Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041434172.1 THAL_RS02350 branched-chain-amino-acid transaminase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_000025605.1:WP_041434172.1 Length = 305 Score = 305 bits (780), Expect = 1e-87 Identities = 149/303 (49%), Positives = 211/303 (69%), Gaps = 2/303 (0%) Query: 14 MKYVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHD 73 M+Y + G+++P +EA I I T++ HYGT++FEGIRAYWN +++ LY+ AR+HY R Sbjct: 1 MEYAFFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEHHQLYILFAREHYQRLLA 60 Query: 74 SAKIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAII 133 + + M +++ YSVD+L++ TVELLR N++ DVYIRPI + + + AI Sbjct: 61 NCRAMFMELPYSVDDLVNITVELLRKNNIKHDVYIRPIAYFKDLALTPKLIGFTPEIAIY 120 Query: 134 TVPFGHYLE-PKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILL 192 T FG YL+ KGI+ K SW+R ++ P + KV+G YVNS +A +A ++G+DEAI+L Sbjct: 121 TYSFGRYLDTSKGIRVKTSSWIRNDDNSIPSRWKVAGAYVNSALAKTEAILAGYDEAIML 180 Query: 193 NRDGYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVI-TIARDLGLTVTEKRITRE 251 N++G+VAEGSGENIF+++ + TPP +D ILEGITR VI I +L L V E+ I+R Sbjct: 181 NQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRSAVIKLIKNELVLEVEERSISRS 240 Query: 252 ELYTADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLT 311 ELY+ADEVF TGTAAE+TPVV ID R IG+G+ GPI +++ Y D V G + +YK WLT Sbjct: 241 ELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGNIERYKGWLT 300 Query: 312 PIY 314 P+Y Sbjct: 301 PVY 303 Lambda K H 0.321 0.139 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: 328 Number of extensions: 21 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: 314 Length of database: 305 Length adjustment: 27 Effective length of query: 287 Effective length of database: 278 Effective search space: 79786 Effective search space used: 79786 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_041434172.1 THAL_RS02350 (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.2594002.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-125 403.3 0.1 3.5e-125 403.1 0.1 1.0 1 NCBI__GCF_000025605.1:WP_041434172.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025605.1:WP_041434172.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.1 0.1 3.5e-125 3.5e-125 1 298 [] 5 302 .. 5 302 .. 0.98 Alignments for each domain: == domain 1 score: 403.1 bits; conditional E-value: 3.5e-125 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk..glaifrlkehveRlydsakilrleipyskeelv 71 +++G++v++e+ak+++ t+++hYGt+vfeGiRaY++++ +l+i++++eh++Rl+ + +++ +e+pys ++lv NCBI__GCF_000025605.1:WP_041434172.1 5 FFEGRIVPIEEAKISIKTNSFHYGTAVFEGIRAYWNEEhhQLYILFAREHYQRLLANCRAMFMELPYSVDDLV 77 79*********************************98866899****************************** PP TIGR01122 72 evtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvkvssfrraa 142 ++t+e+lrknn+k+ +YiRp++y ++dl l+pk ++ ++e++i+++++g+yl++ +kGi+vk+ss+ r++ NCBI__GCF_000025605.1:WP_041434172.1 78 NITVELLRKNNIKHdVYIRPIAY--FKDLALTPKlIGFTPEIAIYTYSFGRYLDT---SKGIRVKTSSWIRND 145 ************988********..9****************************7...7************** PP TIGR01122 143 vnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrd 215 +nsip+++k+ag+Y+ns+lak+ea+ aGydeai+L+++G+vaeGsGenif+v+ +++tPp ++iL+gitr NCBI__GCF_000025605.1:WP_041434172.1 146 DNSIPSRWKVAGAYVNSALAKTEAILAGYDEAIMLNQNGFVAEGSGENIFLVRGRKVVTPPCWDHILEGITRS 218 ************************************************************************* PP TIGR01122 216 aviklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287 avikl+k el++ev+e++isr+ely aDevfltGtaae+tP++e+D+rkig+g +Gp+t++lq+ +fd v+g+ NCBI__GCF_000025605.1:WP_041434172.1 219 AVIKLIKnELVLEVEERSISRSELYSADEVFLTGTAAEITPVVEIDNRKIGSGDIGPITRELQKIYFDAVRGN 291 *****99789*************************************************************** PP TIGR01122 288 tekkeewltyv 298 +e++++wlt+v NCBI__GCF_000025605.1:WP_041434172.1 292 IERYKGWLTPV 302 ********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (305 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: 15.33 // [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