Align ATP-dependent reduction of co(II)balamin (characterized)
to candidate 206336 DVU0908 iron-sulfur cluster-binding protein, putative
Query= reanno::DvH:206336 (543 letters) >MicrobesOnline__882:206336 Length = 543 Score = 1086 bits (2808), Expect = 0.0 Identities = 543/543 (100%), Positives = 543/543 (100%) Query: 1 MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV 60 MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV Sbjct: 1 MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV 60 Query: 61 RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP 120 RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP Sbjct: 61 RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP 120 Query: 121 FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV 180 FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV Sbjct: 121 FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV 180 Query: 181 LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV 240 LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV Sbjct: 181 LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV 240 Query: 241 EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA 300 EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA Sbjct: 241 EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA 300 Query: 301 DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD 360 DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD Sbjct: 301 DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD 360 Query: 361 GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR 420 GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR Sbjct: 361 GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR 420 Query: 421 GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF 480 GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF Sbjct: 421 GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF 480 Query: 481 IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH 540 IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH Sbjct: 481 IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH 540 Query: 541 FHF 543 FHF Sbjct: 541 FHF 543 Lambda K H 0.320 0.136 0.413 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1273 Number of extensions: 46 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 543 Length of database: 543 Length adjustment: 35 Effective length of query: 508 Effective length of database: 508 Effective search space: 258064 Effective search space used: 258064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
Align candidate 206336 DVU0908 (iron-sulfur cluster-binding protein, putative)
to HMM PF14574 (RACo_C_ter)
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/PF14574.10.hmm # target sequence database: /tmp/gapView.24691.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: RACo_C_ter [M=261] Accession: PF14574.10 Description: C-terminal domain of RACo the ASKHA domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-45 139.1 0.0 1.2e-44 138.5 0.0 1.2 1 lcl|MicrobesOnline__882:206336 DVU0908 iron-sulfur cluster-bind Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206336 DVU0908 iron-sulfur cluster-binding protein, putative # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 138.5 0.0 1.2e-44 1.2e-44 4 249 .. 298 541 .. 296 542 .. 0.89 Alignments for each domain: == domain 1 score: 138.5 bits; conditional E-value: 1.2e-44 RACo_C_ter 4 lliDiGTNaEivlg.nkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignekpkGicGsGiid 81 +l D+GTN+E vl + ++ l++s a GPAlEG ++++G+ A++gAi +++++p l + v+++ ++ Gi G+G i+ lcl|MicrobesOnline__882:206336 298 VLADLGTNGEFVLAlSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVP--YVLDGGEADGISGTGYIS 374 678**********736799*************************************555..5678888*********** PP RACo_C_ter 82 liaelleagiidkkgklnkelkserireeeeteeyvlvlaeeset..ekdivitekDidelirakaAiyagvktLleev 158 l+ +ll+ag++d +g++ ++ +s+ ++ + ++ ++ e + +++ +Di+e+++ kaA +++ Ll ++ lcl|MicrobesOnline__882:206336 375 LVHALLRAGLLDVDGRFIQSPSSPLAA---RMARSIVSHRGEPCLplARGLYLAARDIEEILKVKAAFSLAFERLLATA 450 *****************7775444433...3444444333333322378****************************** PP RACo_C_ter 159 glevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAraallsreareeleeiarkityielavek 237 ++ + ++ + laGa G++ +++ +G +P + ++++vGNtsl+gA+ +l+s+ r++l++ ++ t ++l +++ lcl|MicrobesOnline__882:206336 451 QMPSHALSGIHLAGALGQHALPADLEGLGFIPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAP 529 ******************************************************************************* PP RACo_C_ter 238 kFmeefvaalfl 249 +F f++ + + lcl|MicrobesOnline__882:206336 530 DFSAAFLRHMHF 541 ******998865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (543 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 14.57 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory