Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_106718540.1 CU100_RS21135 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_003010935.1:WP_106718540.1 Length = 296 Score = 220 bits (561), Expect = 3e-62 Identities = 115/262 (43%), Positives = 163/262 (62%), Gaps = 5/262 (1%) Query: 7 DGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNS 66 +G IWM+G+ + W DA+IHVLTH LHY VFEG RAY G IF+L EHT+RL S Sbjct: 10 EGYIWMNGEFVRWTDARIHVLTHGLHYASSVFEGERAY-----GGEIFKLNEHTERLHES 64 Query: 67 AKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAW 126 A+I +P+D E L A +++ + + Y+RPI W GSE +GVSA+ N I+VAIA W Sbjct: 65 ARILGFKIPYDVEELNDACRKLLAKQGFQDAYVRPIAWRGSESMGVSAQANKINVAIAIW 124 Query: 127 PWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALL 186 W +Y +GIR+ + + R + ++KA+G Y+ ++ A A GY +AL+ Sbjct: 125 QWPSYFDPAQKLRGIRLDMAEYRRPDPRTAPSKSKAAGLYMICTISKHAAEAKGYADALM 184 Query: 187 LDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDE 246 LD G V+E +G N F V +G ++TP LDGITR TVI LA+ G +V+E+ I +E Sbjct: 185 LDWRGQVAEATGANVFFVKDGIIHTPVPDCFLDGITRRTVIELAKRRGYEVVERVIMPEE 244 Query: 247 VYTCDEAFFTGTAAEVTPIREL 268 + ++ F TGTAAEVTP+ E+ Sbjct: 245 LVDFEQCFLTGTAAEVTPVSEI 266 Lambda K H 0.319 0.136 0.411 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: 251 Number of extensions: 8 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: 296 Length adjustment: 27 Effective length of query: 280 Effective length of database: 269 Effective search space: 75320 Effective search space used: 75320 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_106718540.1 CU100_RS21135 (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.3611243.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-89 284.3 0.0 6.1e-89 284.1 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106718540.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106718540.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 284.1 0.0 6.1e-89 6.1e-89 1 281 [. 14 285 .. 14 295 .. 0.96 Alignments for each domain: == domain 1 score: 284.1 bits; conditional E-value: 6.1e-89 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w++Ge+v++ da++hvlth+lhY ++vfeG RaY + if+l+eh+eRl++sa+il ++ipy eel+++ NCBI__GCF_003010935.1:WP_106718540.1 14 WMNGEFVRWTDARIHVLTHGLHYASSVFEGERAYGG----EIFKLNEHTERLHESARILGFKIPYDVEELNDA 82 9*********************************99....9******************************** PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 ++++l k+++++aY+Rp++++G+e++g++++++ k++v+ia w+w+ y++ +Gi+ ++ +rr ++ + NCBI__GCF_003010935.1:WP_106718540.1 83 CRKLLAKQGFQDAYVRPIAWRGSESMGVSAQAN-KINVAIAIWQWPSYFDPAQKLRGIRLDMAEYRRPDPRTA 154 ******************************777.****************99999****************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 p+k kaag Y+ ++ k+ a ++Gy +a++Ld G vae +G n+f vkdg + tP + L+gitr +vi+ NCBI__GCF_003010935.1:WP_106718540.1 155 PSKSKAAGLYMICTISKHAAEAKGYADALMLDWRGQVAEATGANVFFVKDGIIHTPVP-DCFLDGITRRTVIE 226 ********************************************************99.99************ PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaff 281 lak++g+ev+e++i eel + fltGtaaevtP+ e+ + ++G++ +l++ + NCBI__GCF_003010935.1:WP_106718540.1 227 LAKRRGYEVVERVIMPEELVDFEQCFLTGTAAEVTPVSEISRYRF---TVGEIAINLMNDYA 285 ****************************************98876...46777777777775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (296 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: 19.18 // [ok]
This GapMind analysis is from Jul 26 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