Citrus Sinensis ID: 030084

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180---
Protein Sequence
MACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVPL
Secondary Structure (PSIPRED)
cccccHHHHHHcccccccccccccEEEEcccccccccccHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHcccHHHHccccEEEEEEEccEEEEEEcccccccccHHHHHHHHHHHHHHHHHcccccEEEEcccHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHccEEEcccEEEEEcccEEEEEccccccHccccHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHcccHHHHcccccEEEEEccccEEEEEEEcccccccccHHHHHHHHHHHHHHHcHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
MACLSLTaatrisktptissksqfptkFNERLQfisikpknsvlqksgshetairasnpsapagsspglysahqfdltakNVDLVLEDVRpyliadggnidvvSVEDGVVSVKlqgacgscpsstttmSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLIsdkryyyttavpl
Flexible Loop (DISEMBL)
MACLSLTAatrisktptissksqfptKFNERLQFISIKPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLqgacgscpsstttmsMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLlclisdkryyyttavpl
Low Complexity Region (SEG)
MACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRasnpsapagsspgLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIdvvsvedgvvsvKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVPL
Disordered region (IsUnstruct)
*********************************************************************YSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYTTA***
Disordered Region (DISOPRED)
*****LT*ATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHE*************************LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEV*********************
Disordered Region (DISEMBL)
MACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKN***************************LYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVPL
Disordered Region (DISPRO)
*ACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRA***************AHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYT*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDKRYYYTTAVPL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	183	2.2.26 [Sep-21-2011]
Q93W77	231	NifU-like protein 1, chlo	yes	no	0.781	0.619	0.597	4e-44
Q93W20	235	NifU-like protein 2, chlo	no	no	0.437	0.340	0.518	4e-18
Q84LK7	226	NifU-like protein 1, chlo	no	no	0.502	0.407	0.505	1e-16
Q84RQ7	236	NifU-like protein 3, chlo	no	no	0.420	0.326	0.5	9e-15
P33179	112	Nitrogen fixation protein	N/A	no	0.535	0.875	0.375	9e-13
O32119	111	Putative nitrogen fixatio	yes	no	0.311	0.513	0.526	5e-12
P20628	300	Nitrogen fixation protein	no	no	0.513	0.313	0.388	1e-10
Q43885	300	Nitrogen fixation protein	no	no	0.513	0.313	0.388	1e-10
Q9UMS0	254	NFU1 iron-sulfur cluster	yes	no	0.683	0.492	0.320	4e-10
B4JWR9	298	NFU1 iron-sulfur cluster	N/A	no	0.349	0.214	0.415	3e-09

>sp|Q93W77|NIFU1_ARATH NifU-like protein 1, chloroplastic OS=Arabidopsis thaliana GN=NIFU1 PE=1 SV=1

 Score =  177 bits (449), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 89/149 (59%), Positives = 112/149 (75%), Gaps = 6/149 (4%)

Query: 19  SSKSQFPTKFNERLQFISIKPKNSVLQKSG-SHETAIRASNPSA-----PAGSSPGLYSA 72
           S+++ FP   ++   F+    K   + ++   H +AI  S+         +G S GLYSA
Sbjct: 21  STRNGFPVISDQNPSFVLFANKRRHISRTAIFHRSAISGSSQGEKISPLASGVSSGLYSA 80

Query: 73  HQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGI 132
             FDLT +NVDLVLEDVRP+LI+DGGN+DVVSVEDGVVS+KLQGAC SCPSS+TTM+MGI
Sbjct: 81  QTFDLTPQNVDLVLEDVRPFLISDGGNVDVVSVEDGVVSLKLQGACTSCPSSSTTMTMGI 140

Query: 133 ERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           ERVLKEKFGDA+KDIRQV+DEEV++ TVE
Sbjct: 141 ERVLKEKFGDALKDIRQVFDEEVKQITVE 169

Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins.
Arabidopsis thaliana (taxid: 3702)

>sp|Q93W20|NIFU2_ARATH NifU-like protein 2, chloroplastic OS=Arabidopsis thaliana GN=NIFU2 PE=1 SV=1

 Score = 90.9 bits (224), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/81 (51%), Positives = 59/81 (72%), Gaps = 1/81 (1%)

Query: 74  QFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIE 133
           +  LT +NV+ VL+++RPYL++DGGN+ +  ++  +V VKLQGACGSCPSST TM MGIE
Sbjct: 82  EVPLTEENVESVLDEIRPYLMSDGGNVALHEIDGNIVRVKLQGACGSCPSSTMTMKMGIE 141

Query: 134 RVLKEKFGDAIKDIRQVYDEE 154
           R L EK  + +  +  + DEE
Sbjct: 142 RRLMEKIPEIVA-VEALPDEE 161

Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins. Required for biogenesis of ferredoxin, a major photosynthetic electron carrier containing [2Fe-2S] cluster. Required for the assembly of photosystem I complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84LK7|NIFU1_ORYSJ NifU-like protein 1, chloroplastic OS=Oryza sativa subsp. japonica GN=NIFU1 PE=1 SV=1

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 48/95 (50%), Positives = 60/95 (63%), Gaps = 3/95 (3%)

Query: 60  SAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACG 119
            A AG  P   +A Q  LTA NV+ VL+ VRPYL ADGG++ +  +   VV +KLQGACG
Sbjct: 60  GAIAGLDP--VTAVQLPLTAGNVESVLDQVRPYLTADGGDVALHEIAGNVVRLKLQGACG 117

Query: 120 SCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154
           SCPSS  T+  GIER L EK  D +  +  V D+E
Sbjct: 118 SCPSSLITIKRGIERRLMEKIPD-VAAVEPVTDKE 151

Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84RQ7|NIFU3_ARATH NifU-like protein 3, chloroplastic OS=Arabidopsis thaliana GN=NIFU3 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 39/78 (50%), Positives = 56/78 (71%), Gaps = 1/78 (1%)

Query: 77  LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVL 136
           LT +NV+ VL++VRP L+ADGGN+ +  ++  VV +KLQGACGSCPSS+ T+ MGIE  L
Sbjct: 84  LTEENVERVLDEVRPSLMADGGNVALHEIDGLVVVLKLQGACGSCPSSSMTLKMGIESRL 143

Query: 137 KEKFGDAIKDIRQVYDEE 154
           ++K  + I  + Q  + E
Sbjct: 144 RDKIPE-IMSVEQFLESE 160

Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|P33179|NIFU_ANASL Nitrogen fixation protein NifU (Fragment) OS=Anabaena sp. (strain L31) GN=nifU PE=3 SV=1

 Score = 73.2 bits (178), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 39/104 (37%), Positives = 61/104 (58%), Gaps = 6/104 (5%)

Query: 37  IKPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIAD 96
           +K KN+V   +  +   +  +   A +G    L +  +  L  K +D   E+VRP LIAD
Sbjct: 6   VKEKNAV---TNLNTKGVNLTKEIANSGQKRALTNVQKIALIQKVLD---EEVRPVLIAD 59

Query: 97  GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKF 140
           GG++++  V+  +V V LQGACGSCPSST T+ + IE  L+++ 
Sbjct: 60  GGDVELYDVDGDIVKVVLQGACGSCPSSTATLKIAIESRLRDRI 103

May be involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins.

Anabaena sp. (strain L31) (taxid: 29412)

>sp|O32119|YUTI_BACSU Putative nitrogen fixation protein YutI OS=Bacillus subtilis (strain 168) GN=yutI PE=3 SV=1

 Score = 70.9 bits (172), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 44/57 (77%)

Query: 80  KNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVL 136
           + V  VL+ +RP+L+ DGG+ ++V V++G+V ++L GACGSCPSST T+  GIER L
Sbjct: 41  EQVQEVLDKLRPFLLRDGGDCELVDVDEGIVKLRLLGACGSCPSSTITLKAGIERAL 97

May be involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins.

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|P20628|NIFU_NOSS1 Nitrogen fixation protein NifU OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=nifU PE=3 SV=1

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 40/103 (38%), Positives = 57/103 (55%), Gaps = 9/103 (8%)

Query: 38  KPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADG 97
           K   ++  K GS  T I  S    P      L +  +  L  K +D   E+VRP LIADG
Sbjct: 198 KAATNLNNKGGSKPTNIPNSGQKRP------LTNVQKIALIQKVLD---EEVRPVLIADG 248

Query: 98  GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKF 140
           G++++  V+  +V V LQGACGSC SST T+ + IE  L+++ 
Sbjct: 249 GDVELYDVDGDIVKVVLQGACGSCSSSTATLKIAIESRLRDRI 291

May be involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q43885|NIFU_TRIAZ Nitrogen fixation protein NifU OS=Trichormus azollae GN=nifU PE=3 SV=1

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 40/103 (38%), Positives = 57/103 (55%), Gaps = 9/103 (8%)

Query: 38  KPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADG 97
           K   ++  K GS  T I  S    P      L +  +  L  K +D   E+VRP LIADG
Sbjct: 198 KAATNLNNKGGSKPTNIPNSGQKRP------LTNVQKIALIQKVLD---EEVRPVLIADG 248

Query: 98  GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKF 140
           G++++  V+  +V V LQGACGSC SST T+ + IE  L+++ 
Sbjct: 249 GDVELYDVDGDIVKVVLQGACGSCSSSTATLKIAIESRLRDRI 291

May be involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins.

Anabaena azollae (taxid: 1164)

>sp|Q9UMS0|NFU1_HUMAN NFU1 iron-sulfur cluster scaffold homolog, mitochondrial OS=Homo sapiens GN=NFU1 PE=1 SV=2

 Score = 64.3 bits (155), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 69/134 (51%), Gaps = 9/134 (6%)

Query: 26  TKFNERLQFISIKPK--NSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVD 83
           TK NE L +  +KP    +++    S    +    PS  AGS          ++ A   +
Sbjct: 122 TKENEELDWNLLKPDIYATIMDFFASGLPLVTEETPSGEAGSE------EDDEVVAMIKE 175

Query: 84  LVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDA 143
           L+   +RP +  DGG++     EDG+V +KLQG+C SCPSS  T+  GI+ +L + +   
Sbjct: 176 LLDTRIRPTVQEDGGDVIYKGFEDGIVQLKLQGSCTSCPSSIITLKNGIQNML-QFYIPE 234

Query: 144 IKDIRQVYDEEVRE 157
           ++ + QV D+E  E
Sbjct: 235 VEGVEQVMDDESDE 248

Iron-sulfur cluster scaffold protein which can assemble [4Fe-2S] clusters and deliver them to target proteins.

Homo sapiens (taxid: 9606)

>sp|B4JWR9|NFU1_DROGR NFU1 iron-sulfur cluster scaffold homolog, mitochondrial OS=Drosophila grimshawi GN=GH17809 PE=3 SV=1

 Score = 61.6 bits (148), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 44/65 (67%), Gaps = 1/65 (1%)

Query: 89  VRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIR 148
           +RP +  DGG+I  +S E GVV +K+QG+C SCPSS  T+  G++ +L + +   ++ + 
Sbjct: 202 IRPTVQEDGGDIVFISYEKGVVKLKMQGSCSSCPSSIVTLKNGVQNML-QFYIPEVESVE 260

Query: 149 QVYDE 153
           QV+DE
Sbjct: 261 QVFDE 265

Molecular scaffold for [Fe-S] cluster assembly of mitochondrial iron-sulfur proteins.

