Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011780770.1 MVAN_RS17940 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_000015305.1:WP_011780770.1 Length = 367 Score = 657 bits (1696), Expect = 0.0 Identities = 319/363 (87%), Positives = 345/363 (95%) Query: 6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDP 65 LEFTV N NPA+D VR ILANPGFG+++TDHMVSIDYT +GWH+A+V+PYGPI+LDP Sbjct: 5 LEFTVDRNANPASDEVRAQILANPGFGRFHTDHMVSIDYTDGKGWHDARVMPYGPIELDP 64 Query: 66 SAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQ 125 SAIVLHY QE+FEGLKAYRWADGSIVSFRPEANAARL++SARRLAIPELP+E+FI SLR+ Sbjct: 65 SAIVLHYAQEVFEGLKAYRWADGSIVSFRPEANAARLRTSARRLAIPELPDELFIRSLRE 124 Query: 126 LIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVS 185 LIAVDEKWVP AGGEESLYLRPF+IATEPGLGVRP++EYRYL+I SPAGAYF GIKPVS Sbjct: 125 LIAVDEKWVPAAGGEESLYLRPFIIATEPGLGVRPASEYRYLVIGSPAGAYFPRGIKPVS 184 Query: 186 VWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMN 245 VWLSHEYVRASPGGTGAAKFGGNYAASLLAQA+A+ GCDQVVWLDAIERRY+EEMGGMN Sbjct: 185 VWLSHEYVRASPGGTGAAKFGGNYAASLLAQAEASAHGCDQVVWLDAIERRYIEEMGGMN 244 Query: 246 LFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGE 305 LFFVFGSGG+ARLVTPELSGSLLPGITR+SLLQLATDAGFAVEERKIDVDEWQKKA AGE Sbjct: 245 LFFVFGSGGTARLVTPELSGSLLPGITRNSLLQLATDAGFAVEERKIDVDEWQKKAAAGE 304 Query: 306 ITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMA 365 ITEVFACGTAAVITPVSHVKH DGEFTIADG+PGEITMALRDTLTGIQRGTFADTHGWMA Sbjct: 305 ITEVFACGTAAVITPVSHVKHGDGEFTIADGEPGEITMALRDTLTGIQRGTFADTHGWMA 364 Query: 366 RLN 368 RL+ Sbjct: 365 RLS 367 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: 635 Number of extensions: 18 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: 368 Length of database: 367 Length adjustment: 30 Effective length of query: 338 Effective length of database: 337 Effective search space: 113906 Effective search space used: 113906 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_011780770.1 MVAN_RS17940 (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.2668.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-148 477.2 0.0 1.1e-147 477.0 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011780770.1 MVAN_RS17940 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011780770.1 MVAN_RS17940 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.0 0.0 1.1e-147 1.1e-147 1 312 [. 49 365 .. 49 366 .. 0.99 Alignments for each domain: == domain 1 score: 477.0 bits; conditional E-value: 1.1e-147 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++++++++eld++++vlhY+qevfeGlkayR+adG+i++fRp+ana+Rlr+sa+rl++Pel++el lcl|NCBI__GCF_000015305.1:WP_011780770.1 49 WHDARVMPYGPIELDPSAIVLHYAQEVFEGLKAYRWADGSIVSFRPEANAARLRTSARRLAIPELPDEL 117 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f+++l++l+++d++wvp a++e+sLYlRPf+iate+ lGv++a+ey++lv+ sP+GaYf g++pvs++ lcl|NCBI__GCF_000015305.1:WP_011780770.1 118 FIRSLRELIAVDEKWVPAAGGEESLYLRPFIIATEPGLGVRPASEYRYLVIGSPAGAYFPRGIKPVSVW 186 ********************************************************************* PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg... 204 ++ eyvRa p+GtGa+k+gGnYaasllaq++a+++g+d+vv+ld++e+++iee+G++n+f++ ++g lcl|NCBI__GCF_000015305.1:WP_011780770.1 187 LSHEYVRASPGGTGAAKFGGNYAASLLAQAEASAHGCDQVVWLDAIERRYIEEMGGMNLFFVFGSGgta 255 *****************************************************************9898 PP TIGR01123 205 elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelk 271 +lvt++ls+s+L+g+tr+sll+la d+g++veer+i++de++++++aGei vfacGtaavitPv+++k lcl|NCBI__GCF_000015305.1:WP_011780770.1 256 RLVTPELSGSLLPGITRNSLLQLATDAGFAVEERKIDVDEWQKKAAAGEIteVFACGTAAVITPVSHVK 324 99***********************************************999***************** PP TIGR01123 272 iegkevevkseevGevtkklrdeltdiqyGkledkegWive 312 +++ e++++++e+Ge+t++lrd+lt+iq+G+++d++gW+++ lcl|NCBI__GCF_000015305.1:WP_011780770.1 325 HGDGEFTIADGEPGEITMALRDTLTGIQRGTFADTHGWMAR 365 ***************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (367 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: 7.53 // [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