Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_013257671.1 DEBA_RS04245 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000143965.1:WP_013257671.1 Length = 357 Score = 433 bits (1114), Expect = e-126 Identities = 208/344 (60%), Positives = 262/344 (76%), Gaps = 1/344 (0%) Query: 15 KPKP-DPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEG 73 KPKP D N L FGR+FTDHM +MDY KGW++PR+ PY P ++DPAAM++HYGQ VFEG Sbjct: 14 KPKPADENNLGFGRIFTDHMLLMDYQTGKGWHNPRVEPYGPFTLDPAAMIFHYGQEVFEG 73 Query: 74 LKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEG 133 LKAY E HV +FRP N+ER+N+S DRLCIP + E VLE + +L+ +++DWIP AEG Sbjct: 74 LKAYRGEGGHVYMFRPAANIERMNRSCDRLCIPALPNEVVLEAMYELIRVEQDWIPRAEG 133 Query: 134 TSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGT 193 TSLY+RP IIATE LGV S TY II PVG+YY EG PV+I VE ++VRA GGT Sbjct: 134 TSLYVRPTIIATEACLGVKTSATYLFYIITGPVGAYYAEGFNPVRIWVEEKYVRAAIGGT 193 Query: 194 GNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLN 253 G AKT+GNYASSLKA A EKGF+QVLWL+ +++ IEEVG+MNIFFKI GE++T L+ Sbjct: 194 GEAKTSGNYASSLKAATEAHEKGFTQVLWLNACDRQSIEEVGTMNIFFKIAGEVITSPLD 253 Query: 254 GSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGEL 313 GSIL G+TR+SV+AL +HWG+ VSER++ ID++I A K G LEEAFGTGTAAVISPVG + Sbjct: 254 GSILPGVTRDSVLALCRHWGMNVSERQLTIDDIIAAAKAGTLEEAFGTGTAAVISPVGSI 313 Query: 314 IWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVA 357 ++ + + +G+TG ++ KLYD ITGIQ G D FGW +VA Sbjct: 314 HFKGQDYQVADGQTGALSLKLYDEITGIQLGKKPDPFGWVVKVA 357 Lambda K H 0.316 0.135 0.390 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: 470 Number of extensions: 17 Number of successful extensions: 1 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: 363 Length of database: 357 Length adjustment: 29 Effective length of query: 334 Effective length of database: 328 Effective search space: 109552 Effective search space used: 109552 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_013257671.1 DEBA_RS04245 (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.1233.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-129 415.3 0.0 7.5e-129 415.1 0.0 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013257671.1 DEBA_RS04245 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013257671.1 DEBA_RS04245 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.1 0.0 7.5e-129 7.5e-129 1 313 [] 44 356 .. 44 356 .. 0.99 Alignments for each domain: == domain 1 score: 415.1 bits; conditional E-value: 7.5e-129 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++++++++++++ld++++++hYgqevfeGlkayR + G++++fRp an++R++rs++rl +P l++e+ lcl|NCBI__GCF_000143965.1:WP_013257671.1 44 WHNPRVEPYGPFTLDPAAMIFHYGQEVFEGLKAYRGEGGHVYMFRPAANIERMNRSCDRLCIPALPNEV 112 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 +lea+ +l+++++dw+p a+ ++sLY+RP++iate+ lGvk++ +ylf++++ PvGaY+++g +pv+i+ lcl|NCBI__GCF_000143965.1:WP_013257671.1 113 VLEAMYELIRVEQDWIPRAE-GTSLYVRPTIIATEACLGVKTSATYLFYIITGPVGAYYAEGFNPVRIW 180 *****************999.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 ve++yvRaa +GtG +k++GnYa+sl+a ++a+e+g+ +v++l++ +++ ieevG++nif+ + ge++ lcl|NCBI__GCF_000143965.1:WP_013257671.1 181 VEEKYVRAAIGGTGEAKTSGNYASSLKAATEAHEKGFTQVLWLNACDRQSIEEVGTMNIFFKIA-GEVI 248 ************************************************************9998.8*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl +siL+gvtr+s+l l +++g++v+er+++id++ aa++aG + +f++Gtaavi+Pvg+++ +g lcl|NCBI__GCF_000143965.1:WP_013257671.1 249 TSPLDGSILPGVTRDSVLALCRHWGMNVSERQLTIDDIIAAAKAGTLeeAFGTGTAAVISPVGSIHFKG 317 *********************************************9888******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 + ++v+++++G ++ kl+de+t+iq+Gk+ d++gW+v+v lcl|NCBI__GCF_000143965.1:WP_013257671.1 318 QDYQVADGQTGALSLKLYDEITGIQLGKKPDPFGWVVKV 356 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (357 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: 8.92 // [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