Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011446313.1 SARO_RS13560 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_000013325.1:WP_011446313.1 Length = 367 Score = 435 bits (1119), Expect = e-127 Identities = 211/362 (58%), Positives = 268/362 (74%), Gaps = 5/362 (1%) Query: 6 LEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDP 65 L FT + + P R +LANPGFG +TDHMV IDY +GWH+A+V+PYGPI LDP Sbjct: 10 LTFTRNPHPAPVAADARAQVLANPGFGTTFTDHMVEIDYAEGQGWHDARVVPYGPIALDP 69 Query: 66 SAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQ 125 +A VLHY QEIFEGLKAYR ADG I FRPEANA R +SARRLA+PELPE++F+E++RQ Sbjct: 70 AAAVLHYAQEIFEGLKAYRLADGGIALFRPEANAQRFNASARRLAMPELPEDLFVEAVRQ 129 Query: 126 LIAVDEKWVPPAGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVS 185 + D+ W P G S+YLRPF+ A+E LGVRP+ +Y++++IASPAG YFK G VS Sbjct: 130 QVLADKDWFPTVEG-GSMYLRPFMFASEAFLGVRPARQYKFMVIASPAGNYFKSGAPAVS 188 Query: 186 VWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMN 245 +W+S +Y RA+PGGTGAAK GGNYAASL+ A+A G DQV++LDA E ++VEE+GGMN Sbjct: 189 IWVS-DYTRAAPGGTGAAKCGGNYAASLVPTAEAFSRGHDQVLFLDAAEHKWVEELGGMN 247 Query: 246 LFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGE 305 LFFVF G ++TPEL+G++LPGITR SLL LA + G V E + +D+W+ A +G+ Sbjct: 248 LFFVFDDGS---ILTPELTGTILPGITRSSLLTLAAEEGLTVREGRYSLDQWKADAASGK 304 Query: 306 ITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMA 365 + E FACGTAAV+TPV V DGEFTI G PG++T LR L GIQRG ADTHGW++ Sbjct: 305 LIETFACGTAAVVTPVGKVASRDGEFTIGSGGPGQLTQKLRQKLVGIQRGEIADTHGWVS 364 Query: 366 RL 367 R+ Sbjct: 365 RI 366 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: 473 Number of extensions: 16 Number of successful extensions: 4 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_011446313.1 SARO_RS13560 (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.4099.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-129 416.7 0.0 3e-129 416.5 0.0 1.0 1 lcl|NCBI__GCF_000013325.1:WP_011446313.1 SARO_RS13560 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_011446313.1 SARO_RS13560 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.5 0.0 3e-129 3e-129 1 312 [. 54 365 .. 54 366 .. 0.99 Alignments for each domain: == domain 1 score: 416.5 bits; conditional E-value: 3e-129 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++++++++ ld+++avlhY+qe+feGlkayR adG i lfRp+ana+R++ sa+rl++Pel+e+l lcl|NCBI__GCF_000013325.1:WP_011446313.1 54 WHDARVVPYGPIALDPAAAVLHYAQEIFEGLKAYRLADGGIALFRPEANAQRFNASARRLAMPELPEDL 122 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f+ea++q v adkdw p+ + + s+YlRPf++a e+ lGv++a++y f+v+asP+G+Yfk+g vsi+ lcl|NCBI__GCF_000013325.1:WP_011446313.1 123 FVEAVRQQVLADKDWFPTVE-GGSMYLRPFMFASEAFLGVRPARQYKFMVIASPAGNYFKSGAPAVSIW 190 *****************999.99********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+ +y+Raap+GtGa+k+gGnYaasl + ++a +g d+v++ld++e+k +ee+G++n+f++ +dg+++ lcl|NCBI__GCF_000013325.1:WP_011446313.1 191 VS-DYTRAAPGGTGAAKCGGNYAASLVPTAEAFSRGHDQVLFLDAAEHKWVEELGGMNLFFVFDDGSIL 258 *6.8***************************************************************** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t++l++ iL+g+tr+sll+la + gl+v+e++ ++d++ka +++G++ facGtaav+tPvg+++ + lcl|NCBI__GCF_000013325.1:WP_011446313.1 259 TPELTGTILPGITRSSLLTLAAEEGLTVREGRYSLDQWKADAASGKLieTFACGTAAVVTPVGKVASRD 327 *********************************************99899******************* PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 e+++ s+ +G++t+klr++l++iq+G+++d++gW+ + lcl|NCBI__GCF_000013325.1:WP_011446313.1 328 GEFTIGSGGPGQLTQKLRQKLVGIQRGEIADTHGWVSR 365 ***********************************976 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.40 // [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