Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 243 bits (619), Expect = 9e-69 Identities = 141/376 (37%), Positives = 202/376 (53%), Gaps = 15/376 (3%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 +I +Y V+GE +WD +G+ Y+DF GI V LGH +P + E L Q Sbjct: 14 MIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWH 73 Query: 63 LSTSFST-PIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKI------TGRKK 115 ++ P+ + +D D++ NSG EA EAALK ARK + + Sbjct: 74 TGNGYTNEPVLRLAKKLIDATFADRV---FFCNSGAEANEAALKLARKFAHDRYGSHKSG 130 Query: 116 IIAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSK-IDNETAAVIVE 174 I+AFKNAFHGRT ++S Y + F PL + +N+I S ID+ T AVIVE Sbjct: 131 IVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVE 190 Query: 175 PIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTA 234 PIQGE GV+PA+ F++ L+E +LLIFDE+QTG GRTG+L+AY HY + PD+LT Sbjct: 191 PIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTT 250 Query: 235 GKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQ 294 KA+GGGFPV + + A + G HG+TYGGNP+A A ++I ++ Q Sbjct: 251 AKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQ 310 Query: 295 KGQQFSNILVKNLADLKVVREVRGKGLMIG----IDIRFQPGQVLKYLQEKGILAVKAGS 350 + F L + EVRG GL+IG D Q Q+ + + G++ + AG Sbjct: 311 RHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGG 370 Query: 351 TVIRFLPSYLITYENM 366 V+RF P+ ++ E + Sbjct: 371 NVVRFAPALNVSEEEV 386 Lambda K H 0.317 0.136 0.385 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: 382 Number of extensions: 11 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: 387 Length of database: 406 Length adjustment: 31 Effective length of query: 356 Effective length of database: 375 Effective search space: 133500 Effective search space used: 133500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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