Align aromatic-amino-acid aminotransferase (EC 2.6.1.1) (characterized)
to candidate WP_028997211.1 H537_RS0106295 amino acid aminotransferase
Query= metacyc::PHETRANTHAUERA-MONOMER (404 letters) >NCBI__GCF_000430725.1:WP_028997211.1 Length = 394 Score = 481 bits (1237), Expect = e-140 Identities = 234/395 (59%), Positives = 295/395 (74%), Gaps = 1/395 (0%) Query: 1 MFEHVDAYPGDPILSLVETFHHDPRPRKVNLGIGLYYDEEGRIPLLGSVEKAEAALAANP 60 M +HV A+ GDPILSL E F D RP K+NL IG+Y DE R+P + +V +AEA L A Sbjct: 1 MLQHVPAFAGDPILSLNEAFQQDARPNKINLSIGVYADESLRLPAMAAVLEAEARLTARR 60 Query: 61 GPRPYLPMEGAADYRAAVQKLLFGPDSAALRAGRIATIQTIGGSGALKVGADLLKRYFPA 120 RPYLPMEG A +R AV+ L+FG A+ GR+AT+QTIG SGALK+GA+ ++++ P Sbjct: 61 DARPYLPMEGDAAFREAVRALVFGAAHPAVTQGRVATVQTIGSSGALKLGAEFIRQWLPG 120 Query: 121 SEVWVSDPTWDNHRSIFEGAGIEVHDYPYYDAASGGVRFDEMIETLQSLPAQSIVLLHPC 180 SEVWVSDPTWDNHR+IFE AG+ VH YPY+D A G V FD M++TL+SLPA+S+VLLH C Sbjct: 121 SEVWVSDPTWDNHRAIFESAGLAVHAYPYHDPARG-VAFDAMLDTLRSLPARSVVLLHGC 179 Query: 181 CHNPTGVDLSTAQWQEVIAVVASRGLIPFLDIAYQGFGDNLDDDAYAARAMADAGVSFFV 240 CHNPTG DL AQW + A+ A RGLIPF+D+AYQGFG+ +D DA RA+A+AG++ FV Sbjct: 180 CHNPTGEDLDAAQWGALTALCAQRGLIPFVDLAYQGFGEGVDADAGPVRALAEAGITGFV 239 Query: 241 SNSFSKNLSFYGERCGGLSVVCQDADEAERVLGQLKFTVRRNYSSPPVHGGRVAAAVMND 300 +NS SKN+ YGERCG LSVVC DA +AE VLGQLK VRR+YSSPP+H GRVAA V+ Sbjct: 240 ANSLSKNMGLYGERCGALSVVCGDAGQAEHVLGQLKLAVRRSYSSPPLHAGRVAAQVLGA 299 Query: 301 AGLHEEWVGEVRGMRERIKAMREKLHEVLSSTLPGRDFSYFVKQRGMFSYTGLTPEQVDR 360 L W E+ GMR+RI +MR LH L P +D+SY ++QRGMFSYTGL+ QVDR Sbjct: 300 PELRAAWAQELDGMRQRILSMRRALHAALVQRRPAQDWSYLLRQRGMFSYTGLSAAQVDR 359 Query: 361 LREEFAVYVVQSGRMCVAGLNRGNVDYVAKAMAAV 395 LREE A+Y+V+SGR+C+AGLN + VA+A+A + Sbjct: 360 LREEHAIYLVRSGRICLAGLNATCIGTVAQAIAGL 394 Lambda K H 0.320 0.136 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: 465 Number of extensions: 14 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: 404 Length of database: 394 Length adjustment: 31 Effective length of query: 373 Effective length of database: 363 Effective search space: 135399 Effective search space used: 135399 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: 50 (23.9 bits)
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