Drosophila grimshawi (taxid: 7222)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
225437626	213	PREDICTED: nifU-like protein 1, chloropl	0.781	0.671	0.696	1e-53
224064633	216	predicted protein [Populus trichocarpa]	0.601	0.509	0.794	2e-45
255548369	210	Nitrogen fixation protein nifU, putative	0.808	0.704	0.627	6e-44
4558563	174	putative NifU-like metallocluster assemb	0.792	0.833	0.602	2e-43
351727691	221	uncharacterized protein LOC100527356 [Gl	0.535	0.443	0.820	2e-43
18411785	231	NifU-like protein 1 [Arabidopsis thalian	0.781	0.619	0.597	2e-42
357511421	216	NifU-like protein [Medicago truncatula]	0.639	0.541	0.728	1e-41
449436401	220	PREDICTED: nifU-like protein 1, chloropl	0.595	0.495	0.783	5e-41
224130940	220	predicted protein [Populus trichocarpa]	0.841	0.7	0.557	1e-40
388492810	225	unknown [Lotus japonicus]	0.513	0.417	0.829	2e-39

>gi|225437626|ref|XP_002278510.1| PREDICTED: nifU-like protein 1, chloroplastic [Vitis vinifera] gi|297744011|emb|CBI36981.3| unnamed protein product [Vitis vinifera]

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 110/158 (69%), Positives = 128/158 (81%), Gaps = 15/158 (9%)

Query: 4   LSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRASNPSAPA 63
           LS  +A R+SKT     K+Q           + +KP  +VLQ+     TAI+ASNPSAP+
Sbjct: 9   LSQNSAFRLSKTSVKPQKNQ---------PIVRLKPLRTVLQR-----TAIKASNPSAPS 54

Query: 64  GSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPS 123
           GS PGLYSAH+F+LTAKNVDLVLEDVRPYLI+DGGN+DVVSVEDGV+S+KLQGACGSCPS
Sbjct: 55  GS-PGLYSAHKFELTAKNVDLVLEDVRPYLISDGGNVDVVSVEDGVISLKLQGACGSCPS 113

Query: 124 STTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           STTTM+MGIERVLKEKFGDA+KDIRQVYDE+  ETTVE
Sbjct: 114 STTTMTMGIERVLKEKFGDAVKDIRQVYDEQTGETTVE 151

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064633|ref|XP_002301529.1| predicted protein [Populus trichocarpa] gi|222843255|gb|EEE80802.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 89/112 (79%), Positives = 100/112 (89%), Gaps = 2/112 (1%)

Query: 50  HETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGV 109
           H+TAI+A+ P+    SSPGLYSA QF+L  +NVDLVLE+VRPYLIADGGN+DVVSVEDGV
Sbjct: 45  HKTAIKATAPTG--SSSPGLYSAQQFELNPQNVDLVLEEVRPYLIADGGNVDVVSVEDGV 102

Query: 110 VSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           +S+KLQGACG CPSSTTTM MGIERVLKEKFGDAIKDIRQV DEE +ETTVE
Sbjct: 103 ISLKLQGACGDCPSSTTTMKMGIERVLKEKFGDAIKDIRQVSDEESKETTVE 154

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548369|ref|XP_002515241.1| Nitrogen fixation protein nifU, putative [Ricinus communis] gi|223545721|gb|EEF47225.1| Nitrogen fixation protein nifU, putative [Ricinus communis]

 Score =  182 bits (462), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 101/161 (62%), Positives = 120/161 (74%), Gaps = 13/161 (8%)

Query: 1   MACLSLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRASNPS 60
           MA L+ TA ++I   P    K   P   +   Q I++K +  VL K     TAI+A+  S
Sbjct: 1   MASLAFTAPSKI---PPYCPK--IPANTHRYPQSITMKTR-VVLSK-----TAIKAT--S 47

Query: 61  APAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGS 120
                SPGLYSA +F+LT +NVDLVLEDVRPYLIADGGN+DVVSVEDGV+S++LQGACGS
Sbjct: 48  QTGSQSPGLYSAQKFELTPENVDLVLEDVRPYLIADGGNVDVVSVEDGVISLQLQGACGS 107

Query: 121 CPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           CPSSTTTM MGIERVLKEKFGD++KDIRQV DEEV+ETT E
Sbjct: 108 CPSSTTTMKMGIERVLKEKFGDSVKDIRQVNDEEVKETTPE 148

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4558563|gb|AAD22656.1|AC007138_20 putative NifU-like metallocluster assembly factor [Arabidopsis thaliana] gi|7268578|emb|CAB80687.1| putative NifU-like metallocluster assembly factor [Arabidopsis thaliana]

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 91/151 (60%), Positives = 114/151 (75%), Gaps = 6/151 (3%)

Query: 19  SSKSQFPTKFNERLQFISIKPKNSVLQKSG-SHETAIRASNPSA-----PAGSSPGLYSA 72
           S+++ FP   ++   F+    K   + ++   H +AI  S+         +G S GLYSA
Sbjct: 20  STRNGFPVISDQNPSFVLFANKRRHISRTAIFHRSAISGSSQGEKISPLASGVSSGLYSA 79

Query: 73  HQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGI 132
             FDLT +NVDLVLEDVRP+LI+DGGN+DVVSVEDGVVS+KLQGAC SCPSS+TTM+MGI
Sbjct: 80  QTFDLTPQNVDLVLEDVRPFLISDGGNVDVVSVEDGVVSLKLQGACTSCPSSSTTMTMGI 139

Query: 133 ERVLKEKFGDAIKDIRQVYDEEVRETTVEVS 163
           ERVLKEKFGDA+KDIRQV+DEEV++ TVEVS
Sbjct: 140 ERVLKEKFGDALKDIRQVFDEEVKQITVEVS 170

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727691|ref|NP_001238705.1| uncharacterized protein LOC100527356 [Glycine max] gi|255632161|gb|ACU16433.1| unknown [Glycine max]

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 87/106 (82%), Positives = 96/106 (90%)

Query: 56  ASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQ 115
           ASNP+    SSPGLYSA +FDLTA NVDLVL+DVRPYLIADGGN+DVVSVEDGVVS++L+
Sbjct: 52  ASNPNQNESSSPGLYSAKKFDLTASNVDLVLDDVRPYLIADGGNVDVVSVEDGVVSLRLE 111

Query: 116 GACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           GAC SCPSSTTTM+MGIERVLKEKFGDA+KDIRQVY  E RETTVE
Sbjct: 112 GACESCPSSTTTMTMGIERVLKEKFGDAVKDIRQVYLTEPRETTVE 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18411785|ref|NP_567219.1| NifU-like protein 1 [Arabidopsis thaliana] gi|75163233|sp|Q93W77.1|NIFU1_ARATH RecName: Full=NifU-like protein 1, chloroplastic; Short=AtCNfu1; Short=AtCnfU-IVb; Flags: Precursor gi|14517434|gb|AAK62607.1| AT4g01940/T7B11_20 [Arabidopsis thaliana] gi|15215670|gb|AAK91380.1| AT4g01940/T7B11_20 [Arabidopsis thaliana] gi|20908090|gb|AAM26728.1| AT4g01940/T7B11_20 [Arabidopsis thaliana] gi|28207816|emb|CAD55558.1| NFU1 protein [Arabidopsis thaliana] gi|332656703|gb|AEE82103.1| NifU-like protein 1 [Arabidopsis thaliana]

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 89/149 (59%), Positives = 112/149 (75%), Gaps = 6/149 (4%)

Query: 19  SSKSQFPTKFNERLQFISIKPKNSVLQKSG-SHETAIRASNPSA-----PAGSSPGLYSA 72
           S+++ FP   ++   F+    K   + ++   H +AI  S+         +G S GLYSA
Sbjct: 21  STRNGFPVISDQNPSFVLFANKRRHISRTAIFHRSAISGSSQGEKISPLASGVSSGLYSA 80

Query: 73  HQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGI 132
             FDLT +NVDLVLEDVRP+LI+DGGN+DVVSVEDGVVS+KLQGAC SCPSS+TTM+MGI
Sbjct: 81  QTFDLTPQNVDLVLEDVRPFLISDGGNVDVVSVEDGVVSLKLQGACTSCPSSSTTMTMGI 140

Query: 133 ERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           ERVLKEKFGDA+KDIRQV+DEEV++ TVE
Sbjct: 141 ERVLKEKFGDALKDIRQVFDEEVKQITVE 169

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511421|ref|XP_003625999.1| NifU-like protein [Medicago truncatula] gi|355501014|gb|AES82217.1| NifU-like protein [Medicago truncatula] gi|388517667|gb|AFK46895.1| unknown [Medicago truncatula]

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 45  QKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVS 104
           Q S +  T IR+S+ +    SSPGLYSA +F+LTA NVDLVLEDVRPYLI+DGGN+DVVS
Sbjct: 37  QNSRTSTTVIRSSSTANQNQSSPGLYSAQKFELTASNVDLVLEDVRPYLISDGGNVDVVS 96

Query: 105 VEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVY-DEEVRETTVE 161
           VE+GVVS+KLQGAC SCPSSTTTM MGIERVLKEKFGD+I+DI QV+ D++ RETTVE
Sbjct: 97  VENGVVSLKLQGACESCPSSTTTMKMGIERVLKEKFGDSIEDIVQVFDDDQARETTVE 154

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436401|ref|XP_004135981.1| PREDICTED: nifU-like protein 1, chloroplastic-like [Cucumis sativus] gi|449515245|ref|XP_004164660.1| PREDICTED: nifU-like protein 1, chloroplastic-like [Cucumis sativus]

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 87/111 (78%), Positives = 95/111 (85%), Gaps = 2/111 (1%)

Query: 53  AIRAS--NPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVV 110
           AIRAS  N      SSPGLYSA +F+LT  NVDLVLEDVRPYLIADGGN+DVVSVEDGVV
Sbjct: 48  AIRASPSNSGPSTTSSPGLYSAQKFELTIGNVDLVLEDVRPYLIADGGNVDVVSVEDGVV 107

Query: 111 SVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           S+KL GACGSCPSSTTTM MGIERVLKEKFGD++K+I QVYDEE +ETT E
Sbjct: 108 SLKLVGACGSCPSSTTTMKMGIERVLKEKFGDSVKEICQVYDEEPKETTPE 158

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130940|ref|XP_002320962.1| predicted protein [Populus trichocarpa] gi|222861735|gb|EEE99277.1| predicted protein [Populus trichocarpa]

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/165 (55%), Positives = 117/165 (70%), Gaps = 11/165 (6%)

Query: 1   MACLSLTAATRI----SKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGSHETAIRA 56
           MA L+ TA  +I     K P+I S+   P     + +   +     + QK     TAI+A
Sbjct: 1   MASLASTALPKILPSCPKIPSIISRPCPPQSLTTKQRIPLVGIGRRIFQK-----TAIKA 55

Query: 57  SNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQG 116
           + P+    SSPGL+SA QF+L  +NVDLVLE+VRPYLI+DGGN+DVVSVEDGV+++KLQG
Sbjct: 56  TAPTG--SSSPGLHSAQQFELNPQNVDLVLEEVRPYLISDGGNVDVVSVEDGVITLKLQG 113

