Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate Pf6N2E2_2395 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2395 Length = 470 Score = 229 bits (584), Expect = 1e-64 Identities = 161/443 (36%), Positives = 234/443 (52%), Gaps = 60/443 (13%) Query: 7 NPSKWLAAEKKYDSGVYN---KHDVVMVRGQGATVWDENGRSYIDCVVGYGVATLGHSHP 63 N S LA + + +S + + + + R +G V D GR++IDC+ G G LGH+HP Sbjct: 27 NESPLLARQSRQESNARSYPRRIPLALKRAKGLYVEDVEGRTFIDCLAGAGTLALGHNHP 86 Query: 64 DVVKAVQEQ-AGKLMVMPQTVPNDKRAEFLQELVGVLPQGLD---RVFLCN-SGTEAMEA 118 V++A+Q+ A +L + + + F+Q+L G+LP L ++ C +GT+A+EA Sbjct: 87 VVIEAIQQVLADELPLHTLDLTTPVKDRFVQDLFGLLPAALAAEAKIQFCGPTGTDAVEA 146 Query: 119 AKKFAITATGRSRFVSMKRGFSGRSLGALSFTWEPKYREPFGDAVDNKSVDFVTY----- 173 A K TATGRS +S + G+ G S GALS ++P G + N V F+ Y Sbjct: 147 ALKLVRTATGRSTVLSFQGGYHGMSQGALSLMGSLGPKKPLGALLSN-GVQFMPYPYDYR 205 Query: 174 ------------GNLDELR------AAVTEQTAAVIMEPVQGEGGVRPASAEFIQEARRI 215 NL L A + AAVI+E VQGEGGV PA ++++ RRI Sbjct: 206 CPFGLGGVAGVKANLHYLENLLNDPEAGVQLPAAVIVEVVQGEGGVIPADLDWLRGLRRI 265 Query: 216 TREKGALLILDEIQTGFCRTGKMFACEHFGVIPDGMTLAKAIAGGTPTAAFAMMSEVADR 275 T + G LI+DEIQ+GF RTGKMFA EH G+IPD + L+KAI G P A + Sbjct: 266 TEQAGVALIVDEIQSGFGRTGKMFAFEHAGIIPDVVVLSKAIGGSLPLAVVVYRDWLDTW 325 Query: 276 MPAGGHGTTFGGNPLSMAAGVASLRAMKREGLAEQAREKGAYMMDKLRAIQS--PKIREV 333 +P G H TF GN ++MAAG A +R ++ L A G + + LR +Q P++ ++ Sbjct: 326 LP-GAHAGTFRGNQMAMAAGSAVMRYLQEHALPAHAAAMGERLSEHLRILQRDFPQLGDI 384 Query: 334 RGLGLMIGVELKEKSA-------PYIHA-----MEHDEGVLCLAATPL---------VVR 372 RG GLM+GVEL + + P +HA ++ + CL + VVR Sbjct: 385 RGRGLMLGVELVDPTGKPDALGHPPVHAGLAPRLQRE----CLKRGLILELGGRQGGVVR 440 Query: 373 FLPPAVISKEQIDQVVAAFERVL 395 FLPP +I+K +ID+V F R L Sbjct: 441 FLPPLIITKAEIDRVAEIFGRAL 463 Lambda K H 0.317 0.132 0.380 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: 510 Number of extensions: 21 Number of successful extensions: 6 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: 429 Length of database: 470 Length adjustment: 33 Effective length of query: 396 Effective length of database: 437 Effective search space: 173052 Effective search space used: 173052 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: 51 (24.3 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