Align ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) (characterized)
to candidate WP_011989278.1 CKL_RS03490 ASKHA domain-containing protein
Query= reanno::Phaeo:GFF1501 (698 letters) >NCBI__GCF_000016505.1:WP_011989278.1 Length = 647 Score = 452 bits (1163), Expect = e-131 Identities = 245/651 (37%), Positives = 388/651 (59%), Gaps = 15/651 (2%) Query: 23 VVFTPSGKRGRFPVGTPVLTAARQLGVDLDSVCGGRGICSKCQITPSYGEFSKHGVTVAD 82 V+F P+G RG+ G +L A ++ G++L+S CGG G C KC++ +K ++ Sbjct: 5 VIFQPTGYRGKICSGKTILEACQKFGINLESPCGGNGTCGKCKVKLEKILCNKES-DFSN 63 Query: 83 DALTEWNKVEQRYKDKRGLIDGRRLGCQAQVQGDVVIDVPPESQVHRQVVRKRAEARDIT 142 +++ + E+ K + RL C ++ D+VI VP +S+ +Q + + + ++ Sbjct: 64 SSISPITEKEREILTKEEQLQNFRLACCTKITEDMVIFVPEKSEKGKQRILETSGSKLFH 123 Query: 143 MNPSTRLYYVEVEEPDMHKPTGDMERLIEALDAQWDL--KGVKTDLHILSVLQPALRKGG 200 +NP + YY+E++ P + D R+ +AL ++ K + D ++ L LRK Sbjct: 124 LNPGVKKYYIELKSPTLEDCRDDFTRVKDALLHKYRNLEKHISMDYKVMQTLSSLLRKEK 183 Query: 201 WKVTVAVHLGDENHPPKIMHIWPGFYEGSIYGLAVDLGSTTIAAHLCDLKTGDVVASSGI 260 +K+TV + + E I+ + PGF E +IYG+A+D+G+TTIAA LCDL +G+V+ + Sbjct: 184 YKITVTLWMDKE-----IISVEPGFNE-NIYGVAMDVGTTTIAAALCDLSSGEVITQTSS 237 Query: 261 MNPQIRFGEDLMSRVSYSMMNKGGDQEMTRAVREGMNALFTQIAAEAEIDKALIVDAVFV 320 +NPQI +GED++SR+S+ +NK G +EM + + +N L ++AA + I D V V Sbjct: 238 LNPQIIYGEDILSRISHCSINKNGLEEMHSLIIKEINKLLEELAASINRNVNQIYDMVIV 297 Query: 321 CNPVMHHLFLGIDPFELGQAPFALATSNALALRAVELDLNIHPAARVYLLPCIAGHVGAD 380 N MHH+ L I+P LGQ+PF S L ++A ELD+NI A +Y LP G VG+D Sbjct: 298 FNTAMHHIALNINPEYLGQSPFTPVISQGLNIKARELDINICKGAYMYSLPIEGGFVGSD 357 Query: 381 AAAVALSEAPDKSEDLVLVVDVGTNAEILLGNKDKVLACSSPTGPAFEGAQISSGQRAAP 440 +V +S+ K + +++++D+GTN EI GN++ V + S TGPA EGAQ+ G RA Sbjct: 358 NVSVLISQEIHKQDKMLMIIDIGTNGEIDFGNREGVFSTSCATGPALEGAQMKYGMRAVT 417 Query: 441 GAIERVEINPETKEPRFRVIGSDIWSDEDGFAAAVATTGITGICGSGIIEAIAEMRMAGL 500 GAIERV+IN + E F+VIG D W++ G+ GICGSGII+A+AEM + Sbjct: 418 GAIERVKINSLSLEADFKVIGEDKWNN------TAEVGGVKGICGSGIIDAVAEMYKNSI 471 Query: 501 LDASGLIGSAEQTGTTRCIQDGRTNAYLLWDGSVEGGPTITVTNPDIRAIQMAKAALYSG 560 + G R ++GR L+W G I++T D+RA+Q+AK+ALY+G Sbjct: 472 IGKDGTFNKKIVCPRIRRDEEGRMEYVLVWRRHTSIGEDISITQKDVRAVQLAKSALYAG 531 Query: 561 ARLLMDKFGIDTVDRVVLAGAFGAHISAKHAMVLGMIPDCPLDKVTSAGNAAGTGARIAL 620 A++LM K +D+V+ V+LAGAFG++I+ ++A+V+G+ PDC L+ V GNAAG GA+IAL Sbjct: 532 AKMLMKKRNVDSVEGVILAGAFGSYINKENALVIGLFPDCDLNNVVVVGNAAGEGAKIAL 591 Query: 621 LNTEARSEIEATVQQIEKIETAVEPRFQEHFVNASAIPNSAEPFPILSSIV 671 L+T+ R+E E + ++ +E A E F+ F NA P+S + FP + I+ Sbjct: 592 LSTDKRTEAEEVAKDVQFMECAAEKDFEMEFYNAMNFPHSEDEFPHIKHIL 