Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= curated2:Q7SI94 (388 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 238 bits (608), Expect = 2e-67 Identities = 129/363 (35%), Positives = 209/363 (57%), Gaps = 13/363 (3%) Query: 16 IKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEISTLSLAFDTPIREE 75 +KG G +WD++ +++D G V LGH + ++ L +Q +++ LS Sbjct: 24 VKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLSNTMTNEPALM 83 Query: 76 MIKELDELKPEDLDNLFLLNSGSEAVELALKIARKITKRR------KIVAFKNSFHGRSM 129 + K L + + ++ NSG+EA E ALK+ R++ + +I+AFK FHGR++ Sbjct: 84 LAKHL--VDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFKQGFHGRTL 141 Query: 130 GALSVTWNKKYREPFEPLIGPVEFLEYNNVDSLKSITED-TAAVIVEPVQGEGGVIPAKK 188 +SV Y + F P ++ EYNN+DSLK++ D T AV++EP+QGEGG+I Sbjct: 142 FTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRTCAVVLEPLQGEGGIINPTP 201 Query: 189 EFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAGKAIGGGFPVSAV 248 EF+K +RE+ ++ NALL+ DEVQTG GRTG+++AY + PD+LT KA+GGGFP+ A+ Sbjct: 202 EFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVTPDVLTTAKALGGGFPIGAM 261 Query: 249 FLPNWISEKIEEGDHGSTYGGNPLAAAAVTAACKVAKSEKIAEQAQKKGELFMRILKEKL 308 +++ + G HGSTYGGNPLA A AA + ++ +++ +LF L Sbjct: 262 LTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEVLNGVKEREQLFRDGLNAIN 321 Query: 309 EDFKIVREIRGLGLMIGIDLKVNPSIAIK----VLQDEKVLSLKAGLTTIRFLPPYLITQ 364 + +++ E+RG GL++G L + + + +E VL L AG +RF P +I + Sbjct: 322 DKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVLLLMAGQNVVRFAPSLIIPE 381 Query: 365 SDM 367 +D+ Sbjct: 382 ADV 384 Lambda K H 0.317 0.136 0.386 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: 360 Number of extensions: 13 Number of successful extensions: 3 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: 388 Length of database: 405 Length adjustment: 31 Effective length of query: 357 Effective length of database: 374 Effective search space: 133518 Effective search space used: 133518 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 (21.6 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