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 BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 212 bits (539), Expect = 2e-59 Identities = 139/391 (35%), Positives = 205/391 (52%), Gaps = 32/391 (8%) Query: 16 KGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSFSTPIKD-- 73 + E +WD+EGRR++DF GI V GHR+P IL +++QL++ + + P Sbjct: 28 RAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQI-VPYASYV 86 Query: 74 EMLQALDKVKP-DKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTAGSLS 132 E+ + L++ P D +G EAVE A+K AR TGR +IAF FHGRT ++ Sbjct: 87 ELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMA 146 Query: 133 VTWN-KKYREPFEPLVGPVEFLTFNN-------------IEDLSKID---NETAAVIVEP 175 +T Y+ F P V F N IE L K D AA+I EP Sbjct: 147 LTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTADSLKAIEFLFKADIDPKRVAAIIFEP 206 Query: 176 IQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAG 235 +QGE G PA EF++AL++ G LLI DE+QTGF RTGKL+A HY++VPD++T Sbjct: 207 VQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVPDLMTVA 266 Query: 236 KAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQK 295 K++ GG P+S V + + G G TY GNP+A+AA A +I++E + E+A Sbjct: 267 KSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIIDEEKLCERATLL 326 Query: 296 GQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQPG-----QVLKYLQ----EKGILAV 346 G + L+ +D+ + +VRG G M+ ++ G + K +Q E+G+L + Sbjct: 327 GDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAEFTKRVQTRALERGLLLL 386 Query: 347 KAG--STVIRFLPSYLITYENMEEASNVLRE 375 G S V+RFL I +EA +L + Sbjct: 387 VCGVYSNVVRFLFPLTIQDAVFDEAMAILED 417 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: 426 Number of extensions: 17 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: 387 Length of database: 427 Length adjustment: 31 Effective length of query: 356 Effective length of database: 396 Effective search space: 140976 Effective search space used: 140976 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