Query: 117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           ACG+C SS TTM MGIERVLKEKFGDA++DIRQ+  EE +ETTVE
Sbjct: 114 ACGNCASSETTMKMGIERVLKEKFGDAVQDIRQLSFEEPKETTVE 158

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388492810|gb|AFK34471.1| unknown [Lotus japonicus]

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 78/94 (82%), Positives = 88/94 (93%)

Query: 68  GLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTT 127
           GLYSA +FDLTA NVDLVLEDVRPYLI+DGGN++VVSVE+GV+S+KLQGAC SCPSSTTT
Sbjct: 62  GLYSAAKFDLTAPNVDLVLEDVRPYLISDGGNVEVVSVENGVISLKLQGACESCPSSTTT 121

Query: 128 MSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE 161
           M +GIERVLKEKFGDA+KDI QVYDEE +ETTVE
Sbjct: 122 MKLGIERVLKEKFGDAVKDIVQVYDEEPKETTVE 155

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
TAIR|locus:2141400	231	NFU1 "NFU domain protein 1" [A	0.901	0.714	0.474	7.7e-32
TAIR|locus:2158849	235	NFU2 "NIFU-like protein 2" [Ar	0.420	0.327	0.512	6e-16
UNIPROTKB|P74558	76	ssl2667 "NifU protein" [Synech	0.404	0.973	0.506	3.3e-15
TAIR|locus:2120745	236	NFU3 "NFU domain protein 3" [A	0.420	0.326	0.474	6.2e-14
UNIPROTKB|Q81XP7	78	BAS4821 "NifU domain protein"	0.360	0.846	0.432	3.2e-10
TIGR_CMR|BA_5186	78	BA_5186 "nifU domain protein"	0.360	0.846	0.432	3.2e-10
UNIPROTKB|Q74FX2	74	GSU0480 "Thioredoxin/NifU-like	0.382	0.945	0.458	1.8e-09
TIGR_CMR|GSU_0480	74	GSU_0480 "NifU-like domain pro	0.382	0.945	0.458	1.8e-09
UNIPROTKB|Q3Z623	72	DET1632 "NifU-like protein" [D	0.366	0.930	0.397	2.9e-09
TIGR_CMR|DET_1632	72	DET_1632 "nifU protein, homolo	0.366	0.930	0.397	2.9e-09

TAIR|locus:2141400 NFU1 "NFU domain protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 83/175 (47%), Positives = 108/175 (61%)

Query:     1 MACL--SLTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGS-HETAIRXX 57
             MA L  S++ + RI    + S+++ FP   ++   F+    K   + ++   H +AI   
Sbjct:     2 MASLATSISGSFRIL-VKSSSTRNGFPVISDQNPSFVLFANKRRHISRTAIFHRSAISGS 60

Query:    58 XXXX-----XXXXXXXLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXX 112
                             LYSA  FDLT +NVDLVLEDVRP+LI+DGGN+            
Sbjct:    61 SQGEKISPLASGVSSGLYSAQTFDLTPQNVDLVLEDVRPFLISDGGNVDVVSVEDGVVSL 120

Query:   113 KLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVE-VSALL 166
             KLQGAC SCPSS+TTM+MGIERVLKEKFGDA+KDIRQV+DEEV++ TVE V+A L
Sbjct:   121 KLQGACTSCPSSSTTMTMGIERVLKEKFGDALKDIRQVFDEEVKQITVEAVNAHL 175

GO:0005506 "iron ion binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016226 "iron-sulfur cluster assembly" evidence=IEA;IGI;ISS

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0005198 "structural molecule activity" evidence=TAS

GO:0009658 "chloroplast organization" evidence=ISS

TAIR|locus:2158849 NFU2 "NIFU-like protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 40/78 (51%), Positives = 52/78 (66%)

Query:    77 LTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVL 136
             LT +NV+ VL+++RPYL++DGGN+            KLQGACGSCPSST TM MGIER L
Sbjct:    85 LTEENVESVLDEIRPYLMSDGGNVALHEIDGNIVRVKLQGACGSCPSSTMTMKMGIERRL 144

Query:   137 KEKFGDAIKDIRQVYDEE 154
              EK  + +  +  + DEE
Sbjct:   145 MEKIPEIVA-VEALPDEE 161

GO:0005506 "iron ion binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016226 "iron-sulfur cluster assembly" evidence=IEA;IGI;IMP

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0005198 "structural molecule activity" evidence=TAS

GO:0009658 "chloroplast organization" evidence=IMP

GO:0009570 "chloroplast stroma" evidence=IDA

UNIPROTKB|P74558 ssl2667 "NifU protein" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 38/75 (50%), Positives = 51/75 (68%)

Query:    76 DLTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERV 135
             +LT  NV+ VL+++RPYL+ADGGN+            +LQGACGSCPSST T+ MGIER 
Sbjct:     2 ELTLNNVETVLDELRPYLMADGGNVEVVELDGPIVKVRLQGACGSCPSSTMTLKMGIERK 61

Query:   136 LKEKFGDAIKDIRQV 150
             L+E   + I ++ QV
Sbjct:    62 LREMIPE-IAEVEQV 75

GO:0016226 "iron-sulfur cluster assembly" evidence=IDA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IDA

TAIR|locus:2120745 NFU3 "NFU domain protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 37/78 (47%), Positives = 50/78 (64%)

Query:    77 LTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVL 136
             LT +NV+ VL++VRP L+ADGGN+            KLQGACGSCPSS+ T+ MGIE  L
Sbjct:    84 LTEENVERVLDEVRPSLMADGGNVALHEIDGLVVVLKLQGACGSCPSSSMTLKMGIESRL 143

Query:   137 KEKFGDAIKDIRQVYDEE 154
             ++K  + I  + Q  + E
Sbjct:   144 RDKIPE-IMSVEQFLESE 160

GO:0005506 "iron ion binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;ISS;IDA

GO:0016226 "iron-sulfur cluster assembly" evidence=IEA;IGI;ISS

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0005198 "structural molecule activity" evidence=TAS

GO:0009658 "chloroplast organization" evidence=ISS

GO:0009570 "chloroplast stroma" evidence=IDA

UNIPROTKB|Q81XP7 BAS4821 "NifU domain protein" [Bacillus anthracis (taxid:1392)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 29/67 (43%), Positives = 41/67 (61%)

Query:    85 VLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVLKEKFGDAI 144
             VL+ +RP+L+ DGG++            +L GACGSCPSST T+  GIER L E+    I
Sbjct:    13 VLDKLRPFLLRDGGDVELVDIEEGIVKLRLMGACGSCPSSTITLKAGIERALLEEVPGVI 72

Query:   145 KDIRQVY 151
              ++ QV+
Sbjct:    73 -EVEQVF 78

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_5186 BA_5186 "nifU domain protein" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 29/67 (43%), Positives = 41/67 (61%)

Query:    85 VLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVLKEKFGDAI 144
             VL+ +RP+L+ DGG++            +L GACGSCPSST T+  GIER L E+    I
Sbjct:    13 VLDKLRPFLLRDGGDVELVDIEEGIVKLRLMGACGSCPSSTITLKAGIERALLEEVPGVI 72

Query:   145 KDIRQVY 151
              ++ QV+
Sbjct:    73 -EVEQVF 78

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q74FX2 GSU0480 "Thioredoxin/NifU-like domain protein" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 33/72 (45%), Positives = 42/72 (58%)

Query:    80 KNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXX-KLQGACGSCPSSTTTMSMGIERVLKE 138
             ++V  VL+ VRP L ADGG++             KL GACG CP ST T+ MGIER LKE
Sbjct:     3 EDVKKVLDLVRPALQADGGDVELVEVTEDGVVKVKLVGACGHCPMSTMTLKMGIERTLKE 62

Query:   139 KFGDAIKDIRQV 150
             K    +K++  V
Sbjct:    63 KV-PGVKEVVSV 73

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|GSU_0480 GSU_0480 "NifU-like domain protein" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 33/72 (45%), Positives = 42/72 (58%)

Query:    80 KNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXX-KLQGACGSCPSSTTTMSMGIERVLKE 138
             ++V  VL+ VRP L ADGG++             KL GACG CP ST T+ MGIER LKE
Sbjct:     3 EDVKKVLDLVRPALQADGGDVELVEVTEDGVVKVKLVGACGHCPMSTMTLKMGIERTLKE 62

Query:   139 KFGDAIKDIRQV 150
             K    +K++  V
Sbjct:    63 KV-PGVKEVVSV 73

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q3Z623 DET1632 "NifU-like protein" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 27/68 (39%), Positives = 40/68 (58%)

Query:    80 KNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVLKEK 139
             + V+ VL+ +RP L ADGGN+            KL GAC  CP ST T+  GIE++LK +
Sbjct:     3 EKVEAVLDKIRPALEADGGNVELVEVVDGVVKVKLVGACAGCPMSTMTLKNGIEKILKRE 62

Query:   140 FGDAIKDI 147
               + +K++
Sbjct:    63 IPE-VKEV 69

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|DET_1632 DET_1632 "nifU protein, homolog" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 27/68 (39%), Positives = 40/68 (58%)

Query:    80 KNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVLKEK 139
             + V+ VL+ +RP L ADGGN+            KL GAC  CP ST T+  GIE++LK +
Sbjct:     3 EKVEAVLDKIRPALEADGGNVELVEVVDGVVKVKLVGACAGCPMSTMTLKNGIEKILKRE 62

Query:   140 FGDAIKDI 147
               + +K++
Sbjct:    63 IPE-VKEV 69

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q93W77	NIFU1_ARATH	No assigned EC number	0.5973	0.7814	0.6190	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	183
pfam01106	68	pfam01106, NifU, NifU-like domain	4e-24
COG0694	93	COG0694, COG0694, Thioredoxin-like proteins and do	1e-21
TIGR02000	290	TIGR02000, NifU_proper, Fe-S cluster assembly prot	3e-14
PRK11190	192	PRK11190, PRK11190, Fe/S biogenesis protein NfuA;	2e-04
TIGR03341	190	TIGR03341, YhgI_GntY, IscR-regulated protein YhgI	3e-04

>gnl|CDD|144628 pfam01106, NifU, NifU-like domain

 Score = 89.6 bits (223), Expect = 4e-24
 Identities = 30/64 (46%), Positives = 49/64 (76%)

Query: 82  VDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFG 141
           ++ V++++RP L  DGG+I++V V+  +V V+LQGACG C SST T+  GIER L+E+ G
Sbjct: 1   IEEVIDEIRPMLQRDGGDIELVDVDGDIVKVRLQGACGGCMSSTMTLKGGIERKLRERLG 60

Query: 142 DAIK 145
           ++++
Sbjct: 61  ESLR 64

This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown. Length = 68

>gnl|CDD|223766 COG0694, COG0694, Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]

 Score = 83.9 bits (208), Expect = 1e-21
 Identities = 32/73 (43%), Positives = 50/73 (68%), Gaps = 3/73 (4%)

Query: 82  VDLVLEDVRPYLIADGGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK 139
            +++ E +RP L  DGG++++V ++  DGVV ++L GAC  CPSST T+  GIER LKE+
Sbjct: 15  EEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEE 74

