Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_013258202.1 DEBA_RS06895 alanine transaminase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000143965.1:WP_013258202.1 Length = 389 Score = 366 bits (939), Expect = e-106 Identities = 169/388 (43%), Positives = 248/388 (63%), Gaps = 3/388 (0%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 MQE RR++ LPPY+FA + + AR RG DII LG+G+PD+PTP H+++KLV A Sbjct: 1 MQEFRRMKRLPPYVFAVVTELKMAARRRGEDIIDLGMGNPDLPTPDHIVEKLVEAARKGA 60 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120 NHRY S+G+ R A+A WY+R Y VD+DP E V IG KEG++H+ L + PGD+ L Sbjct: 61 NHRYSASKGITKLRHAIAAWYKRRYDVDIDPETEAVATIGVKEGLSHLVLATISPGDVVL 120 Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180 P P YP++ ++AGG+ +P+ F DL + K++ ++P+NPT Sbjct: 121 APSPTYPIHPYSVVIAGGDLRNVPILPDRDFFEDLQTALRQTWPQPKMLITSFPHNPTTV 180 Query: 181 VADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPY 240 DL F ++VEF + + + HD AY+++T+DGY APS LQ PGAK++ +EF S SK Y Sbjct: 181 CVDLAFMTKLVEFCKENQIWLVHDFAYADLTFDGYEAPSVLQVPGAKDIAVEFFSASKSY 240 Query: 241 NMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQER 300 +M GWRLG+ G +++ AL RIKS +D G FQ +Q AGI AL QE + ++ VY+ R Sbjct: 241 SMAGWRLGFCVGNREMVNALTRIKSYLDYGVFQPIQIAGIIALNEDQECVKQIVEVYRSR 300 Query: 301 RDIIVEGFNSLGWHLEKPKATFYVWAPVPRGYTSA---SFAEMVLEKAGVIITPGNGYGN 357 RD+++ G +GWH+ PK T +VWA +P Y +A F + ++E+A V ++PG G+G Sbjct: 301 RDVLINGLERIGWHVPSPKGTMFVWAKIPEPYRAAGSVEFCKKLVEEAKVAVSPGIGFGE 360 Query: 358 YGEGYFRIALTISKERMQEAIERLRRVL 385 YG+ Y R AL +++R+ +AI LR+ L Sbjct: 361 YGDEYVRFALVENEQRINQAIRGLRKFL 388 Lambda K H 0.320 0.139 0.421 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: 430 Number of extensions: 19 Number of successful extensions: 2 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: 390 Length of database: 389 Length adjustment: 30 Effective length of query: 360 Effective length of database: 359 Effective search space: 129240 Effective search space used: 129240 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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