Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate HSERO_RS10805 HSERO_RS10805 succinyldiaminopimelate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__HerbieS:HSERO_RS10805 Length = 403 Score = 105 bits (263), Expect = 2e-27 Identities = 112/377 (29%), Positives = 170/377 (45%), Gaps = 27/377 (7%) Query: 37 LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSG--QAVDAEQ 94 L +G+P TPA I QA ID+L AG Y G ALR IA+ ++R + A + Sbjct: 34 LGIGEPKHPTPAFIQQALIDNL-AGLASYPATLGSDALRGAIADWLQKRYDIPRPDPATE 92 Query: 95 VVVLAGAQCALYAVVQCLLNP---GDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGF 151 ++ + G++ AL+++ Q +++P G V+ P Y YE GA+ V + F Sbjct: 93 ILPVNGSREALFSLTQTVVDPTRPGALVMCPNPFYQIYEGSAYLAGAQPYFVNSDPKRNF 152 Query: 152 RVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELL 211 +V + R + + + SP NP+GA L W+ L L + + SDE YSE+ Sbjct: 153 APDFSQVPQDVWERVQLLFVCSPGNPTGAVLTLEDWKELFALSDRYGFVIASDECYSEIY 212 Query: 212 FDGE----HVSPASLPGM-ADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266 F+ + + A L G R + +SLSK + G R G+V G AA+ L+ L Sbjct: 213 FNEDPPLGGMQAARLLGRDYRRLISFSSLSKRSNVPGMRSGFVAGDAAI---LKKFLLYR 269 Query: 267 LY---GSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMF 323 Y IQ A+ A + ++ Y + V L + L PD + Sbjct: 270 TYHGAAMSPVIQAASVLAWQDE-THVQGNIAKYVTKFSQVTPLLQEV--LEVALPDAAFY 326 Query: 324 VMVDI-RPTGLSAQAFADRLLDRHGVSVLAG-----EAFGPS-AAGHIRLGLVLGAEPLR 376 + + + +S FA RL + V+VL G EA G + AG IR+ LV E Sbjct: 327 LWAKVDKLVNISDTEFAQRLYAEYNVTVLPGSYLAREAHGVNPGAGRIRMALVAEVEECL 386 Query: 377 EACRRIALCAAELLGQA 393 EA +RI +L GQA Sbjct: 387 EAAQRIVAFTRKLAGQA 403 Lambda K H 0.322 0.136 0.411 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: 423 Number of extensions: 23 Number of successful extensions: 5 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: 393 Length of database: 403 Length adjustment: 31 Effective length of query: 362 Effective length of database: 372 Effective search space: 134664 Effective search space used: 134664 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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