Query: 140 FGDAIKDIRQVYD 152
               +K++ QV +
Sbjct: 75  I-PEVKEVEQVTE 86

Length = 93

>gnl|CDD|233679 TIGR02000, NifU_proper, Fe-S cluster assembly protein NifU

 Score = 68.4 bits (167), Expect = 3e-14
 Identities = 33/108 (30%), Positives = 51/108 (47%), Gaps = 11/108 (10%)

Query: 38  KPKNSVLQKSGSHETAIRASNPSAPAGSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADG 97
           K   +     GS  T    S    P  +   +            +  VLE+VRP L ADG
Sbjct: 190 KGATNPANAGGSKPTNKPNSGQKRPLTNVQRIQL----------IQKVLEEVRPVLQADG 239

Query: 98  GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIK 145
           G++++  V+  +V V L GAC  C  ST T+  GI++ L+E+ G+ + 
Sbjct: 240 GDVELYDVDGKIVYVVLTGACSGCSMSTMTL-KGIQQRLRERLGEFVV 286

Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]. Length = 290

>gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 82  VDLVLE-DVRPYLIADGGNIDVVSV-EDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK 139
           V+ VL+  + P L   GG + ++ + EDG   ++  G C  C     T+  GIE+ L  +
Sbjct: 111 VEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNE 170

Query: 140 FGDAIKDIRQVYDEE 154
           F   +K +R + + +
Sbjct: 171 FPGELKGVRDLTEHQ 185

Length = 192

>gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 32/119 (26%), Positives = 56/119 (47%), Gaps = 16/119 (13%)

Query: 43  VLQKSGSHETAIRASNPSAP--AGSSPGLYSAHQFDLTAKNVDLVLE-DVRPYLIADGGN 99
           V  + G   T ++A N   P  A  +P         L  + ++ VL+ ++ P L + GG 
Sbjct: 80  VTDRMGGQLT-LKAPNAKMPKVADDAP---------LEER-INYVLQSEINPQLASHGGK 128

Query: 100 IDVVSV-EDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRE 157
           + +V + +DGV  ++  G C  C     T+  G+E+ L E+F + +K +R   D    E
Sbjct: 129 VTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPE-LKGVRDATDHTRGE 186

IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]. Length = 190

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
COG0694	93	Thioredoxin-like proteins and domains [Posttransla	99.93
PF01106	68	NifU: NifU-like domain; InterPro: IPR001075 Iron-s	99.92
TIGR03341	190	YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR0	99.9
PRK11190	192	Fe/S biogenesis protein NfuA; Provisional	99.9
KOG2358	213	consensus NifU-like domain-containing proteins [Po	99.84
TIGR02000	290	NifU_proper Fe-S cluster assembly protein NifU. Th	99.83
KOG2358	213	consensus NifU-like domain-containing proteins [Po	98.63
PF01883	72	DUF59: Domain of unknown function DUF59; InterPro:	93.77
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	89.83
TIGR02945	99	SUF_assoc FeS assembly SUF system protein. Members	87.97
PF07315	93	DUF1462: Protein of unknown function (DUF1462); In	85.52

>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]

Probab=99.93  E-value=1.3e-25  Score=169.77  Aligned_cols=80  Identities=43%  Similarity=0.748  Sum_probs=73.2

Q ss_pred             hhchHHHHHHHHH-hhcchhhhCCCcEEEEEee--CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecc
Q 030084           75 FDLTAKNVDLVLE-DVRPYLIADGGNIDVVSVE--DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVY  151 (183)
Q Consensus        75 ~el~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe--dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~  151 (183)
                      .....++|+.+|+ +|||+|+.|||||+|++|+  +|+|+|||.|||+|||||++||+++||++|++.+| ++.+|++++
T Consensus         7 ~~~~~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~-ev~~V~~v~   85 (93)
T COG0694           7 DAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIP-EVKEVEQVT   85 (93)
T ss_pred             cHHHHHHHHHHHHhccCcceeccCCeEEEEEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCC-ccceEEEcc
Confidence            3445678899985 9999999999999999998  88999999999999999999999999999999999 699999998


Q ss_pred             cccc
Q 030084          152 DEEV  155 (183)
Q Consensus       152 d~e~  155 (183)
                      ++..
T Consensus        86 ~~~~   89 (93)
T COG0694          86 EHAR   89 (93)
T ss_pred             Cccc
Confidence            8754

>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron

Probab=99.92  E-value=3.7e-25  Score=157.32  Aligned_cols=68  Identities=50%  Similarity=0.933  Sum_probs=63.2

Q ss_pred             HHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084           82 VDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV  150 (183)
Q Consensus        82 Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V  150 (183)
                      |+.+|++|||+|++||||++|+++++++|+|||+|+|+|||++..||+++||++|++++| ++..|+.|
T Consensus         1 V~~~l~~IrP~L~~dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~-~v~~V~~v   68 (68)
T PF01106_consen    1 VEEVLEEIRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVP-EVKRVVPV   68 (68)
T ss_dssp             HHHHHHHCHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHST-T-SEEEEC
T ss_pred             CHHHHHHhChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCC-CCceEEEC
Confidence            678998899999999999999999999999999999999999999999999999999999 57777654

These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.

>TIGR03341 YhgI_GntY IscR-regulated protein YhgI

Probab=99.90  E-value=5.5e-24  Score=176.92  Aligned_cols=81  Identities=28%  Similarity=0.625  Sum_probs=74.6

Q ss_pred             hchHHHHHHHHH-hhcchhhhCCCcEEEEEee-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084           76 DLTAKNVDLVLE-DVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE  153 (183)
Q Consensus        76 el~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe-dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~  153 (183)
                      +.+.++|+.+|+ +|||+|++|||||||++|+ +++|+|||+|+|+|||++.+||+++||++|++++| +|++|+.+++|
T Consensus       104 ~~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p-~v~~V~~~~~~  182 (190)
T TIGR03341       104 APLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFP-ELKGVRDATDH  182 (190)
T ss_pred             hHHHHHHHHHHHhccCHHHHhcCCceEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCC-CcceEEEecCc
Confidence            446788999996 8999999999999999997 57999999999999999999999999999999999 69999999999


Q ss_pred             cccc
Q 030084          154 EVRE  157 (183)
Q Consensus       154 e~~e  157 (183)
                      +...
T Consensus       183 ~~~~  186 (190)
T TIGR03341       183 TRGE  186 (190)
T ss_pred             cccC
Confidence            7643

IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.

>PRK11190 Fe/S biogenesis protein NfuA; Provisional

Probab=99.90  E-value=4e-24  Score=178.28  Aligned_cols=81  Identities=26%  Similarity=0.579  Sum_probs=74.9

Q ss_pred             chHHHHHHHHH-hhcchhhhCCCcEEEEEee-CCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccc
Q 030084           77 LTAKNVDLVLE-DVRPYLIADGGNIDVVSVE-DGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE  154 (183)
Q Consensus        77 l~~e~Ve~vLe-~IRP~LqsdGGDVELVdVe-dg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e  154 (183)
                      .+.++|+.+|+ +|||+|++|||||||++|+ +++|+|||+|+|+|||||.+||+++||++|++++|++|++|++|++|.
T Consensus       106 ~~~~~i~~~l~~~irP~l~~dGGdielv~v~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~v~~~~  185 (192)
T PRK11190        106 PLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRDLTEHQ  185 (192)
T ss_pred             HHHHHHHHHHHhccChhHHhcCCcEEEEEEcCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEEecccc
Confidence            35678999995 9999999999999999997 689999999999999999999999999999999998899999999997


Q ss_pred             ccc
Q 030084          155 VRE  157 (183)
Q Consensus       155 ~~e  157 (183)
                      ...
T Consensus       186 ~~~  188 (192)
T PRK11190        186 RGE  188 (192)
T ss_pred             cCC
Confidence            543

>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]

Probab=99.84  E-value=3.7e-22  Score=169.23  Aligned_cols=154  Identities=30%  Similarity=0.301  Sum_probs=123.1

Q ss_pred             cccceeeeecccccCCCCCCccccCccceEEeccCCcceeeccc-eeeecccCCCCC-----CCCCCCCCcc----ccch
Q 030084            6 LTAATRISKTPTISSKSQFPTKFNERLQFISIKPKNSVLQKSGS-HETAIRASNPSA-----PAGSSPGLYS----AHQF   75 (183)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-----~~~~~~~l~s----~~~~   75 (183)
                      .++.||.+.++ +.++++++++...++.||.+.|++.++..+-. +...+.-+...+     -++....++.    ++..
T Consensus        44 ~s~~~s~La~s-~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~  122 (213)
T KOG2358|consen   44 CSAFFSPLAKS-ILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDP  122 (213)
T ss_pred             cchhhcHHHHH-HHhhcCCcEEEEecCCeEEEeccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCCh
Confidence            45667888887 88899999999999999999999995544433 332222222221     1223333333    6667


Q ss_pred             hchHHHHHHHHHhhcchhhhCCCcEEEEEeeC--CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084           76 DLTAKNVDLVLEDVRPYLIADGGNIDVVSVED--GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE  153 (183)
Q Consensus        76 el~~e~Ve~vLe~IRP~LqsdGGDVELVdVed--g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~  153 (183)
                      |.+....+.+..+|||.++.||||++++++++  |.|++||+|+|.+||++..||+++||.+|+.++| +|++|+++.|.
T Consensus       123 e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lklqgact~cpss~vtlk~Gie~mL~~y~~-eVK~v~qv~d~  201 (213)
T KOG2358|consen  123 ESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKLQGACTECPSSLVTLKNGIENMLEIYVP-EVKGVIQVPDA  201 (213)
T ss_pred             hHHHHHHHHHHHhhhhhhhccCCceeeccccCccchHHHHHhhhhccCCcccchhhhhHHHHHHhhcc-eeeEEEeccCc
Confidence            77777788888999999999999999999998  5999999999999999999999999999999999 89999999999


Q ss_pred             ccccccHH
Q 030084          154 EVRETTVE  161 (183)
Q Consensus       154 e~~e~s~E  161 (183)
                      |.+++..|
T Consensus       202 e~~~v~~e  209 (213)
T KOG2358|consen  202 EVMTVTVE  209 (213)
T ss_pred             cceEEeee
Confidence            88777655

>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU

Probab=99.83  E-value=1.6e-20  Score=164.82  Aligned_cols=71  Identities=38%  Similarity=0.669  Sum_probs=65.5

Q ss_pred             hHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084           78 TAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV  150 (183)
Q Consensus        78 ~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V  150 (183)
                      ..++|+.+|++|||+|+.|||||+|++|++++|+|||+|+|+|||++.+||+. ||++|++++| ++..|+.|
T Consensus       220 ~~~~v~~~l~~irP~l~~dGGdv~lv~v~~~~v~v~l~GaC~gC~~s~~Tl~~-Ie~~l~~~~p-~~~~V~~v  290 (290)
T TIGR02000       220 RIQLIQKVLEEVRPVLQADGGDVELYDVDGKIVYVVLTGACSGCSMSTMTLKG-IQQRLRERLG-EFVVVEAV  290 (290)
T ss_pred             HHHHHHHHHHHhCchHhhcCCcEEEEEEeCCEEEEEEeeCCCCCcchHHHHHH-HHHHHHHhCC-CceEEEeC
Confidence            34668999999999999999999999999999999999999999999999998 9999999999 57777654

Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.

