Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate RR42_RS05990 RR42_RS05990 aromatic amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__Cup4G11:RR42_RS05990 Length = 398 Score = 409 bits (1050), Expect = e-118 Identities = 207/399 (51%), Positives = 275/399 (68%), Gaps = 5/399 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLN-A 58 +F V+ DPIL L E F D R+ KVNL +G+Y+ ++G IP L+AV EAE ARL A Sbjct: 3 LFSAVEMAPRDPILGLNEAFNADTRATKVNLGVGVYFTDEGKIPLLRAVQEAEKARLTTA 62 Query: 59 QPHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRY 118 P G YLP+EG+ Y A+ LLFG + P++ + RV T Q LGG+GALK+GADFLKR Sbjct: 63 TPRG---YLPIEGIAAYDQAVQTLLFGKESPLITEGRVVTAQALGGTGALKIGADFLKRL 119 Query: 119 FPESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLL 178 +P++ V +SDP+WENH A+F AGF V Y +YD A++G+ F ++ +LK+ A +IV+L Sbjct: 120 YPDAKVAISDPSWENHRALFEAAGFPVINYAYYDAASHGLNFAGMVESLKSYAANTIVVL 179 Query: 179 HPCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLP 238 H CCHNPTG DL+ +QW V+E++K R LIPFLD+AYQGF G+E D A+R A +GLP Sbjct: 180 HACCHNPTGVDLSAEQWKQVVELIKERNLIPFLDMAYQGFAEGIEPDGAAVRLFAESGLP 239 Query: 239 ALVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAV 298 VS+SFSK FSLYGERVG LS++ E A RV+ Q+K +R NYS+PP G VVA V Sbjct: 240 FFVSSSFSKSFSLYGERVGALSIVTTGKEEAQRVMSQVKRVIRTNYSNPPTHGGTVVATV 299 Query: 299 LNDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQ 358 LN L+A W E+ EMR RI MR LV L+ + +F ++ +QRGMFSY+GL++AQ Sbjct: 300 LNSPELRAMWEQELGEMRDRIKLMRHALVDKLAAKGVPGDFSFVKSQRGMFSYSGLNSAQ 359 Query: 359 VDRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 VD LR E G+Y + +GR+CVA LN+ N+ V A AAV+ Sbjct: 360 VDVLRNEHGIYAVGTGRICVAALNSRNIDAVVNAIAAVL 398 Lambda K H 0.320 0.135 0.401 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: 429 Number of extensions: 12 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: 397 Length of database: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 Apr 09 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