Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Length = 413 Score = 128 bits (322), Expect = 3e-34 Identities = 122/404 (30%), Positives = 189/404 (46%), Gaps = 43/404 (10%) Query: 33 IVVDLDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTPEFEAALVRAGRVKPSN 92 + + + G G RL D + G EYLD + +GH HP + A +AG + ++ Sbjct: 35 LALSFNKGLGTRLWD-QAGREYLDAVAGVAVTNVGHSHPKI----VAAITEQAGLLLHTS 89 Query: 93 PDFATVEQARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVA--FDWKTKVNARKGVA 150 ++ Q R A+ ++AG + FF + G A E ALK+A W KG Sbjct: 90 NLYSIDWQQRLAQKLTQLAG---MDRAFFNNSGAEANETALKIARLHGW------HKG-- 138 Query: 151 IRGSRVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPSPAV-VPGDDWDDPELL 209 I V+ +E AFHGR+ TLS ++ ++ + ++P V VP D Sbjct: 139 IEQPLVVVMENAFHGRTLGTLSASDGPAVRL------GFNKLPGDFVKVPFGD------- 185 Query: 210 PHERVAVEAAEAALRRYGREIACFVYEPIQGEGGDRHLRPRFLRAVQELCREHDVLTVAD 269 + A + + +G I + EPIQGE G + P +L AV+ELC L + D Sbjct: 186 ------LGALDKVQQAFGSRIVAVLMEPIQGESGVQLAPPGYLSAVRELCNRRSWLLMLD 239 Query: 270 EVQTG-ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVLEVEENAFREASRISSTW 328 E+QTG TG+ +A+Q G+ PD++ K + +G F S S+ Sbjct: 240 EIQTGIGRTGQWFAFQHEGIVPDVMTLAKGLGNGVPIGACLARGKAAELFTPGSHGSTFG 299 Query: 329 GGSLTDMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEFPSVVRDARGRGLMCAI 388 G L V T +L+++E + L E++R G LL LR +A P+ V RG+GLM I Sbjct: 300 GNPLACRVGCT-VLDIVEEQGLLENARLQGARLLERLRTELAGNPN-VSQIRGQGLMIGI 357 Query: 389 SFADPDKRNRALAVARDHHRTLFLPSGTDSLRCRPPLSVRPEEV 432 P R+ +L ARDH + + G +++R PPL++ EV Sbjct: 358 ELKQP-IRDLSLIAARDHGLLINVTRG-NTIRLLPPLTLDEREV 399 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: 412 Number of extensions: 22 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: 447 Length of database: 413 Length adjustment: 32 Effective length of query: 415 Effective length of database: 381 Effective search space: 158115 Effective search space used: 158115 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: 51 (24.3 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