>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]

Probab=98.63  E-value=2.2e-08  Score=85.71  Aligned_cols=105  Identities=29%  Similarity=0.250  Sum_probs=89.2

Q ss_pred             hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccc
Q 030084           75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE  154 (183)
Q Consensus        75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e  154 (183)
                      +.+++++++.+|...+|++.+|||++-+--+++..+.+++.|+|..||.+++|++.+||..||.++++..-+|..+..+.
T Consensus        75 ~k~~ee~~w~~L~p~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~  154 (213)
T KOG2358|consen   75 TKLTEENVWSVLDPEIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFET  154 (213)
T ss_pred             eccchhhhHhhhchhhHHHHhccccccchhhccchhhhhhcccccCChhHHHHHHHHHHHhhhhhhhccCCceeeccccC
Confidence            34566789999999999999999999999999999999999999999999999999999999999996555555554443


Q ss_pred             cccccHHHHHHHHHHhhhhhhccCC
Q 030084          155 VRETTVEVSALLLCLISDKRYYYTT  179 (183)
Q Consensus       155 ~~e~s~E~In~al~~Lr~a~~~~~~  179 (183)
                      -.++..+.+..|+.-.+.+.-..++
T Consensus       155 g~g~v~lklqgact~cpss~vtlk~  179 (213)
T KOG2358|consen  155 GLGLVSLKLQGACTECPSSLVTLKN  179 (213)
T ss_pred             ccchHHHHHhhhhccCCcccchhhh
Confidence            4589999999999888877655443

>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function

Probab=93.77  E-value=0.41  Score=33.08  Aligned_cols=65  Identities=29%  Similarity=0.407  Sum_probs=47.5

Q ss_pred             HHHHHHH-HhhcchhhhC---CCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           80 KNVDLVL-EDVRPYLIAD---GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        80 e~Ve~vL-e~IRP~Lqsd---GGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      +.|..+| .-.-|.+..+   =|-|+=+.+++|.|+|.|.-...+|+ ....|+.-|+++|+ .+|. +++|
T Consensus         2 ~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i~~~~V~v~l~l~~~~~~-~~~~l~~~i~~~l~-~l~g-v~~V   70 (72)
T PF01883_consen    2 QAVRDALKQVKDPELGKDIVELGMVRDISIEGGKVSVSLELPTPACP-AAEPLREEIREALK-ALPG-VKSV   70 (72)
T ss_dssp             HHHHHHHTT-BETTTSSBTTTTTSEEEEEECTCEEEEEE--SSTTHT-THHHHHHHHHHHHH-TSTT--SEE
T ss_pred             HHHHHHHhCCCCCCCCCCHHHcCCeeEEEEECCEEEEEEEECCCCch-HHHHHHHHHHHHHH-hCCC-CceE
Confidence            5567777 3445666544   47788899999999999999999999 77788899999999 5774 5555

The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.

>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit

Probab=89.83  E-value=1.9  Score=35.02  Aligned_cols=73  Identities=18%  Similarity=0.204  Sum_probs=49.7

Q ss_pred             CCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHhhhh
Q 030084           97 GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLISDK  173 (183)
Q Consensus        97 GGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~Lr~a  173 (183)
                      =|-|.=++++++.|.|.|.-.=.+||... .|++.|+++|++. +  ++.|.-...-.+.=.++=.-++++++||.+
T Consensus        14 LG~Vr~V~v~gd~V~VtIt~Ty~gcpa~e-~L~~~I~~aL~~~-G--v~~V~V~i~~~p~Wt~d~it~~gr~~l~~~   86 (146)
T TIGR02159        14 LGMVREVDVDGGGVVVKFTPTYSGCPALE-VIRQDIRDAVRAL-G--VEVVEVSTSLDPPWTTDWITEDAREKLREY   86 (146)
T ss_pred             cCCeeEEEEECCEEEEEEEeCCCCCchHH-HHHHHHHHHHHhc-C--CCeEEEeEeeCCCCChHHCCHHHHHHHHhc
Confidence            36677778888999999998889999655 7888999999883 4  555533222223344444455667777653

Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.

>TIGR02945 SUF_assoc FeS assembly SUF system protein

Probab=87.97  E-value=4.4  Score=29.63  Aligned_cols=66  Identities=20%  Similarity=0.330  Sum_probs=44.8

Q ss_pred             HHHHHHHHH-hhcchhhhC---CCcEEEEEeeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           79 AKNVDLVLE-DVRPYLIAD---GGNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        79 ~e~Ve~vLe-~IRP~Lqsd---GGDVELVdVed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      .+.|..+|+ -.-|.+..+   =|-|.=+.+++ +.|+|.|.-...+|+.... ++..++++|.. ++ .++.|
T Consensus         3 ~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v~~~~~v~i~l~l~~p~~~~~~~-l~~~i~~al~~-l~-gv~~v   73 (99)
T TIGR02945         3 KDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGS-MPGEVENAVRA-VP-GVGSV   73 (99)
T ss_pred             HHHHHHHHcCCCCCCCCCCeecCCCeeEEEECCCCeEEEEEEECCCCCChHHH-HHHHHHHHHHh-CC-CCceE
Confidence            456777774 444555542   34555567775 8999999988888886554 77888888876 55 35655

Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.

>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues

Probab=85.52  E-value=2.3  Score=32.84  Aligned_cols=52  Identities=23%  Similarity=0.245  Sum_probs=30.9

Q ss_pred             cCCCCcchHHHHHHHHHHHHHHHccccccceeeccccccccccHHHHHHHHHHh
Q 030084          117 ACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVRETTVEVSALLLCLI  170 (183)
Q Consensus       117 ACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~e~s~E~In~al~~L  170 (183)
                      +|.+=|||..|. .++|.+|++++|+.--.+.-|+-+++.+- ++.-+-+.+|+
T Consensus        11 SCVn~PsSkeTy-eWL~aal~RKyp~~~f~~~YiDi~~p~~~-~~~~~~a~~I~   62 (93)
T PF07315_consen   11 SCVNAPSSKETY-EWLEAALKRKYPDQPFEFTYIDIENPPEN-DHDQQFAERIL   62 (93)
T ss_dssp             GGSSS--HHHHH-HHHHHHHHHH-TTS-EEEEEEETTT-----HHHHHHHHHHH
T ss_pred             hhcCCCCchhHH-HHHHHHHhCcCCCCceEEEEEecCCCCcc-HHHHHHHHHHH
Confidence            455668899998 79999999999975456666765554333 44444454544

A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
2z51_A	154	Crystal Structure Of Arabidopsis Cnfu Involved In I		1e-16
2jnv_A	91	Solution Structure Of C-Terminal Domain Of Nifu-Lik		2e-14
1xhj_A	88	Solution Structure Of The Staphylococcus Epidermidi		7e-10
1veh_A	92	Solution Structure Of Rsgi Ruh-018, A Nifu-Like Dom		2e-04

>pdb|2Z51|A Chain A, Crystal Structure Of Arabidopsis Cnfu Involved In Iron- Sulfur Cluster Biosynthesis Length = 154

Iteration: 1
 Score = 82.4 bits (202), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/78 (51%), Positives = 52/78 (66%), Gaps = 1/78 (1%)
Query: 77  LTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVL 136
           LT +NV+ VL+++RPYL++DGGN+            KLQGACGSCPSST TM MGIER L
Sbjct: 4   LTEENVESVLDEIRPYLMSDGGNVALHEIDGNVVRVKLQGACGSCPSSTMTMKMGIERRL 63
Query: 137 KEKFGDAIKDIRQVYDEE 154
            EK  + +  +  + DEE
Sbjct: 64  MEKIPEIVA-VEALPDEE 80

>pdb|2JNV|A Chain A, Solution Structure Of C-Terminal Domain Of Nifu-Like Protein From Oryza Sativa Length = 91

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/80 (50%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 75  FDLTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIER 134
             LTA NV+ VL+ VRPYL ADGG++            KLQGACGSCPSS  T+  GIER
Sbjct: 3   LPLTAGNVESVLDQVRPYLTADGGDVALHEIAGNVVRLKLQGACGSCPSSLITIKRGIER 62
Query: 135 VLKEKFGDAIKDIRQVYDEE 154
            L EK  D +  +  V D+E
Sbjct: 63  RLMEKIPD-VAAVEPVTDKE 81

>pdb|1XHJ|A Chain A, Solution Structure Of The Staphylococcus Epidermidis Protein Se0630. Northest Structural Genomics Consortium Target Ser8 Length = 88

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 45/79 (56%), Gaps = 5/79 (6%)
Query: 75  FDLTAKNVDLVLEDVRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIER 134
           FD  A+    V+E +RP+L+ DGG+             +L GACG+CPSST T+  GIER
Sbjct: 9   FDQVAE----VIERLRPFLLRDGGDCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIER 64
Query: 135 VLKEKFGDAIKDIRQVYDE 153
            L E+    I ++ QV+ E
Sbjct: 65  ALHEEVPGVI-EVEQVFLE 82

>pdb|1VEH|A Chain A, Solution Structure Of Rsgi Ruh-018, A Nifu-Like Domain Of Hirip5 Protein From Mouse Cdna Length = 92

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 89  VRPYLIADGGNIXXXXXXXXXXXXKLQGACGSCPSSTTTMSMGIERVLK 137
           +RP +  DGG++            KLQG+C SCPSS  T+  GI+ +L+
Sbjct: 26  IRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNMLQ 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
1xhj_A	88	Nitrogen fixation protein NIFU; alpha-beta, NIFU-l	5e-33
2z51_A	154	NIFU-like protein 2, chloroplast; CNFU, iron-sulfu	6e-32
2z51_A	154	NIFU-like protein 2, chloroplast; CNFU, iron-sulfu	2e-17
1veh_A	92	NIFU-like protein hirip5; structural genomics, mou	6e-27
1th5_A	74	NIFU1; iron-sulfur cluster binding, structural gen	2e-25

>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structur initiative, NESG, PSI; NMR {Staphylococcus epidermidis} SCOP: d.52.8.1 Length = 88

 Score =  112 bits (282), Expect = 5e-33
 Identities = 35/79 (44%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 76  DLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERV 135
                 V  V+E +RP+L+ DGG+  +V VEDG+V ++L GACG+CPSST T+  GIER 
Sbjct: 6   PTMFDQVAEVIERLRPFLLRDGGDCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERA 65

Query: 136 LKEKFGDAIKDIRQVYDEE 154
           L E+    + ++ QV+ E 
Sbjct: 66  LHEEV-PGVIEVEQVFLEH 83

>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Length = 154

 Score =  111 bits (279), Expect = 6e-32
 Identities = 44/79 (55%), Positives = 58/79 (73%), Gaps = 1/79 (1%)

Query: 76  DLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERV 135
            LT +NV+ VL+++RPYL++DGGN+ +  ++  VV VKLQGACGSCPSST TM MGIER 
Sbjct: 3   PLTEENVESVLDEIRPYLMSDGGNVALHEIDGNVVRVKLQGACGSCPSSTMTMKMGIERR 62

