Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012114576.1 XAUT_RS12870 branched-chain amino acid aminotransferase
Query= BRENDA::O86428 (307 letters) >NCBI__GCF_000017645.1:WP_012114576.1 Length = 297 Score = 222 bits (565), Expect = 9e-63 Identities = 122/294 (41%), Positives = 173/294 (58%), Gaps = 9/294 (3%) Query: 6 RDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTDRLFDS 65 RDG IWYDG V W DA HVL+H LHYG VFEG RAY G IF+ H++RL S Sbjct: 11 RDGWIWYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAY----GGTIFKSAEHSERLRLS 66 Query: 66 AHIMNMQIPYSRDEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIIAAW 125 A +++ IPY+ EI+ A +A + +NNL AYIRP+ + GSE MG+ A +H+ I W Sbjct: 67 AEMLDFTIPYTIGEIDAAKKATLEKNNLVDAYIRPVAWRGSEMMGVAAQKNTIHLAIGVW 126 Query: 126 SWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGADEAMM 185 W +Y E Q+G+++ S + R +AK+ G Y+ ++ A G +A+M Sbjct: 127 EWPSYFDPEQRQKGLRLDLSEWRRPDPATIPCKAKAAGLYMICTISKHRAERRGFADALM 186 Query: 186 LDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKRITRDE 245 LD GYVAE +G N+F +KDGVI+TP L+G+TR T++ +A HG ++VE+ I +E Sbjct: 187 LDYRGYVAECTGANVFFVKDGVIHTPTPDCFLDGLTRRTVIDIARRHGMEVVERHIKPEE 246 Query: 246 VYIADEAFFTGTAAEVTPIREV-DGRKIGAGRRGPVTEKLQKAYFDLVSGKTEA 298 + E F TGTAAEVTP+ + D +G +T +L +Y V K +A Sbjct: 247 LSSFTECFITGTAAEVTPVGSIADWHFAPSG----ITHQLMDSYTAEVRPKQQA 296 Lambda K H 0.319 0.134 0.394 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: 281 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: 307 Length of database: 297 Length adjustment: 27 Effective length of query: 280 Effective length of database: 270 Effective search space: 75600 Effective search space used: 75600 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_012114576.1 XAUT_RS12870 (branched-chain amino acid aminotransferase)
to HMM TIGR01122 (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/TIGR01122.hmm # target sequence database: /tmp/gapView.1505101.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-88 281.9 0.0 3.1e-88 281.8 0.0 1.0 1 NCBI__GCF_000017645.1:WP_012114576.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000017645.1:WP_012114576.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.8 0.0 3.1e-88 3.1e-88 1 287 [. 16 293 .. 16 297 .] 0.97 Alignments for each domain: == domain 1 score: 281.8 bits; conditional E-value: 3.1e-88 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w+dG +v+++dak+hvl+h+lhYG++vfeG RaY + +if+ eh eRl sa++l++ ipy+ e+ + NCBI__GCF_000017645.1:WP_012114576.1 16 WYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAYGG----TIFKSAEHSERLRLSAEMLDFTIPYTIGEIDAA 84 9*********************************99....9******************************** PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 k +l knnl +aYiRp++++G+e +g+ + + +++++i +wew+ y++ e +kG++ +s +rr ++ +i NCBI__GCF_000017645.1:WP_012114576.1 85 KKATLEKNNLVDAYIRPVAWRGSEMMGVAA-QKNTIHLAIGVWEWPSYFDPEQRQKGLRLDLSEWRRPDPATI 156 ******************************.6669************************************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 p kakaag Y+ ++ k+ a r+G+ +a++Ld Gyvae +G n+f vkdgv+ tP + L+g+tr +vi+ NCBI__GCF_000017645.1:WP_012114576.1 157 PCKAKAAGLYMICTISKHRAERRGFADALMLDYRGYVAECTGANVFFVKDGVIHTPTP-DCFLDGLTRRTVID 228 *********************************************************9.99************ PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287 +a+++g+ev+e++i eel e f+tGtaaevtP+ ++ + + +t++l++++ v+ k NCBI__GCF_000017645.1:WP_012114576.1 229 IARRHGMEVVERHIKPEELSSFTECFITGTAAEVTPVGSIADWHFAP---SGITHQLMDSYTAEVRPK 293 ****************************************9998865...469999999998777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (297 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: 14.97 // [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