Solution Structure Of Rsgi Ruh-018, A Nifu-Like Dom 4e-18
2z51_A154 Crystal Structure Of Arabidopsis Cnfu Involved In I 7e-15
1xhj_A88 Solution Structure Of The Staphylococcus Epidermidi 9e-15
2jnv_A91 Solution Structure Of C-Terminal Domain Of Nifu-Lik 5e-14
>gi|159163237|pdb|1VEH|A Chain A, Solution Structure Of Rsgi Ruh-018, A Nifu-Like Domain Of Hirip5 Protein From Mouse Cdna Length = 92 Back     alignment and structure
 Score = 94.9 bits (234), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 36/73 (49%), Positives = 54/73 (73%)

Query: 117 VVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANIL 176
           VV  IKE+LD R+RP V  DGGD++++G+ DGIV L ++G+C+ CPS+  TLK G+ N+L
Sbjct: 14  VVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNML 73

Query: 177 NHFVPEVKDIRTV 189
             ++PEV+ +  V
Sbjct: 74  QFYIPEVEGVEQV 86


>gi|194319991|pdb|2Z51|A Chain A, Crystal Structure Of Arabidopsis Cnfu Involved In Iron- Sulfur Cluster Biosynthesis Length = 154 Back     alignment and structure
>gi|58177342|pdb|1XHJ|A Chain A, Solution Structure Of The Staphylococcus Epidermidis Protein Se0630. Northest Structural Genomics Consortium Target Ser8 Length = 88 Back     alignment and structure
>gi|163310812|pdb|2JNV|A Chain A, Solution Structure Of C-Terminal Domain Of Nifu-Like Protein From Oryza Sativa Length = 91 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
1veh_A92 NIFU-like protein hirip5; structural genomics, mouse cD 3e-23
1xhj_A88 Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, 5e-22
2z51_A154 NIFU-like protein 2, chloroplast; CNFU, iron-sulfur clu 3e-15
2z51_A154 NIFU-like protein 2, chloroplast; CNFU, iron-sulfur clu 8e-11
1th5_A74 NIFU1; iron-sulfur cluster binding, structural genomics 2e-14
1pqx_A91 Conserved hypothetical protein; ZR18,structure, autostr 3e-22
2k1h_A94 Uncharacterized protein Ser13; structural genomics, unk 5e-22
>1veh_A NIFU-like protein hirip5; structural genomics, mouse cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.52.8.1 Length = 92 Back     alignment and structure
 Score =  103 bits (258), Expect = 3e-23
 Identities = 38/78 (48%), Positives = 56/78 (71%)

Query: 112 ESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYG 171
           E D  VV  IKE+LD R+RP V  DGGD++++G+ DGIV L ++G+C+ CPS+  TLK G
Sbjct: 9   EEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSG 68