Query: 136 LKEKFGDAIKDIRQVYDEE 154
           L EK  + I  +  + DEE
Sbjct: 63  LMEKIPE-IVAVEALPDEE 80

>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A Length = 154

 Score = 74.1 bits (182), Expect = 2e-17
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 6/82 (7%)

Query: 70  YSAHQFDLTAKNVDLVLEDVRPYLIAD-GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTM 128
                 +L  +N++ VLE++RPYLI    G++D+V +ED +V +++ G      +   T+
Sbjct: 78  DEETGLELNEENIEKVLEEIRPYLIGTADGSLDLVEIEDPIVKIRITGPA----AGVMTV 133

Query: 129 SMGIERVLKEKFGDAIKDIRQV 150
            + + + L+EK    I  ++ +
Sbjct: 134 RVAVTQKLREKIPS-IAAVQLI 154

>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

 Score = 97.0 bits (242), Expect = 6e-27
 Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 64  GSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPS 123
           GSS    S    ++ A   +L+   +RP +  DGG++     EDG+V +KLQG+C SCPS
Sbjct: 1   GSSGSSGSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPS 60

Query: 124 STTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154
           S  T+  GI+ +L+    + ++ + QV    
Sbjct: 61  SIITLKSGIQNMLQFYIPE-VEGVEQVSGPS 90

>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

 Score = 92.3 bits (230), Expect = 2e-25
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 76  DLTAKNVDLVLEDVRPYLIAD-GGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIER 134
           +L  +NV+ VL ++RPYL    GG +  + ++  +V V+L G      +   T+ + + +
Sbjct: 3   ELNEENVEKVLNEIRPYLAGTGGGGLQFLMIKGPIVKVRLTGPA----AVVRTVRIAVSK 58

Query: 135 VLKEKFGDAIKDIRQV 150
            L+EK    I+ ++ +
Sbjct: 59  KLREKIPS-IQIVQLL 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
2z51_A	154	NIFU-like protein 2, chloroplast; CNFU, iron-sulfu	99.96
1xhj_A	88	Nitrogen fixation protein NIFU; alpha-beta, NIFU-l	99.95
1veh_A	92	NIFU-like protein hirip5; structural genomics, mou	99.93
1th5_A	74	NIFU1; iron-sulfur cluster binding, structural gen	99.89
2z51_A	154	NIFU-like protein 2, chloroplast; CNFU, iron-sulfu	99.82
3cq1_A	103	Putative uncharacterized protein TTHB138; DTDP-4-k	97.05
1uwd_A	103	Hypothetical protein TM0487; similar to PAAD prote	96.6
3lno_A	108	Putative uncharacterized protein; alpha-beta fold,	96.39
1xg8_A	111	Hypothetical protein SA0798; structural genomics,	86.88
1th5_A	74	NIFU1; iron-sulfur cluster binding, structural gen	84.13

>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A

Probab=99.96  E-value=2.4e-30  Score=208.38  Aligned_cols=107  Identities=45%  Similarity=0.642  Sum_probs=99.3

Q ss_pred             hhchHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeeccccc
Q 030084           75 FDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE  154 (183)
Q Consensus        75 ~el~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e  154 (183)
                      ++++.++|+.+|++|||+|++|||||+|++|++++|+|||+|+|+|||+|.+||+++||++|++++| +++.|+.+.+++
T Consensus         2 ~~~~~e~v~~~L~~iRP~l~~dGGdvelv~v~~~~V~v~l~GaC~gC~ss~~Tlk~~Ie~~L~~~vp-ev~~V~~v~~~~   80 (154)
T 2z51_A            2 VPLTEENVESVLDEIRPYLMSDGGNVALHEIDGNVVRVKLQGACGSCPSSTMTMKMGIERRLMEKIP-EIVAVEALPDEE   80 (154)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHTTEEEEEEEEETTEEEEEEEHHHHTCHHHHHHHHHHHHHHHHHHCT-TCCEEEECCSSC
T ss_pred             CcchHHHHHHHHHHhChHHHhcCCeEEEEEEECCEEEEEEECCCCCCCccHhHHHHHHHHHHHHhCC-CceEEEEccCch
Confidence            3567889999999999999999999999999999999999999999999999999999999999998 699999998876


Q ss_pred             c-ccccHHHHHHHHHHhhhhhhc-cCCccc
Q 030084          155 V-RETTVEVSALLLCLISDKRYY-YTTAVP  182 (183)
Q Consensus       155 ~-~e~s~E~In~al~~Lr~a~~~-~~~~~~  182 (183)
                      . .+++.|.|+++|+.+||++.. .||.|-
T Consensus        81 e~l~L~~~~v~~~L~~iRP~L~~~dGGdve  110 (154)
T 2z51_A           81 TGLELNEENIEKVLEEIRPYLIGTADGSLD  110 (154)
T ss_dssp             CSCCSSHHHHHHHHHHHGGGCCGGGCCEEE
T ss_pred             hhhHHHHHHHHHHHHHHHHHhhhcCCCCeE
Confidence            5 378999999999999999997 898763

>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structur initiative, NESG, PSI; NMR {Staphylococcus epidermidis} SCOP: d.52.8.1

Probab=99.95  E-value=6.8e-28  Score=179.06  Aligned_cols=76  Identities=46%  Similarity=0.852  Sum_probs=71.6

Q ss_pred             chHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084           77 LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE  153 (183)
Q Consensus        77 l~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~  153 (183)
                      .+.++|+.+|++|||+|++|||||+|++|++|+|+|||+|||+|||||++||+++||++|++++| +|+.|++++++
T Consensus         7 ~~~~~I~~~L~~IRP~L~~dGGdvelv~v~~g~V~V~L~GaC~gCpss~~TLk~gIE~~L~~~vP-ev~~V~~v~~~   82 (88)
T 1xhj_A            7 TMFDQVAEVIERLRPFLLRDGGDCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHEEVP-GVIEVEQVFLE   82 (88)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHSCEEEEEECCSSEEEEEEESSCCSSCHHHHHHHHHHHHHHHHHST-TCCEEEEEECC
T ss_pred             HHHHHHHHHHHHhcHHHHhcCCeEEEEEEECCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCC-CceEEEecccc
Confidence            44677999998899999999999999999999999999999999999999999999999999997 79999999765

>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

Probab=99.93  E-value=1.4e-26  Score=173.11  Aligned_cols=78  Identities=33%  Similarity=0.588  Sum_probs=72.5

Q ss_pred             chHHHHHHHHH-hhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccccc
Q 030084           77 LTAKNVDLVLE-DVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEV  155 (183)
Q Consensus        77 l~~e~Ve~vLe-~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~  155 (183)
                      .+.++|+.+|+ +|||+|++|||||+|++|++|+|+|||+|||+|||||.+||+++||++|++++| +++.|++|.+++.
T Consensus        13 ~~~~~I~~~L~~~IRP~L~~dGGdvelv~v~~g~V~v~l~GaC~gC~ss~~Tlk~gIE~~L~~~vp-ev~~V~~v~~~~~   91 (92)
T 1veh_A           13 EVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNMLQFYIP-EVEGVEQVSGPSS   91 (92)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHSCCCCEEEEETTEEEECCCCCCCCCHHHHHHTHHHHHHHHHHHCS-SCCCEEECSCSCC
T ss_pred             HHHHHHHHHHHHHhhHHHHhcCCeEEEEEEeCCEEEEEEeecCCCCCCcHHHHHHHHHHHHHHHCC-CCCEEEEcCCCCC
Confidence            44677999996 699999999999999999999999999999999999999999999999999998 6999999987753

>1th5_A NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa} SCOP: d.52.8.1

Probab=99.89  E-value=4.4e-24  Score=154.07  Aligned_cols=71  Identities=28%  Similarity=0.619  Sum_probs=66.7

Q ss_pred             hhchHHHHHHHHHhhcchhhhCC-CcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084           75 FDLTAKNVDLVLEDVRPYLIADG-GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV  150 (183)
Q Consensus        75 ~el~~e~Ve~vLe~IRP~LqsdG-GDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V  150 (183)
                      ++++.++|+.+|++|||+|++|| ||++|++|++|+|+|||+|||+||    +||+++||++|++++| +++.|+.|
T Consensus         2 ~~~~~~~V~~~L~~iRP~L~~dGGGdvelv~v~~g~V~v~l~GaC~gc----~Tlk~gIe~~L~~~vp-ei~~V~~v   73 (74)
T 1th5_A            2 LELNEENVEKVLNEIRPYLAGTGGGGLQFLMIKGPIVKVRLTGPAAVV----RTVRIAVSKKLREKIP-SIQIVQLL   73 (74)
T ss_dssp             CCCSHHHHHHHHTTTHHHHTTTTCCCCCCCEEETTEEEECCCSSSSSS----SSHHHHHHHHHHHHCT-TCSEEEEC
T ss_pred             hhHHHHHHHHHHHHHhHHHHhcCCCcEEEEEEeCCEEEEEEecCCcch----HHHHHHHHHHHHHHCC-CCcEEEeC
Confidence            46778999999999999999999 999999999999999999999999    6999999999999998 59999876

>2z51_A NIFU-like protein 2, chloroplast; CNFU, iron-sulfur cluster biosynthesis, metal transport; 1.35A {Arabidopsis thaliana} PDB: 2jnv_A

Probab=99.82  E-value=1.4e-20  Score=151.42  Aligned_cols=72  Identities=31%  Similarity=0.683  Sum_probs=66.6

Q ss_pred             chhchHHHHHHHHHhhcchhhh-CCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084           74 QFDLTAKNVDLVLEDVRPYLIA-DGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV  150 (183)
Q Consensus        74 ~~el~~e~Ve~vLe~IRP~Lqs-dGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V  150 (183)
                      .++++.++|+.+|++|||+|++ ||||+||++|++++|+|||+|+|+||    +|++.+||++|++++| +|++|+++
T Consensus        82 ~l~L~~~~v~~~L~~iRP~L~~~dGGdvelv~v~~~~v~v~l~Gac~~~----~Tlk~~Ie~~l~e~vP-~i~~V~~~  154 (154)
T 2z51_A           82 GLELNEENIEKVLEEIRPYLIGTADGSLDLVEIEDPIVKIRITGPAAGV----MTVRVAVTQKLREKIP-SIAAVQLI  154 (154)
T ss_dssp             SCCSSHHHHHHHHHHHGGGCCGGGCCEEEEEEEETTEEEEEEESGGGGC----HHHHHHHHHHHHHHCT-TCCEEEEC
T ss_pred             hhHHHHHHHHHHHHHHHHHhhhcCCCCeEEEEEECCEEEEEEecCCccc----HhHHHHHHHHHHHHCC-CccEEEeC
Confidence            3567889999999999999997 99999999999999999999999998    7999999999999998 69988764

>3cq1_A Putative uncharacterized protein TTHB138; DTDP-4-keto-L-rhamnose reductase, plasmid, oxidoreductase, structural genomics, NPPSFA; 1.90A {Thermus thermophilus} PDB: 2cu6_A 3cq2_A 3cq3_A*

Probab=97.05  E-value=0.0016  Score=47.62  Aligned_cols=67  Identities=19%  Similarity=0.250  Sum_probs=55.9

