Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_011951625.1 SWIT_RS03965 branched-chain amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS25890 (363 letters) >NCBI__GCF_000016765.1:WP_011951625.1 Length = 359 Score = 472 bits (1214), Expect = e-138 Identities = 233/361 (64%), Positives = 273/361 (75%), Gaps = 3/361 (0%) Query: 1 MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF 60 MT Q F++ PN A R L+ +P FGRVFTDHMV + + EG+GW DA+V AR P Sbjct: 1 MTSQ--FTILPNAAPTPAEDRAKLLENPGFGRVFTDHMVVVRYVEGKGWHDAEVKARGPL 58 Query: 61 SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE 120 IDPA +VLHY QEIFEGMKAYR DG + LFRP NA RF SA+RMAMP +PE LF+E Sbjct: 59 QIDPASAVLHYAQEIFEGMKAYRLDDG-LALFRPEANAARFNLSARRMAMPDVPEELFIE 117 Query: 121 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA 180 A+EQLVRID+ WVP G GSLYLRPFMFANEVFLG+KP+SE++F VIA VG YFKGG + Sbjct: 118 AVEQLVRIDRDWVPGGGGSLYLRPFMFANEVFLGVKPSSEYLFMVIASSVGAYFKGGKDS 177 Query: 181 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG 240 V+VWVS +YTRAAPGGTG AKCGGNYA SL+AQ +AT +GCDQVVFLDAAE +W+EELGG Sbjct: 178 VTVWVSTDYTRAAPGGTGSAKCGGNYAASLLAQKQATEHGCDQVVFLDAAERKWIEELGG 237 Query: 241 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL 300 MN+FFVMDDG++VTPPL G+ILPGITR S+I LAR+ G+ V E YSY +W+ADA+SG+L Sbjct: 238 MNVFFVMDDGSMVTPPLQGTILPGITRDSIIRLARDEGIAVREEPYSYEQWKADARSGKL 297 Query: 301 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH 360 E F CGTAA + AIG V+ F IG G G T LRDRL IQR A P GWV Sbjct: 298 VETFACGTAAVVTAIGTVKGDDGEFTIGAGGTGQTTARLRDRLTGIQRGTVADPYGWVRR 357 Query: 361 V 361 V Sbjct: 358 V 358 Lambda K H 0.321 0.135 0.415 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: 487 Number of extensions: 16 Number of successful extensions: 2 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: 363 Length of database: 359 Length adjustment: 29 Effective length of query: 334 Effective length of database: 330 Effective search space: 110220 Effective search space used: 110220 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_011951625.1 SWIT_RS03965 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01123.hmm # target sequence database: /tmp/gapView.29892.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01123 [M=313] Accession: TIGR01123 Description: ilvE_II: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-129 415.9 0.0 5e-129 415.7 0.0 1.0 1 lcl|NCBI__GCF_000016765.1:WP_011951625.1 SWIT_RS03965 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016765.1:WP_011951625.1 SWIT_RS03965 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.7 0.0 5e-129 5e-129 1 313 [] 47 358 .. 47 358 .. 0.99 Alignments for each domain: == domain 1 score: 415.7 bits; conditional E-value: 5e-129 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++ae+++ ++l++d++savlhY+qe+feG+kayR +dG + lfRp+ana+R++ sa+r+++P+++eel lcl|NCBI__GCF_000016765.1:WP_011951625.1 47 WHDAEVKARGPLQIDPASAVLHYAQEIFEGMKAYRLDDG-LALFRPEANAARFNLSARRMAMPDVPEEL 114 ***************************************.579************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f+ea++qlv++d+dwvp +++ sLYlRPf++a e lGvk+++eylf+v+as vGaYfkgg + v+++ lcl|NCBI__GCF_000016765.1:WP_011951625.1 115 FIEAVEQLVRIDRDWVP--GGGGSLYLRPFMFANEVFLGVKPSSEYLFMVIASSVGAYFKGGKDSVTVW 181 *****************..788*********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+t+y+Raap+GtG +k+gGnYaasllaqk+a+e+g+d+vv+ld++e+k iee+G++n+f++++dg++v lcl|NCBI__GCF_000016765.1:WP_011951625.1 182 VSTDYTRAAPGGTGSAKCGGNYAASLLAQKQATEHGCDQVVFLDAAERKWIEELGGMNVFFVMDDGSMV 250 ********************************************************************* PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl + iL+g+tr+s+++la+d g++v+e+ + +++ka + +G++ facGtaav+t +g +k ++ lcl|NCBI__GCF_000016765.1:WP_011951625.1 251 TPPLQGTILPGITRDSIIRLARDEGIAVREEPYSYEQWKADARSGKLveTFACGTAAVVTAIGTVKGDD 319 *********************************************99888******************* PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 e+++ ++ +G+ t +lrd lt+iq+G+++d++gW+ +v lcl|NCBI__GCF_000016765.1:WP_011951625.1 320 GEFTIGAGGTGQTTARLRDRLTGIQRGTVADPYGWVRRV 358 ***********************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (359 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: 11.37 // [ok]
This GapMind analysis is from Apr 10 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