Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 177 bits (448), Expect = 6e-49 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 26/396 (6%) Query: 3 VSRLRPYATTVF--AEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60 ++R++P AT + A + V+L G PD P + +AA+ AI G +Y Sbjct: 7 LTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTRYTQV 66 Query: 61 PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120 PG LR+A+ R +GV+ E V VT G +A+ L+ PG EVL+ P++ Sbjct: 67 PGIPELRQAVCGYFARFYGVEAPMEATV-VTNGGKQALYNLFQCLLNPGDEVLVPAPYWV 125 Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 SY +V +AG V V P RGF + + L RAVTP+TR L++NSP NPTGA S E Sbjct: 126 SYPALVELAGGVPVFVAS-PAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRAE 184 Query: 181 LAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAG-FDGMAERTITISSAAKMFNCTGW 239 AI E A+A +L V++DE+Y+ LV++ A + + ++ E ++ AK F TGW Sbjct: 185 TDAIMEWAIARDLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAMTGW 244 Query: 240 KIGWACGPAELI-AGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRL 298 ++G+A +LI A + Q S + + A+A DA V ++ S R RRD L Sbjct: 245 RVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDA-VEEMKKSFRRRRD-L 302 Query: 299 AAGLTEI--GFAVHDSYGTYFLCADPRPL---GYDDSTEFCAALPEKVGVAAIPMSAFCD 353 A G+ G G ++L AD R L DS C + E+ VA +P +AF D Sbjct: 303 AHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAFGD 362 Query: 354 PAAGQASQQADVWNHLVRFTFCKRDDTLDEAIRRLS 389 A +RF++ DDTL A+ +++ Sbjct: 363 DAC-------------LRFSYAVSDDTLMIALDKVA 385 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: 350 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: 397 Length of database: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 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