Q ss_pred             hHHHHHHHHH-hhcchhhhCC---CcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           78 TAKNVDLVLE-DVRPYLIADG---GNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        78 ~~e~Ve~vLe-~IRP~LqsdG---GDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      +.+.|..+|. -+.|.+..+-   |-|.=++++++.|+|.|...+.+||. ..+++..|+++|++ +| .++.|
T Consensus         7 ~~~~V~~aL~~V~DPel~~~iv~lG~V~~v~v~~~~V~v~l~lt~~~cp~-~~~l~~~i~~al~~-l~-gv~~V   77 (103)
T 3cq1_A            7 LEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPL-HDSLGEAVRQALSR-LP-GVEEV   77 (103)
T ss_dssp             HHHHHHHHHTTCBCTTTCSBTTTTTCEEEEEEETTEEEEEECCSSSSCCS-SCHHHHHHHHHHHT-ST-TCCEE
T ss_pred             HHHHHHHHHhCCCCCCCCcCchhcCceEEEEEECCEEEEEEEECCCCCcH-HHHHHHHHHHHHHh-CC-CceeE
Confidence            4567888885 4779998887   88888999999999999999999998 66888999999985 66 36665

>1uwd_A Hypothetical protein TM0487; similar to PAAD protein, alpha/beta fold,structural genomics joint center for structural genomics, JCSG; NMR {Thermotoga maritima} SCOP: d.52.8.2 PDB: 1wcj_A

Probab=96.60  E-value=0.0054  Score=44.60  Aligned_cols=68  Identities=21%  Similarity=0.271  Sum_probs=54.6

Q ss_pred             chHHHHHHHHHhhc-chhhhCC---CcEEEEEeeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           77 LTAKNVDLVLEDVR-PYLIADG---GNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        77 l~~e~Ve~vLe~IR-P~LqsdG---GDVELVdVed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      .+.+.|..+|..|. |.+..+-   |-|.=+++++ |.|+|.|.-.+.+||. ...++..|+++|++ +| .++.|
T Consensus         6 ~~~~~V~~aL~~V~DPel~~~iv~lG~V~~v~v~~~~~V~v~l~lt~~~cp~-~~~l~~~i~~al~~-l~-gv~~v   78 (103)
T 1uwd_A            6 VTKEDVLNALKNVIDFELGLDVVSLGLVYDIQIDDQNNVKVLMTMTTPMCPL-AGMILSDAEEAIKK-IE-GVNNV   78 (103)
T ss_dssp             CCHHHHHHHHTTCBCTTTSSBTTTTTCCCCEEECTTCEEEEEECCSSSCCSS-HHHHHHHHHHHHHT-SS-SCCEE
T ss_pred             chHHHHHHHHcCCCCCCCCcChhhcCCeeEEEEcCCCEEEEEEEECCCCCcH-HHHHHHHHHHHHHh-CC-CcceE
Confidence            34677889997666 9887765   6677778875 8999999999999997 67888999999986 65 36665

>3lno_A Putative uncharacterized protein; alpha-beta fold, structural genomics, center for structural genomics of infectious diseases, csgid; 2.10A {Bacillus anthracis} SCOP: d.52.8.0

Probab=96.39  E-value=0.0074  Score=44.59  Aligned_cols=88  Identities=15%  Similarity=0.195  Sum_probs=62.6

Q ss_pred             cchhchHHHHHHHHHh-hcchhhhC---CCcEEEEEeeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           73 HQFDLTAKNVDLVLED-VRPYLIAD---GGNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        73 ~~~el~~e~Ve~vLe~-IRP~Lqsd---GGDVELVdVed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      ..-+.+.+.|..+|.. +-|.+..+   -|-|.=+.+++ |.|+|.|.-...+||.. ..++..|+++|+..+| .++.|
T Consensus         4 ~~~~~~~~~V~~aL~~V~DPe~~~~Iv~lG~V~~I~v~~~~~V~V~ltlt~p~cp~~-~~i~~~i~~al~~~l~-Gv~~V   81 (108)
T 3lno_A            4 MSQEAFENKLYANLEAVIDPELGVDIVNLGLVYDVTADENNNAVITMTMTSIGCPMA-GQIVSDVKKVLSTNVP-EVNEI   81 (108)
T ss_dssp             HHHHHHHHHHHHHGGGCEETTTTEEHHHHTCEEEEEECTTCCEEEEECCSCTTCTTH-HHHHHHHHHHHHHHCT-TCCCE
T ss_pred             cchhhhHHHHHHHHcCCCCCCCCCCHHHcCCceEEEECCCCeEEEEEEECCCCCcHH-HHHHHHHHHHHHHhCC-CCceE
Confidence            3445667788888854 47777544   57788888875 89999999999999976 4888999999955577 47776


Q ss_pred             ee-cccc---ccccccHHH
Q 030084          148 RQ-VYDE---EVRETTVEV  162 (183)
Q Consensus       148 ~~-V~d~---e~~e~s~E~  162 (183)
                      .- ++.+   .++-+|+|.
T Consensus        82 ~V~l~~~p~W~~~~~s~~~  100 (108)
T 3lno_A           82 EVNVVWNPPWSKERMSRMA  100 (108)
T ss_dssp             EEEECCSSCCCGGGSCHHH
T ss_pred             EEEEEecCCCChHHCCHHH
Confidence            33 3322   144566554

>1xg8_A Hypothetical protein SA0798; structural genomics, protein structure initative, MCSG, PSI, protein structure initiative; 2.10A {Staphylococcus aureus subsp} SCOP: c.47.1.17

Probab=86.88  E-value=1.2  Score=34.16  Aligned_cols=53  Identities=13%  Similarity=0.107  Sum_probs=35.1

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHccccccceeeccccc-cccccHHHHHHHHHHhh
Q 030084          118 CGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEE-VRETTVEVSALLLCLIS  171 (183)
Q Consensus       118 CsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e-~~e~s~E~In~al~~Lr  171 (183)
                      |.+=|||..|. .++|.+|++++|+.--.+.-|+-++ +++++++.-+-+.+|+.
T Consensus        22 CVnaPSSkeTy-EWLqAal~RKyp~~~f~~~YIDI~~~~~~l~d~~~~~ae~I~e   75 (111)
T 1xg8_A           22 CVNAPTSKDIY-DWLQPLLKRKYPNISFKYTYIDITKDNDNLTDHDLQFIERIEQ   75 (111)
T ss_dssp             GSSSCCHHHHH-HHHHHHHHHHCTTSCEEEEEEETTTC---CCHHHHHHHHHHHT
T ss_pred             ccCCCCchhHH-HHHHHHHhCcCCCCceEEEEEeccCCccchhHHHHHHHHHHhh
Confidence            44558888888 7999999999997656676775554 33445555555555543

>1th5_A NIFU1; iron-sulfur cluster binding, structural genomics, program for RICE genome research, unknown function; NMR {Oryza sativa} SCOP: d.52.8.1

Probab=84.13  E-value=0.56  Score=33.16  Aligned_cols=26  Identities=15%  Similarity=-0.112  Sum_probs=23.0

Q ss_pred             cccHHHHHHHHHHhhhhhhccC-Cccc
Q 030084          157 ETTVEVSALLLCLISDKRYYYT-TAVP  182 (183)
Q Consensus       157 e~s~E~In~al~~Lr~a~~~~~-~~~~  182 (183)
                      +...|.|+++|+.+||+++..| |.+-
T Consensus         3 ~~~~~~V~~~L~~iRP~L~~dGGGdve   29 (74)
T 1th5_A            3 ELNEENVEKVLNEIRPYLAGTGGGGLQ   29 (74)
T ss_dssp             CCSHHHHHHHHTTTHHHHTTTTCCCCC
T ss_pred             hHHHHHHHHHHHHHhHHHHhcCCCcEE
Confidence            4678999999999999999999 7664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	183
d1xhja_	88	d.52.8.1 (A:) Nitrogen fixation protein NifU homol	2e-25
d1veha_	92	d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {	7e-22
d1th5a1	73	d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {	8e-22

>d1xhja_ d.52.8.1 (A:) Nitrogen fixation protein NifU homolog SE0630 {Staphylococcus epidermidis [TaxId: 1282]} Length = 88

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: Nitrogen fixation protein NifU homolog SE0630
species: Staphylococcus epidermidis [TaxId: 1282]

 Score = 91.8 bits (228), Expect = 2e-25
 Identities = 35/74 (47%), Positives = 51/74 (68%), Gaps = 1/74 (1%)

Query: 80  KNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEK 139
             V  V+E +RP+L+ DGG+  +V VEDG+V ++L GACG+CPSST T+  GIER L E+
Sbjct: 10  DQVAEVIERLRPFLLRDGGDCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHEE 69

Query: 140 FGDAIKDIRQVYDE 153
               + ++ QV+ E
Sbjct: 70  VPG-VIEVEQVFLE 82

>d1veha_ d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 92

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 = 82.6 bits (204), Expect = 7e-22
 Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 64  GSSPGLYSAHQFDLTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPS 123
           GSS    S    ++ A   +L+   +RP +  DGG++     EDG+V +KLQG+C SCPS
Sbjct: 1   GSSGSSGSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPS 60

Query: 124 STTTMSMGIERVLKEKFGDAIKDIRQVYDEE 154
           S  T+  GI+ +L+    + ++ + QV    
Sbjct: 61  SIITLKSGIQNMLQFYIPE-VEGVEQVSGPS 90

>d1th5a1 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId: 4530]} Length = 73

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: NifU-like protein 1, NIFUL1
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 82.1 bits (203), Expect = 8e-22
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 76  DLTAKNVDLVLEDVRPYLIA-DGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIER 134
           +L  +NV+ VL ++RPYL    GG +  + ++  +V V+L G          T+ + + +
Sbjct: 2   ELNEENVEKVLNEIRPYLAGTGGGGLQFLMIKGPIVKVRLTGPAAVVR----TVRIAVSK 57

Query: 135 VLKEKFGDAIKDIRQV 150
            L+EK    I+ ++ +
Sbjct: 58  KLREKIPS-IQIVQLL 72

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	183
d1xhja_	88	Nitrogen fixation protein NifU homolog SE0630 {Sta	99.94
d1veha_	92	HIRA-interacting protein 5, HIRIP5 {Mouse (Mus mus	99.93
d1th5a1	73	NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [	99.89
d2cu6a1	91	Hypothetical protein TTHB138 {Thermus thermophilus	93.89
d1uwda_	102	Hypothetical protein TM0487 {Thermotoga maritima [	90.65
d1xg8a_	111	Hypothetical protein SA0798 {Staphylococcus aureus	85.41
d1th5a1	73	NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [	85.32

>d1xhja_ d.52.8.1 (A:) Nitrogen fixation protein NifU homolog SE0630 {Staphylococcus epidermidis [TaxId: 1282]}

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: Nitrogen fixation protein NifU homolog SE0630
species: Staphylococcus epidermidis [TaxId: 1282]

Probab=99.94  E-value=5.3e-27  Score=172.39  Aligned_cols=76  Identities=45%  Similarity=0.845  Sum_probs=70.9

