Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_025274501.1 HALAL_RS0113470 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_000527155.1:WP_025274501.1 Length = 366 Score = 415 bits (1066), Expect = e-120 Identities = 200/357 (56%), Positives = 260/357 (72%), Gaps = 3/357 (0%) Query: 7 EFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPS 66 +F V AN P + R +LA PGFG +TDHM ++ ++ D GWH+A+V P+GP+ L P+ Sbjct: 8 DFEVIANERPRSADERAELLAEPGFGSVFTDHMFTMRWSADRGWHSARVEPFGPLTLSPA 67 Query: 67 AIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQL 126 VLHY QEIFEGLKAY +DG++ FRPEANA R SARRLA+PELPE+ F+ S+R+L Sbjct: 68 TAVLHYAQEIFEGLKAYHRSDGTVGLFRPEANAQRFNGSARRLAMPELPEKWFLASIREL 127 Query: 127 IAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSV 186 I+VD WVP G E SLY+RPF+IATE LGVRPS EY Y +I SPAGAYFK G KPV++ Sbjct: 128 ISVDRDWVPTEG-ESSLYVRPFMIATESFLGVRPSQEYLYGVITSPAGAYFKTGPKPVTL 186 Query: 187 WLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNL 246 W+S +Y RA+PGGTGAAK GGNYAASL +QA E GCDQVV+LDA+E +Y++E+GGMNL Sbjct: 187 WVSEDYTRAAPGGTGAAKCGGNYAASLAPHSQAIEKGCDQVVFLDAVEHKYIDELGGMNL 246 Query: 247 FFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEI 306 FFV+G + TP L+GS+LPGITRD+++ L ++ G+ V E +++W+ A +G + Sbjct: 247 FFVYGD--EKVIYTPRLTGSILPGITRDAIITLLSEEGWDVHETDYSLEKWRADAQSGRL 304 Query: 307 TEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGW 363 TE FACGTAAVITPV ++ GEF+I + + GE+T LR + IQ G DTH W Sbjct: 305 TETFACGTAAVITPVGMIREQGGEFSINESKTGELTRRLRSRILDIQHGRAEDTHNW 361 Lambda K H 0.318 0.135 0.409 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: 460 Number of extensions: 9 Number of successful extensions: 3 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: 368 Length of database: 366 Length adjustment: 30 Effective length of query: 338 Effective length of database: 336 Effective search space: 113568 Effective search space used: 113568 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: 49 (23.5 bits)
Align candidate WP_025274501.1 HALAL_RS0113470 (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.1058936.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-127 408.6 0.0 8.2e-127 408.5 0.0 1.0 1 NCBI__GCF_000527155.1:WP_025274501.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000527155.1:WP_025274501.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.5 0.0 8.2e-127 8.2e-127 1 311 [. 51 363 .. 51 365 .. 0.98 Alignments for each domain: == domain 1 score: 408.5 bits; conditional E-value: 8.2e-127 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W++a++++ ++l+l++++avlhY+qe+feGlkay +dG + lfRp+ana+R++ sa+rl++Pel+e+ fl + NCBI__GCF_000527155.1:WP_025274501.1 51 WHSARVEPFGPLTLSPATAVLHYAQEIFEGLKAYHRSDGTVGLFRPEANAQRFNGSARRLAMPELPEKWFLAS 123 ************************************************************************* PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 +++l+ +d+dwvp+++ e+sLY+RPf+iate lGv++++eyl+ v++sP+GaYfk+g +pv+ +v+++y+Ra NCBI__GCF_000527155.1:WP_025274501.1 124 IRELISVDRDWVPTEG-ESSLYVRPFMIATESFLGVRPSQEYLYGVITSPAGAYFKTGPKPVTLWVSEDYTRA 195 *************776.******************************************************** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv.ttplsesiLeg 218 ap+GtGa+k+gGnYaasl ++++a e+g+d+vv+ld+ve+k+i+e+G++n+f++++d +++ t+ l++siL+g NCBI__GCF_000527155.1:WP_025274501.1 196 APGGTGAAKCGGNYAASLAPHSQAIEKGCDQVVFLDAVEHKYIDELGGMNLFFVYGDEKVIyTPRLTGSILPG 268 *********************************************************765535779******* PP TIGR01123 219 vtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtk 289 +tr+++++l + g v+e + ++++++a +++G + facGtaavitPvg ++ +g e++++++++Ge+t+ NCBI__GCF_000527155.1:WP_025274501.1 269 ITRDAIITLLSEEGWDVHETDYSLEKWRADAQSGRLteTFACGTAAVITPVGMIREQGGEFSINESKTGELTR 341 **********************************99999********************************** PP TIGR01123 290 klrdeltdiqyGkledkegWiv 311 +lr ++diq+G++ed+++W+ NCBI__GCF_000527155.1:WP_025274501.1 342 RLRSRILDIQHGRAEDTHNWTQ 363 ********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (366 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 19.13 // [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