Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_086511983.1 BZY95_RS21775 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_002151265.1:WP_086511983.1 Length = 322 Score = 343 bits (880), Expect = 3e-99 Identities = 167/304 (54%), Positives = 220/304 (72%), Gaps = 11/304 (3%) Query: 5 DRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDRLFD 64 DRDG IW DGE + WRDA TH+LTHTLHYGMG FEGVRAY GT +FR+ HT RL D Sbjct: 6 DRDGWIWLDGEWLPWRDAKTHLLTHTLHYGMGCFEGVRAYAGAHGTHLFRVAEHTRRLLD 65 Query: 65 SAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIVAA 124 SAH +++P+ + +E + EA R + N L +AY++P VF+G+EG+GLRA GL VHV++AA Sbjct: 66 SAHALDIPVAFDEEVLIEAQRQCLVRNELRNAYLKPTVFFGAEGLGLRAKGLSVHVMIAA 125 Query: 125 WHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGADEAL 184 W G Y+ EA LG++ TSS+ RHHVNI++ RAK+NG Y+NS+LAL A+ G DEA+ Sbjct: 126 WDLGDYVSSEAATLGLRALTSSWARHHVNISLCRAKTNGHYVNSILALNTAVKAGFDEAI 185 Query: 185 MLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAE-HGLKIVEKRITR 243 MLDPEGYVAE S N+F+++DG ++TPEVT+CL GITR +V+ LA E GL++ E+RITR Sbjct: 186 MLDPEGYVAEASAANVFLLRDGALHTPEVTSCLQGITRDSVIHLAREVLGLEVRERRITR 245 Query: 244 DEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGP----------ITEKLQKAYFDLVT 293 DE+Y ADEAF TGTAAE+ P+RE+DGR IG P +T +LQ+ Y + Sbjct: 246 DELYTADEAFVTGTAAEILPLRELDGRHIGARAGAPLPGQPIDANSVTAQLQQLYRQVTR 305 Query: 294 GKTD 297 G+ + Sbjct: 306 GELE 309 Lambda K H 0.319 0.135 0.400 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: 339 Number of extensions: 11 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: 307 Length of database: 322 Length adjustment: 27 Effective length of query: 280 Effective length of database: 295 Effective search space: 82600 Effective search space used: 82600 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_086511983.1 BZY95_RS21775 (branched-chain amino acid transaminase)
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.11813.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-107 343.8 0.0 4.8e-107 343.5 0.0 1.1 1 lcl|NCBI__GCF_002151265.1:WP_086511983.1 BZY95_RS21775 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511983.1 BZY95_RS21775 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.5 0.0 4.8e-107 4.8e-107 1 290 [. 12 310 .. 12 321 .. 0.94 Alignments for each domain: == domain 1 score: 343.5 bits; conditional E-value: 4.8e-107 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wldGe ++++dak+h+lth+lhYG+g feG+RaY + +g+ +fr+ eh+ Rl+dsa++l++++ + +e lcl|NCBI__GCF_002151265.1:WP_086511983.1 12 WLDGEWLPWRDAKTHLLTHTLHYGMGCFEGVRAYAGAHGTHLFRVAEHTRRLLDSAHALDIPVAFDEEV 80 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+e++++ l +n+l++aY++p v+ Gae+lgl++ +l+v+v+iaaw++g y+ ea G+++ +ss+ lcl|NCBI__GCF_002151265.1:WP_086511983.1 81 LIEAQRQCLVRNELRNAYLKPTVFFGAEGLGLRA-KGLSVHVMIAAWDLGDYVSSEAATLGLRALTSSW 148 **********************************.789******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ +ak++g Y+ns+la a++aG+deai+Ld eGyvae s n+f+++dg+l tP+v +s lcl|NCBI__GCF_002151265.1:WP_086511983.1 149 ARHHVNISLCRAKTNGHYVNSILALNTAVKAGFDEAIMLDPEGYVAEASAANVFLLRDGALHTPEV-TS 216 ******************************************************************.78 PP TIGR01122 208 iLkgitrdaviklake.lgievkeerisreelytaDevfltGtaaevtPirevDgrkigegk....... 268 +L+gitrd+vi+la+e lg+ev+e+ri+r+elytaDe+f+tGtaae+ P+re+Dgr+ig+ lcl|NCBI__GCF_002151265.1:WP_086511983.1 217 CLQGITRDSVIHLAREvLGLEVRERRITRDELYTADEAFVTGTAAEILPLRELDGRHIGARAgaplpgq 285 **************9647*****************************************8641122111 PP TIGR01122 269 ...rGpvtkklqeaffdlvegktek 290 + +vt +lq+ + ++++g+ e+ lcl|NCBI__GCF_002151265.1:WP_086511983.1 286 pidANSVTAQLQQLYRQVTRGELED 310 222456999******9999998775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (322 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: 8.99 // [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