Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_011159904.1 TX73_RS22285 branched-chain amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS25890 (363 letters) >NCBI__GCF_000195775.1:WP_011159904.1 Length = 370 Score = 417 bits (1071), Expect = e-121 Identities = 209/355 (58%), Positives = 253/355 (71%), Gaps = 1/355 (0%) Query: 7 FSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPFSIDPAC 66 F ++P + A R A + +P FGRVFTDHM + + + GW A+V AR F + A Sbjct: 16 FDVQPTASPTPDADRAAKLENPGFGRVFTDHMAVVRYDQTNGWHAARVEARANFPLHTAT 75 Query: 67 SVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLEAIEQLV 126 +VLHY QEIFEG+KAY+ DG V LFRP NA+RF+ SA RMAM LPE++F+EA+EQ+V Sbjct: 76 AVLHYAQEIFEGLKAYKREDGGVNLFRPDANAKRFRDSADRMAMAPLPEAVFIEAVEQVV 135 Query: 127 RIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKAVSVWVS 186 +ID+ W+P G GSLYLRPFM A+EVFLG+KP++E+IF VIA PVG YFKGG VS+WVS Sbjct: 136 KIDRNWIPGGEGSLYLRPFMIASEVFLGVKPSAEYIFAVIASPVGSYFKGGPAPVSIWVS 195 Query: 187 ENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGGMNIFFV 246 E YTRAA GGTG KCGGNYA SL AQ EA GCDQVVFLDA E R+VEELGGMN+FFV Sbjct: 196 ETYTRAAIGGTGGVKCGGNYAASLRAQAEAIERGCDQVVFLDAIERRYVEELGGMNVFFV 255 Query: 247 MDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRLAEAFVC 306 +DG+L TPPL G+ILPGITR S+I LARE G V E Y+ +W ADA SG+L EAF C Sbjct: 256 FEDGSLSTPPL-GTILPGITRDSIIALAREAGRKVREEAYTIDQWRADAASGKLKEAFAC 314 Query: 307 GTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHHV 361 GTAA + IG+V S F I G AG LR +LV+IQ +AA GW+ V Sbjct: 315 GTAAVISPIGKVCSNHGDFVINGGQAGEVAMGLRKQLVDIQYGRAADTHGWIKKV 369 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: 450 Number of extensions: 15 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: 370 Length adjustment: 30 Effective length of query: 333 Effective length of database: 340 Effective search space: 113220 Effective search space used: 113220 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_011159904.1 TX73_RS22285 (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.6874.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-127 411.3 0.0 1.3e-127 411.1 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011159904.1 TX73_RS22285 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011159904.1 TX73_RS22285 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.1 0.0 1.3e-127 1.3e-127 1 313 [] 58 369 .. 58 369 .. 0.99 Alignments for each domain: == domain 1 score: 411.1 bits; conditional E-value: 1.3e-127 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++++ a++ l+ ++avlhY+qe+feGlkay+ +dG ++lfRpdanakR+r sa+r+++ l+e++ lcl|NCBI__GCF_000195775.1:WP_011159904.1 58 WHAARVEARANFPLHTATAVLHYAQEIFEGLKAYKREDGGVNLFRPDANAKRFRDSADRMAMAPLPEAV 126 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f+ea++q+vk+d++w+p ++e sLYlRPf+ia e lGvk++ ey+f v+asPvG+Yfkgg apvsi+ lcl|NCBI__GCF_000195775.1:WP_011159904.1 127 FIEAVEQVVKIDRNWIP--GGEGSLYLRPFMIASEVFLGVKPSAEYIFAVIASPVGSYFKGGPAPVSIW 193 *****************..788*********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v++ y+Raa +GtG+vk+gGnYaasl+aq++a e+g+d+vv+ld++e++++ee+G++n+f++ +dg+l lcl|NCBI__GCF_000195775.1:WP_011159904.1 194 VSETYTRAAIGGTGGVKCGGNYAASLRAQAEAIERGCDQVVFLDAIERRYVEELGGMNVFFVFEDGSLS 262 *****************************************************************9999 PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl + iL+g+tr+s++ la+++g +v+e+ +id+++a +++G++ +facGtaavi+P+g++ + lcl|NCBI__GCF_000195775.1:WP_011159904.1 263 TPPL-GTILPGITRDSIIALAREAGRKVREEAYTIDQWRADAASGKLkeAFACGTAAVISPIGKVCSNH 330 9887.78**************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 ++++ ++ Gev++ lr++l+diqyG+++d++gWi +v lcl|NCBI__GCF_000195775.1:WP_011159904.1 331 GDFVINGGQAGEVAMGLRKQLVDIQYGRAADTHGWIKKV 369 ************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (370 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: 00:00:00.01 # Mc/sec: 8.15 // [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