Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate YP_002828121.1 NGR_c36470 aromatic amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000018545.1:YP_002828121.1 Length = 389 Score = 254 bits (649), Expect = 3e-72 Identities = 148/396 (37%), Positives = 220/396 (55%), Gaps = 7/396 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + DP+L L+ F++D R KV+L +G+Y +E G P +AV EAE RL + Sbjct: 1 MFDALARQPDDPLLALIGLFRKDERPGKVDLGVGVYRDETGRTPIFRAVKEAEKRL-LET 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 Y+ EG + + L+ G +++ VA +QT GGSGAL++ AD + R Sbjct: 60 QETKAYVGPEGDLVFLDHLWRLVGG---DTVERSHVAGVQTPGGSGALRLAADLIYRMGG 116 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 +W+ P+W NH IF AG E++TY ++D + V F+++++ L+ VLLH Sbjct: 117 RK-IWLGLPSWPNHAPIFKAAGLEIATYDFFDMPSQSVIFDNVVSALEGAAPGDAVLLHA 175 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CHNPTG LT QW + ++ R L+P +D+AYQGFG G+E+D +R + + AL Sbjct: 176 SCHNPTGGVLTEAQWMEIAALVAERGLLPLVDLAYQGFGRGLEQDVAGLRHLLTVVPEAL 235 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+ S SK F LY ER G + + +A V L R +YS PP+ GA VV +L Sbjct: 236 VAVSCSKSFGLYRERTGAIFGVTPSTSSADTVRSNLAGLARTSYSMPPDHGAAVVRTILA 295 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D L W E+E MR R+ +RQ L + L + ++ + +Q GMFS L+ A+V Sbjct: 296 DPDLARDWAEELEGMRLRMTGIRQALAEGLRSRW--QSLGAVADQEGMFSMLPLTEAEVM 353 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 RLR E G+Y+ SGR+ +AGL TA V V + F ++ Sbjct: 354 RLRTEHGLYMPGSGRINIAGLKTAEVADVIQKFTSL 389 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: 381 Number of extensions: 17 Number of successful extensions: 4 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: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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 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