Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 271 bits (692), Expect = 3e-77 Identities = 156/385 (40%), Positives = 223/385 (57%), Gaps = 21/385 (5%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY + ++ VRG+G + G Y+D G V LGHG+P+ +A+ QA TLM + Sbjct: 9 VYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSN 68 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAH------TGRKKFVAA 136 +P + + + + VF NSG EA E A+K AR + R K + Sbjct: 69 LYGSPQGEALAQRI--VDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITF 126 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQG 196 F GR++G++S T +PK R+ F PL+ +++ +ND+E +D+ETA ++E VQG Sbjct: 127 KNAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVETVQG 186 Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256 EGG+ T EF++ R+ E G LLILDEIQ G GRTGK +A+EH+GI PDILT AK + Sbjct: 187 EGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGI 246 Query: 257 GGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316 G G PLGA + EE A+ M G HG+T+GGNPLAMAAG A + + +E ++G Sbjct: 247 GNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMG-- 304 Query: 317 FMEKLRA-----IPSPK--IREVRGMGLMVGLELKEKAA--PYIARLEKEHRVLALQAGP 367 E+LRA IP+ E+RG GLM+G++LKE A ++A L + H +L + AG Sbjct: 305 --ERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLTVAAGE 362 Query: 368 TVIRFLPPLVIEKEDLERVVEAVRA 392 V R LPPLVIE+ + +E + A Sbjct: 363 NVFRVLPPLVIEESHIAECIEKLSA 387 Lambda K H 0.319 0.137 0.402 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: 414 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: 395 Length of database: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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