Q ss_pred             chHHHHHHHHHhhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec-ccc
Q 030084           77 LTAKNVDLVLEDVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV-YDE  153 (183)
Q Consensus        77 l~~e~Ve~vLe~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V-~d~  153 (183)
                      .+.++|+.+|++|||+|++|||||+|++|++|+|+|||+|||+|||++.+||+++||++|++++| ++..|+.| +++
T Consensus         7 ~l~~~I~~vLe~IRP~l~~dGGdvelv~v~~g~V~v~l~GaC~gC~~s~~Tlk~~Ie~~L~~~vp-ev~~V~~V~~~~   83 (88)
T d1xhja_           7 TMFDQVAEVIERLRPFLLRDGGDCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHEEVP-GVIEVEQVFLEH   83 (88)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHSCEEEEEECCSSEEEEEEESSCCSSCHHHHHHHHHHHHHHHHHST-TCCEEEEEECCC
T ss_pred             HHHHHHHHHHHHhhHHHHhCCCcEEEEeccCCEEEEEecCCCCCCccHHHHHHHHHHHHHHHHCC-CCceEEEecCCC
Confidence            34678999999999999999999999999999999999999999999999999999999999999 69999997 444

>d1veha_ d.52.8.1 (A:) HIRA-interacting protein 5, HIRIP5 {Mouse (Mus musculus) [TaxId: 10090]}

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=99.93  E-value=9.5e-27  Score=172.24  Aligned_cols=79  Identities=34%  Similarity=0.585  Sum_probs=73.5

Q ss_pred             hhchHHHHHHHHH-hhcchhhhCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeecccc
Q 030084           75 FDLTAKNVDLVLE-DVRPYLIADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDE  153 (183)
Q Consensus        75 ~el~~e~Ve~vLe-~IRP~LqsdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~  153 (183)
                      -+.+.++|+.+|+ +|||+|++|||||+|++|++|+|+|||.|+|+|||++.+||+++||++|++++| +|+.|++|++|
T Consensus        11 d~e~~~~I~~vL~~~IrP~l~~dGGdv~lv~v~~g~V~v~l~GaC~gCp~s~~Tlk~~Ie~~L~~~vp-ev~~V~~v~~~   89 (92)
T d1veha_          11 DDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGIQNMLQFYIP-EVEGVEQVSGP   89 (92)
T ss_dssp             CCHHHHHHHHHHHHTTHHHHHHHSCCCCEEEEETTEEEECCCCCCCCCHHHHHHTHHHHHHHHHHHCS-SCCCEEECSCS
T ss_pred             cHHHHHHHHHHHHHhcChHHHHcCCceEEEEeeCCeEEEEEccCCCCChhHHHHHHHHHHHHHHHHCC-CcceEEEcCCC
Confidence            3456678999995 799999999999999999999999999999999999999999999999999998 69999999887


Q ss_pred             c
Q 030084          154 E  154 (183)
Q Consensus       154 e  154 (183)
                      +
T Consensus        90 ~   90 (92)
T d1veha_          90 S   90 (92)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1th5a1 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId: 4530]}

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: NifU-like protein 1, NIFUL1
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.89  E-value=2.4e-24  Score=153.32  Aligned_cols=71  Identities=28%  Similarity=0.617  Sum_probs=66.3

Q ss_pred             hhchHHHHHHHHHhhcchhh-hCCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccceeec
Q 030084           75 FDLTAKNVDLVLEDVRPYLI-ADGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQV  150 (183)
Q Consensus        75 ~el~~e~Ve~vLe~IRP~Lq-sdGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V  150 (183)
                      ||+++++|+.+|++|||+|+ .|||||+|+++++|+|+|||+|+|+||+    ||+++||++|++++| +|+.|+.+
T Consensus         1 mel~ee~V~~vL~eirP~l~a~dGGdvelv~i~~~~v~v~l~GaC~gC~----Tl~~gIe~~L~~~iP-ei~~V~~v   72 (73)
T d1th5a1           1 LELNEENVEKVLNEIRPYLAGTGGGGLQFLMIKGPIVKVRLTGPAAVVR----TVRIAVSKKLREKIP-SIQIVQLL   72 (73)
T ss_dssp             CCCSHHHHHHHHTTTHHHHTTTTCCCCCCCEEETTEEEECCCSSSSSSS----SHHHHHHHHHHHHCT-TCSEEEEC
T ss_pred             CCCCHHHHHHHHHHhcccccccCCceEEEEEecCCEEEEEecCCCcccc----hHHHHHHHHHHHHCC-CccEEEec
Confidence            57889999999999999998 6999999999999999999999999994    999999999999998 69988765

>d2cu6a1 d.52.8.2 (A:6-96) Hypothetical protein TTHB138 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Fe-S cluster assembly (FSCA) domain-like
family: PaaD-like
domain: Hypothetical protein TTHB138
species: Thermus thermophilus [TaxId: 274]

Probab=93.89  E-value=0.063  Score=36.98  Aligned_cols=67  Identities=16%  Similarity=0.215  Sum_probs=51.1

Q ss_pred             hHHHHHHHH-Hhhcchhhh---CCCcEEEEEeeCCEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce
Q 030084           78 TAKNVDLVL-EDVRPYLIA---DGGNIDVVSVEDGVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI  147 (183)
Q Consensus        78 ~~e~Ve~vL-e~IRP~Lqs---dGGDVELVdVedg~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V  147 (183)
                      ++++|..+| .-+-|.+..   +=|-|.=+.+++|.|.|.|.-.+.+||.... +.+.|+++|+. ++ .++.|
T Consensus         2 le~~v~eaL~~V~DPe~~~dIv~LGlV~~i~i~~~~v~v~l~lt~~~cp~~~~-i~~~i~~al~~-l~-gv~~V   72 (91)
T d2cu6a1           2 LEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDS-LGEAVRQALSR-LP-GVEEV   72 (91)
T ss_dssp             HHHHHHHHHTTCEETTTTEETTTTTCEEEEEEETTEEEEEECCSSSSCCSSCH-HHHHHHHHHHT-ST-TCCEE
T ss_pred             hHHHHHHHHhcCCCCCCCcChhhccceeEEEEeccccEEEEEcCCCCCcHHHH-HHHHHHHHHHc-CC-CCceE
Confidence            355667777 455676653   3577888889999999999999999997665 77888888876 65 37776

>d1uwda_ d.52.8.2 (A:) Hypothetical protein TM0487 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Fe-S cluster assembly (FSCA) domain-like
family: PaaD-like
domain: Hypothetical protein TM0487
species: Thermotoga maritima [TaxId: 2336]

Probab=90.65  E-value=0.29  Score=34.38  Aligned_cols=83  Identities=17%  Similarity=0.205  Sum_probs=55.6

Q ss_pred             hchHHHHHHHH-HhhcchhhhC---CCcEEEEEeeC-CEEEEEEcccCCCCcchHHHHHHHHHHHHHHHccccccce-ee
Q 030084           76 DLTAKNVDLVL-EDVRPYLIAD---GGNIDVVSVED-GVVSVKLQGACGSCPSSTTTMSMGIERVLKEKFGDAIKDI-RQ  149 (183)
Q Consensus        76 el~~e~Ve~vL-e~IRP~Lqsd---GGDVELVdVed-g~V~VrL~GACsGCpsS~~TLk~~IE~~Lre~~P~eV~~V-~~  149 (183)
                      +.+++.|..+| .-+-|.+..+   =|-|.=+.|++ |.|.|.|.=.+.+||... .+...|+++|++ ++ .|.+| +.
T Consensus         4 ~vt~~~V~~aL~~V~DPe~~~dIV~LGlV~~i~I~~~g~V~v~~~lt~~~Cp~~~-~i~~~i~~al~~-~~-gV~~v~V~   80 (102)
T d1uwda_           4 KVTKEDVLNALKNVIDFELGLDVVSLGLVYDIQIDDQNNVKVLMTMTTPMCPLAG-MILSDAEEAIKK-IE-GVNNVEVE   80 (102)
T ss_dssp             CCCHHHHHHHHTTCBCTTTSSBTTTTTCCCCEEECTTCEEEEEECCSSSCCSSHH-HHHHHHHHHHHT-SS-SCCEEEEE
T ss_pred             ccCHHHHHHHHhCCCCCCCCcceeeccceeeEEeccccceEEEEecCCCCCchHH-HHHHHHHHHHHc-CC-CCceEEEE
Confidence            34566788888 5666776432   34455567776 799999999999999754 566889999986 65 37666 33


Q ss_pred             cccc---ccccccHH
Q 030084          150 VYDE---EVRETTVE  161 (183)
Q Consensus       150 V~d~---e~~e~s~E  161 (183)
                      ++.+   .++-+|.|
T Consensus        81 i~~~p~W~~~~~s~~   95 (102)
T d1uwda_          81 LTFDPPWTPERMSPE   95 (102)
T ss_dssp             ECCSSCCCGGGSCHH
T ss_pred             EEecCCCChHHCCHH
Confidence            4433   23345554

>d1xg8a_ c.47.1.17 (A:) Hypothetical protein SA0798 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: YuzD-like
domain: Hypothetical protein SA0798
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.41  E-value=0.78  Score=33.44  Aligned_cols=53  Identities=13%  Similarity=0.107  Sum_probs=35.2

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHccccccceeeccccccc-cccHHHHHHHHHHhh
Q 030084          118 CGSCPSSTTTMSMGIERVLKEKFGDAIKDIRQVYDEEVR-ETTVEVSALLLCLIS  171 (183)
Q Consensus       118 CsGCpsS~~TLk~~IE~~Lre~~P~eV~~V~~V~d~e~~-e~s~E~In~al~~Lr  171 (183)
                      |.+=|||..|. .+++.+|++++|+.--.+..|+-+++. +.+++.-+-+-+|+.
T Consensus        22 CV~aPSSkeTy-EWLqaal~RKyp~~~f~~~YiDi~~~~~~~~~~~~~~ae~I~e   75 (111)
T d1xg8a_          22 CVNAPTSKDIY-DWLQPLLKRKYPNISFKYTYIDITKDNDNLTDHDLQFIERIEQ   75 (111)
T ss_dssp             GSSSCCHHHHH-HHHHHHHHHHCTTSCEEEEEEETTTC---CCHHHHHHHHHHHT
T ss_pred             hcCCCCchhHH-HHHHHHHhCcCCCCceEEEEEeccCCcccccHHHHHHHHHHhh
Confidence            55558888888 799999999999755566666655433 345555555555543

>d1th5a1 d.52.8.1 (A:154-226) NifU-like protein 1, NIFUL1 {Rice (Oryza sativa) [TaxId: 4530]}

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: NifU-like protein 1, NIFUL1
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=85.32  E-value=0.22  Score=33.51  Aligned_cols=27  Identities=15%  Similarity=-0.084  Sum_probs=23.5

Q ss_pred             cccHHHHHHHHHHhhhhhh-ccCCcccC
Q 030084          157 ETTVEVSALLLCLISDKRY-YYTTAVPL  183 (183)
Q Consensus       157 e~s~E~In~al~~Lr~a~~-~~~~~~~~  183 (183)
                      +.++|.|+.+|+.+||++. ..||.|-|
T Consensus         2 el~ee~V~~vL~eirP~l~a~dGGdvel   29 (73)
T d1th5a1           2 ELNEENVEKVLNEIRPYLAGTGGGGLQF   29 (73)
T ss_dssp             CCSHHHHHHHHTTTHHHHTTTTCCCCCC
T ss_pred             CCCHHHHHHHHHHhcccccccCCceEEE
Confidence            5789999999999999996 78998743