Query: 172 VANILNHFVPEVKDIRTV 189
           + N+L  ++PEV+ +  V
Sbjct: 69  IQNMLQFYIPEVEGVEQV 86


>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structure initiative, NESG, PSI; NMR {Staphylococcus epidermidis atcc 12228} SCOP: d.52.8.1 Length = 88 Back     alignment and structure
>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Length = 154 Back     alignment and structure
>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Length = 154 Back     alignment and structure
>1th5_A NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa} SCOP: d.52.8.1 Length = 74 Back     alignment and structure
>1pqx_A Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp} SCOP: d.267.1.1 PDB: 2ffm_A Length = 91 Back     alignment and structure
>2k1h_A Uncharacterized protein Ser13; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Staphylococcus epidermidis atcc 12228} Length = 94 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
1veh_A92 NIFU-like protein hirip5; structural genomics, mouse cD 99.93
1xhj_A88 Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, 99.92
2z51_A154 NIFU-like protein 2, chloroplast; CNFU, iron-sulfur clu 99.9
1th5_A74 NIFU1; iron-sulfur cluster binding, structural genomics 99.78
3lno_A108 Putative uncharacterized protein; alpha-beta fold, stru 94.57
2k1h_A94 Uncharacterized protein Ser13; structural genomics, unk 99.9
1pqx_A91 Conserved hypothetical protein; ZR18,structure, autostr 99.9
2z51_A154 NIFU-like protein 2, chloroplast; CNFU, iron-sulfur clu 98.79
>1veh_A NIFU-like protein hirip5; structural genomics, mouse cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.52.8.1 Back     alignment and structure
Probab=99.93  E-value=1.8e-26  Score=184.84  Aligned_cols=80  Identities=48%  Similarity=0.932  Sum_probs=76.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             45440268899999999987777875289759996433479999636646666689999999999999978970035539
Q gi|254780430|r  110 FIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       110 ~~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      ..++|++++++|+++|+++|||+|++|||||+|++|++|+|+|+|+|||+|||+|++||+++||++||+++|||+.|++|
T Consensus         7 ~~~~d~e~~~~I~~~L~~~IrP~l~~dGGdv~~v~~~~g~V~v~l~GaC~gC~~s~~Tl~~~Ie~~L~~~vpev~~V~~v   86 (92)
T 1veh_A            7 GSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNMLQFYIPEVEGVEQV   86 (92)
T ss_dssp             SCSSCCHHHHHHHHHHHHTTHHHHHHHSCCCCEEEEETTEEEECCCCCCCCCHHHHHHTHHHHHHHHHHHCSSCCCEEEC
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             89763899999999999751678996599369999518879999653578876189999999999999978995569982



>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structure initiative, NESG, PSI; NMR {Staphylococcus epidermidis atcc 12228} SCOP: d.52.8.1 Back     alignment and structure
>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Back     alignment and structure
>1th5_A NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa} SCOP: d.52.8.1 Back     alignment and structure
>3lno_A Putative uncharacterized protein; alpha-beta fold, structural genomics, center for structural genomics of infectious diseases, csgid; 2.10A {Bacillus anthracis} Back     alignment and structure
>2k1h_A Uncharacterized protein Ser13; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Staphylococcus epidermidis atcc 12228} Back     alignment and structure
>1pqx_A Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp} SCOP: d.267.1.1 PDB: 2ffm_A Back     alignment and structure
>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_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 189 nitrogen fixation protein [Candidatus Liberibacter asia
d1veha_92 d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {Mouse 6e-24
d1xhja_88 d.52.8.1 (A:) Nitrogen fixation protein NifU homolog SE 3e-21
d1th5a173 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice 8e-15
d2ffma183 d.267.1.1 (A:1-83) Hypothetical protein SAV1430 {Staphy 2e-22
>d1veha_ d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 92 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Fe-S cluster assembly (FSCA) domain-like
family: NifU C-terminal domain-like
domain: HIRA-interacting protein 5, HIRIP5
species: Mouse (Mus musculus) [TaxId: 10090]
 Score =  104 bits (260), Expect = 6e-24
 Identities = 38/78 (48%), Positives = 56/78 (71%)

Query: 112 ESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYG 171
           E D  VV  IKE+LD R+RP V  DGGD++++G+ DGIV L ++G+C+ CPS+  TLK G
Sbjct: 9   EEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSG 68

