Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Pf1N1B4_849 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_849 Length = 382 Score = 256 bits (653), Expect = 1e-72 Identities = 154/393 (39%), Positives = 216/393 (54%), Gaps = 13/393 (3%) Query: 1 MTVSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60 M S+L T+F +MS LA + GA+NL QGFPD DGP + A IA G NQY P Sbjct: 1 MITSKLPNVGITIFTQMSQLAAQTGAINLSQGFPDFDGPQALRDAVGRHIASGHNQYSPM 60 Query: 61 PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120 G LR+ IAA+ R +G D ++EV VT GAT+AI A+ ++ G EV++ +P YD Sbjct: 61 TGLPVLRQQIAAKIARSYGAHVDADSEVTVTPGATQAIFCAIQAVIHSGDEVIVFDPAYD 120 Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 SY P V +AG V V L + F++D L A++PRTR +I+NSPHNP+GA++S E Sbjct: 121 SYEPSVELAGGRCVHVQLGLND--FSIDFQKLADALSPRTRMIILNSPHNPSGALISRAE 178 Query: 181 LAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWK 240 L +A + ++ VI+DEVYEHLVFD H+ + + + +R +SS K ++ TGWK Sbjct: 179 LDQLAALIRDRDIYVISDEVYEHLVFDGVSHVSVLAHEELYQRAFVVSSFGKTYHVTGWK 238 Query: 241 IGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAA 300 G+ P L A +R QY+S+ G P Q A+A + V L +A+RD Sbjct: 239 TGYVVAPPALTAELRKVHQYVSFCGVTPLQYALADYMAEHPEHVEELPGFYQAKRDLFCD 298 Query: 301 GLTEIGFAVHDSYGTYFLCADPRPLGYD-DSTEFCAALPEKVGVAAIPMSAFCD-PAAGQ 358 L+ F+ GTYF D + D + E + + GVA+IP+S F P GQ Sbjct: 299 LLSPSRFSFTRVAGTYFQLVDYSQIRPDLNDVEMALWMTREHGVASIPISVFYQTPPEGQ 358 Query: 359 ASQQADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391 LVR F KR++TL EA +L V+ Sbjct: 359 ---------RLVRLCFAKREETLREAAAKLCVI 382 Lambda K H 0.321 0.135 0.405 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: 351 Number of extensions: 15 Number of successful extensions: 3 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: 397 Length of database: 382 Length adjustment: 30 Effective length of query: 367 Effective length of database: 352 Effective search space: 129184 Effective search space used: 129184 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 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