Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate Pf1N1B4_2980 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2980 Length = 391 Score = 135 bits (339), Expect = 3e-36 Identities = 125/404 (30%), Positives = 191/404 (47%), Gaps = 43/404 (10%) Query: 33 IVVDLDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTPEFEAALVRAGRVKPSN 92 + + G G RL D + G EYLD + +GH HP + A +AG + ++ Sbjct: 13 LALSFSKGLGTRLWD-QAGREYLDAVAGVAVTNVGHSHPRI----VAAISEQAGLLLHTS 67 Query: 93 PDFATVEQARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVA--FDWKTKVNARKGVA 150 ++ Q R A R++G + FF + G A E ALK+A + W KG Sbjct: 68 NLYSIDWQQRLARKLVRLSG---MDRAFFNNSGAEANETALKLARLYGW------HKG-- 116 Query: 151 IRGSRVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPSPAV-VPGDDWDDPELL 209 I V+ +E AFHGR+ TLS ++ ++ + +P + VP D Sbjct: 117 IEQPLVVVMENAFHGRTLGTLSASDGPAVRL------GFNELPGDFIKVPFGD------- 163 Query: 210 PHERVAVEAAEAALRRYGREIACFVYEPIQGEGGDRHLRPRFLRAVQELCREHDVLTVAD 269 + A EA + +G I + EP+QGE G + P +L+AV+ELC L + D Sbjct: 164 ------LAALEAVQQAHGPRIVAILMEPVQGESGVQVAPPGYLKAVRELCNRRAWLLMLD 217 Query: 270 EVQTG-ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVLEVEENAFREASRISSTW 328 E+QTG TG+ +A+Q G+ PD++ K + +G + F S S+ Sbjct: 218 EIQTGIGRTGQWFAFQHEGIVPDVMTLAKGLGNGIPIGACLARGKAADLFTPGSHGSTFG 277 Query: 329 GGSLTDMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEFPSVVRDARGRGLMCAI 388 G L V T +LE+IE + L E++R GE LL LR +A+ P+V+ RG+GLM I Sbjct: 278 GNPLACRVGCT-VLEIIEEQGLLENARLQGERLLARLRIELADDPNVLA-IRGQGLMIGI 335 Query: 389 SFADPDKRNRALAVARDHHRTLFLPSGTDSLRCRPPLSVRPEEV 432 P R+ L ARDH + + G ++R PPL++ EV Sbjct: 336 ELKQP-IRDLTLIAARDHGLLINVTRG-KTIRLLPPLTIDEREV 377 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: 21 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: 391 Length adjustment: 32 Effective length of query: 415 Effective length of database: 359 Effective search space: 148985 Effective search space used: 148985 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