Query: 172 VANILNHFVPEVKDIRTV 189
           + N+L  ++PEV+ +  V
Sbjct: 69  IQNMLQFYIPEVEGVEQV 86


>d1xhja_ d.52.8.1 (A:) Nitrogen fixation protein NifU homolog SE0630 {Staphylococcus epidermidis [TaxId: 1282]} Length = 88 Back     information, alignment and structure
>d1th5a1 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId: 4530]} Length = 73 Back     information, alignment and structure
>d2ffma1 d.267.1.1 (A:1-83) Hypothetical protein SAV1430 {Staphylococcus aureus [TaxId: 1280]} Length = 83 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
d1veha_92 HIRA-interacting protein 5, HIRIP5 {Mouse (Mus musculus 99.94
d1xhja_88 Nitrogen fixation protein NifU homolog SE0630 {Staphylo 99.92
d1th5a173 NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId 99.78
d2ffma183 Hypothetical protein SAV1430 {Staphylococcus aureus [Ta 99.89
>d1veha_ d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Fe-S cluster assembly (FSCA) domain-like
family: NifU C-terminal domain-like
domain: HIRA-interacting protein 5, HIRIP5
species: Mouse (Mus musculus) [TaxId: 10090]
Probab=99.94  E-value=6.8e-27  Score=185.94  Aligned_cols=80  Identities=48%  Similarity=0.932  Sum_probs=76.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             45440268899999999987777875289759996433479999636646666689999999999999978970035539
Q gi|254780430|r  110 FIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       110 ~~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      ..++|+++.++|+++|+++|||+|++|||||+|++|++|+|||+|+|||+|||||++|||++||++||+++|||+.|++|
T Consensus         7 ~~~~d~e~~~~I~~vL~~~IrP~l~~dGGdv~lv~v~~g~V~v~l~GaC~gCp~s~~Tlk~~Ie~~L~~~vpev~~V~~v   86 (92)
T d1veha_           7 GSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNMLQFYIPEVEGVEQV   86 (92)
T ss_dssp             SCSSCCHHHHHHHHHHHHTTHHHHHHHSCCCCEEEEETTEEEECCCCCCCCCHHHHHHTHHHHHHHHHHHCSSCCCEEEC
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             88761899999999999740758997599469998508868999766778975189999999999999878985569882



>d1xhja_ d.52.8.1 (A:) Nitrogen fixation protein NifU homolog SE0630 {Staphylococcus epidermidis [TaxId: 1282]} Back     information, alignment and structure
>d1th5a1 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId: 4530]} Back     information, alignment and structure
>d2ffma1 d.267.1.1 (A:1-83) Hypothetical protein SAV1430 {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 189 nitrogen fixation protein [Candidatus Liberibacter
1pqx_A_91 (A:) Conserved hypothetical protein; ZR18,structur 1e-30
2k1h_A_94 (A:) Uncharacterized protein Ser13; structural gen 2e-29
1veh_A_92 (A:) NIFU-like protein hirip5; structural genomics 6e-23
1xhj_A_88 (A:) Nitrogen fixation protein NIFU; alpha-beta, N 8e-22
2z51_A_1-8181 (A:1-81) NIFU-like protein 2, chloroplast; CNFU, i 1e-21
1th5_A_74 (A:) NIFU1; iron-sulfur cluster binding, structura 3e-18
2z51_A_82-15473 (A:82-154) NIFU-like protein 2, chloroplast; CNFU, 1e-17
>1pqx_A (A:) Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp}Length = 91 Back     alignment and structure
 Score =  127 bits (320), Expect = 1e-30
 Identities = 18/90 (20%), Positives = 32/90 (35%), Gaps = 2/90 (2%)

Query: 1  MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDF 60
            I   +TPN  T+K    +              +       + I  + G+ S++   DF
Sbjct: 2  KIISISETPNHNTMKITLSESRE-GMTSDTYTKVDDSQPAFINDILKVEGVKSIFHVMDF 60

Query: 61 ITVGK-DQYDWEHLRPPVLGMIMEHFISGD 89
          I+V K +  +WE + P V  +         
Sbjct: 61 ISVDKENDANWETVLPKVEAVFELEHHHHH 90


