Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate Pf6N2E2_5326 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5326 Length = 396 Score = 138 bits (348), Expect = 3e-37 Identities = 132/433 (30%), Positives = 204/433 (47%), Gaps = 45/433 (10%) Query: 17 DAVTSLKAQVTGDLMDIVVDLDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTP 76 DA+T+ T + + G G RL D +DG EYLD + +GH HP L Sbjct: 4 DAMTAACLMTT--YQPLALSFTHGLGTRLWD-QDGREYLDAVAGVAVTNVGHSHPRL--- 57 Query: 77 EFEAALVRAGRVKPSNPDFATVEQARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVA 136 A +AG + ++ ++ Q R A+ +++G L FF + G A E ALK+A Sbjct: 58 -VAAISEQAGLLLHTSNLYSIDWQQRLAQKLTQLSG---LERAFFNNSGAEANETALKLA 113 Query: 137 --FDWKTKVNARKGVAIRGSRVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPS 194 + W KG I V+ ++ AFHGR+ T+ + D +R + R+P Sbjct: 114 RLYGW------HKG--IEQPLVVVMDNAFHGRTLGTMCAS--DGPSVR----LGFNRLPG 159 Query: 195 PAV-VPGDDWDDPELLPHERVAVEAAEAALRRYGREIACFVYEPIQGEGGDRHLRPRFLR 253 + VP D + A EA + + I + EPIQGE G + P +L+ Sbjct: 160 DFIKVPFGD-------------LAALEAIQQAHAERIVAVLVEPIQGESGVQLAPPGYLK 206 Query: 254 AVQELCREHDVLTVADEVQTG-ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVLE 312 A++ELC L + DE+QTG TG+ +A+Q G+ PD++ K + +G Sbjct: 207 ALRELCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKGLGNGVPIGACLARG 266 Query: 313 VEENAFREASRISSTWGGSLTDMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEF 372 F S S+ G L V T +LE+IE + L +++R G+ LLG LR +A+ Sbjct: 267 KAAELFTPGSHGSTFGGNPLACRVGCT-VLEIIEQQALVDNARHQGDQLLGRLRIELADN 325 Query: 373 PSVVRDARGRGLMCAISFADPDKRNRALAVARDHHRTLFLPSGTDSLRCRPPLSVRPEEV 432 P+V+ RG+GLM I P R+ AL ARDH + + G ++R PPL++ EV Sbjct: 326 PNVLA-IRGQGLMIGIELKQP-VRDLALRAARDHGLLINITRG-QTIRLLPPLTIDGREV 382 Query: 433 VDAVSALRKTLVE 445 V + + L + Sbjct: 383 EMIVRGVSRCLAQ 395 Lambda K H 0.321 0.137 0.410 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: 421 Number of extensions: 22 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: 447 Length of database: 396 Length adjustment: 32 Effective length of query: 415 Effective length of database: 364 Effective search space: 151060 Effective search space used: 151060 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