Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate RR42_RS05770 RR42_RS05770 aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Cup4G11:RR42_RS05770 Length = 395 Score = 168 bits (426), Expect = 2e-46 Identities = 117/376 (31%), Positives = 180/376 (47%), Gaps = 18/376 (4%) Query: 12 KPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIP 71 K T+ AL R V+L G PDFD + +A A+ G +Y P AG+P Sbjct: 24 KVGTTIFTVMSALAAERNAVNL---GQGFPDFDCDPKIVDAVAHAMRSGLNQYPPMAGVP 80 Query: 72 ELREALAEKFRRENGLSVT-PEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPE 130 +LR+A+A K + G + E VT G Q + + PGDEVIVL P + SY Sbjct: 81 KLRQAIAGKIGKLYGHAYDWDSEITVTAGATQGILTTILCAVHPGDEVIVLEPCYDSYIP 140 Query: 131 MVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALA 190 + AGG VV V +P +R+ AITPRT+ L++N+P+NPTG ++ ++ LA Sbjct: 141 AIEMAGGKVVSVALDAPHFHIPF-DRLAAAITPRTRMLLINTPHNPTGTIWRAGDMDRLA 199 Query: 191 RLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPE---HTLTVNGAAKAFAMTGWRIGYAC 247 L D L+SDE+YEH++++G+ PE + V+ K + +TGW++GY Sbjct: 200 GLLAGTDILLLSDEVYEHMVFDGQPHQSVSRHPELARRSFVVSSFGKTYHVTGWKVGYVA 259 Query: 248 GPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGL 307 P + V + + +T Q + + + ++++A Y+ +RD GL Sbjct: 260 APAALSAEFRKVHQFNVFTVNTPVQHGLADYMAD---PAPYLDLA-AFYQAKRDFFRAGL 315 Query: 308 TALGLKAVRPSGAFYVLMDTSPIAPDEVRAAERLL--EAGVAVVPGTDFAA----FGHVR 361 A K + G ++ +D S I+ L E GVA +P + F + G VR Sbjct: 316 AATRFKLLPSDGTYFQCVDYSAISDMSEADFSMWLTREIGVAAIPVSAFYSQPRESGVVR 375 Query: 362 LSYATSEENLRKALER 377 +A EE L AL R Sbjct: 376 FCFAKKEETLALALAR 391 Lambda K H 0.317 0.133 0.379 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: 342 Number of extensions: 19 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: 385 Length of database: 395 Length adjustment: 31 Effective length of query: 354 Effective length of database: 364 Effective search space: 128856 Effective search space used: 128856 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 (21.7 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