642 Lambda K H 0.318 0.135 0.396 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: 930 Number of extensions: 46 Number of successful extensions: 5 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: 698 Length of database: 647 Length adjustment: 39 Effective length of query: 659 Effective length of database: 608 Effective search space: 400672 Effective search space used: 400672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_011989278.1 CKL_RS03490 (ASKHA domain-containing protein)
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.3083115.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-97 310.0 2.1 9.8e-97 309.1 2.1 1.5 1 NCBI__GCF_000016505.1:WP_011989278.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016505.1:WP_011989278.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.1 2.1 9.8e-97 9.8e-97 2 260 .. 373 638 .. 372 639 .. 0.98 Alignments for each domain: == domain 1 score: 309.1 bits; conditional E-value: 9.8e-97 RACo_C_ter 2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek.... 70 + ++iDiGTN+Ei +gn++ ++++s+a+GPAlEG+++k+GmrA +gAierv+i++ +le ++kvig++k NCBI__GCF_000016505.1:WP_011989278.1 373 MLMIIDIGTNGEIDFGNREGVFSTSCATGPALEGAQMKYGMRAVTGAIERVKINSLSLEADFKVIGEDKwnnt 445 789****************************************************************999*** PP RACo_C_ter 71 .....pkGicGsGiidliaelleagiidkkgklnkelkserireee.eteeyvlvlaeesetekdivitekDi 137 +kGicGsGiid++ae++++ ii k+g++nk++ +rir++e +++eyvlv+++++++++di+it+kD+ NCBI__GCF_000016505.1:WP_011989278.1 446 aevggVKGICGSGIIDAVAEMYKNSIIGKDGTFNKKIVCPRIRRDEeGRMEYVLVWRRHTSIGEDISITQKDV 518 *******************************************976599************************ PP RACo_C_ter 138 delirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNtslagAra 210 ++++ ak+A+yag+k+L+++ + v++++ v+laGafGsyi+ e+A++iGl+Pd++l++v+ vGN++++gA++ NCBI__GCF_000016505.1:WP_011989278.1 519 RAVQLAKSALYAGAKMLMKKRN--VDSVEGVILAGAFGSYINKENALVIGLFPDCDLNNVVVVGNAAGEGAKI 589 ********************99..9************************************************ PP RACo_C_ter 211 allsreareeleeiarkityielavekkFmeefvaalflphtdlelfpsv 260 alls+++r+e+ee+a++++ +e+a+ek+F+ ef +a+ +ph++ fp++ NCBI__GCF_000016505.1:WP_011989278.1 590 ALLSTDKRTEAEEVAKDVQFMECAAEKDFEMEFYNAMNFPHSED-EFPHI 638 *****************************************877.69986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (647 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.31 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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