Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_085217296.1 B9N75_RS02070 aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_900177405.1:WP_085217296.1 Length = 384 Score = 297 bits (760), Expect = 4e-85 Identities = 160/384 (41%), Positives = 230/384 (59%), Gaps = 13/384 (3%) Query: 7 RPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPL 66 R T+VF MS A +GAVNLGQGFPD P ++ A + + G +QYPP G L Sbjct: 6 RDIPTSVFERMSLAARELGAVNLGQGFPDFGWPEDVVAKAAELLTGAASQYPPMRGLPEL 65 Query: 67 RRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVV 126 R A+A +H G+ Y P+ E+ VT GATEA+A+A+L L+EPG EVLL +P YD+Y P+V Sbjct: 66 RAAVADHYSQHQGIAYAPD-EITVTSGATEALASALLALIEPGDEVLLFQPLYDAYVPMV 124 Query: 127 AMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAE 186 G V L P + + +A+ A+TPRTR ++ N+PHNPTG S EL A+AE Sbjct: 125 RRGGGVPRYVALRPPE--WRITREAIEAALTPRTRLVVFNNPHNPTGRAFSQDELTALAE 182 Query: 187 IAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACG 246 + VA +L+V++DEV+EH++ A HLPLA GM++RT+ + SA K+F+ TGWK+GW Sbjct: 183 VCVARDLIVLSDEVWEHVMPGGAAHLPLASLPGMSDRTVKVGSAGKIFSLTGWKVGWIAA 242 Query: 247 PAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIG 306 PA L + A Q++++ Q AVA L ++A+ +R + RDRLA GL + G Sbjct: 243 PAALGDPITKAHQFVTFTTPPNLQAAVAYGLGKDEAYYRDMRAAFAVARDRLADGLADAG 302 Query: 307 FAVHDSYGTYFLCADPRPLGY-DDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADV 365 + V G+YFLC D G D FC + G+AAIP++AF ++ V Sbjct: 303 YVVLPGEGSYFLCVDLTASGIAADDLTFCERAVREAGIAAIPLTAF--------FEETPV 354 Query: 366 WNHLVRFTFCKRDDTLDEAIRRLS 389 N ++R F K+ +T+DE ++RL+ Sbjct: 355 TN-VIRLCFAKKQETIDEGLKRLA 377 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: 411 Number of extensions: 24 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: 397 Length of database: 384 Length adjustment: 31 Effective length of query: 366 Effective length of database: 353 Effective search space: 129198 Effective search space used: 129198 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 Jul 26 2024. The underlying query database was built on Jul 25 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