>2k1h_A (A:) Uncharacterized protein Ser13; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Staphylococcus epidermidis atcc 12228}Length = 94 Back     alignment and structure
>1veh_A (A:) NIFU-like protein hirip5; structural genomics, mouse cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus}Length = 92 Back     alignment and structure
>1xhj_A (A:) Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structure initiative, NESG, PSI; NMR {Staphylococcus epidermidis atcc 12228}Length = 88 Back     alignment and structure
>2z51_A (A:1-81) NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_ALength = 81 Back     alignment and structure
>1th5_A (A:) NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa}Length = 74 Back     alignment and structure
>2z51_A (A:82-154) NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_ALength = 73 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target189 nitrogen fixation protein [Candidatus Liberibacter asia
2k1h_A_94 Uncharacterized protein Ser13; structural genomics 99.94
1pqx_A_91 Conserved hypothetical protein; ZR18,structure, au 99.94
1veh_A_92 NIFU-like protein hirip5; structural genomics, mou 99.91
1xhj_A_88 Nitrogen fixation protein NIFU; alpha-beta, NIFU-l 99.89
2z51_A_1-8181 NIFU-like protein 2, chloroplast; CNFU, iron-sulfu 99.88
2z51_A_82-15473 NIFU-like protein 2, chloroplast; CNFU, iron-sulfu 99.8
1th5_A_74 NIFU1; iron-sulfur cluster binding, structural gen 99.76
3lno_A_1-9292 Putative uncharacterized protein; alpha-beta fold, 92.98
>2k1h_A (A:) Uncharacterized protein Ser13; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Staphylococcus epidermidis atcc 12228} Back     alignment and structure
Probab=99.94  E-value=9.8e-28  Score=193.64  Aligned_cols=89  Identities=21%  Similarity=0.429  Sum_probs=83.5

Q ss_pred             CEEECCCCCCHHHHHHHCCCEECCCCCEECCCHHHCCCCHHHHHHHHCCCCEEEEECCCEEEEEEC-CCCCHHHHHHHHH
Q ss_conf             910211488722435417975437886430696670134688987416881079980877998314-6682123489999
Q gi|254780430|r    1 MFIQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKD-QYDWEHLRPPVLG   79 (189)
Q Consensus         1 m~I~~e~TPNPn~lKFi~~~~i~~~g~~~f~~~~~a~~spLa~~Lf~i~GV~~Vfi~~nFITVtK~-~~eW~~i~p~I~~   79 (189)
                      |||++|+|||||+|||++++.+.+.|+..|+ .+++..+|||++||+++||++||++.|||||+|+ +++|++|+|+|++
T Consensus         2 ~~i~~e~TPNPn~lKF~~~~~l~~~~~~~~~-~~~a~~spLa~~LF~i~gV~~Vf~~~dfItVtK~~~~dW~~l~~~I~~   80 (94)
T 2k1h_A            2 EIIAISETPNHNTMKVSLSEPRQDNSFTTYT-AAQEGQPEFINRLFEIEGVKSIFYVLDFISIDKEDNANWNELLPQIEN   80 (94)
T ss_dssp             CCCCCBCCSSSSCEEEECCCCCTTCCCCEEC-CCCTTSCHHHHHHHTSTTEEEEEEETTEEEEEECTTCCHHHHHHHHHH
T ss_pred             CEEEECCCCCCCCEEEECCCEEECCCCEEEC-CCCCCCCHHHHHHHCCCCCCEEEECCCEEEEEECCCCCHHHHHHHHHH
T ss_conf             7797025889577787179716448714506-401014999999876889636997198899985899998999999999


Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999740143
Q gi|254780430|r   80 MIMEHFISGDP   90 (189)
Q Consensus        80 ~I~~~l~~g~~   90 (189)
                      +|++||.+|..
T Consensus        81 ~i~~~l~sg~~   91 (94)
T 2k1h_A           81 TFAKSNLEHHH   91 (94)
T ss_dssp             HHHHHC-----
T ss_pred             HHHHHCCCCCC
T ss_conf             98660530012



>1pqx_A (A:) Conserved hypothetical protein; ZR18,structure, autostructure,spins,autoassign, northeast structural genomics consortium; NMR {Staphylococcus aureus subsp} Back     alignment and structure
>1veh_A (A:) NIFU-like protein hirip5; structural genomics, mouse cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} Back     alignment and structure
>1xhj_A (A:) Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structure initiative, NESG, PSI; NMR {Staphylococcus epidermidis atcc 12228} Back     alignment and structure
>2z51_A (A:1-81) NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Back     alignment and structure
>2z51_A (A:82-154) NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Back     alignment and structure
>1th5_A (A:) NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa} Back     alignment and structure
>3lno_A (A:1-92) Putative uncharacterized protein; alpha-beta fold, structural genomics, center for structural genomics of infectious diseases, csgid; 2.10A {Bacillus anthracis} Back     alignment and structure