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 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 209 bits (532), Expect = 1e-58 Identities = 133/381 (34%), Positives = 209/381 (54%), Gaps = 36/381 (9%) Query: 22 VWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENIS---ILSTSFSTPIKDEMLQA 78 +WD+EG+RY+DF TGI V GH +P ++ +K QL+N S ++ + + + + + Sbjct: 34 LWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPYESAVA--LAEQ 91 Query: 79 LDKVKPDKMDN-AMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTAGSLSVTWN- 136 L+++ P D A+ + +G EAVE +K AR TGR+ +IAF FHGRT ++++T Sbjct: 92 LNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVIAFNGGFHGRTNLTMALTGKI 151 Query: 137 KKYREPFEPLVG-------PVEFL------TFNNIEDLSKIDN---ETAAVIVEPIQGES 180 Y+ F P G PV F + IE L K+D + AA++VEP+QGE Sbjct: 152 TPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFKVDIAPCDVAAIVVEPVQGEG 211 Query: 181 GVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGG 240 G A EF++AL+ + G +L+ DEIQTGFGRTGK+++ +H + PD++T K I G Sbjct: 212 GFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMFSCEHAGVEPDLMTMAKGIAG 271 Query: 241 GFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQFS 300 GFP++ V I + G G TYGG+P+ A A +V+++E +VE+A + G F+ Sbjct: 272 GFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVMQEEQLVERAVKIGDSFN 331 Query: 301 NILVKNLADL-KVVREVRGKGLMIGIDIRF-----QPG-----QVLKYLQEKGILAVKAG 349 L +++ EVR +G MI +++ QP ++ G++ + G Sbjct: 332 QALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTALTQAIIANAAAHGLVLLACG 391 Query: 350 --STVIRFLPSYLITYENMEE 368 VIRFLP+ I+ E M E Sbjct: 392 FYGNVIRFLPALTISDEIMAE 412 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: 416 Number of extensions: 19 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: 387 Length of database: 426 Length adjustment: 31 Effective length of query: 356 Effective length of database: 395 Effective search space: 140620 Effective search space used: 140620 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