Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 214 bits (545), Expect = 4e-60 Identities = 145/412 (35%), Positives = 208/412 (50%), Gaps = 48/412 (11%) Query: 11 ALLEAEKT--LDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVE 68 A L+A K + G N + + + R A +WD EG YID G V N GH +P+VV Sbjct: 4 AELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVA 63 Query: 69 AVKRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFP---------VNSGTEANEA 119 AVK Q + T + Y + A L +LNR+ P V +G EA E Sbjct: 64 AVKAQLDNFSH------TCVMVNPYESAVA-LAEQLNRIAPGGSDKKAIFVTTGAEAVEN 116 Query: 120 ALKFARAHTGRKKFVAAMRGFSGRTMGSLSVTWE-PKYREPFLPLVEPVEFIPYN----- 173 +K ARAHTGR+ +A GF GRT ++++T + Y+ F P + PY Sbjct: 117 CVKIARAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHG 176 Query: 174 -DVEALKRAVDE---------ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLI 223 V+ +A++ + AA+++EPVQGEGG A PEFL+A R + + G +L+ Sbjct: 177 VSVKDSLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLV 236 Query: 224 LDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTT 283 +DEIQTG GRTGK F+ EH G+ PD++T+AK + GG PL V + E+ + GG G T Sbjct: 237 MDEIQTGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGT 296 Query: 284 FGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS---PKIREVRGMGLMVG 340 +GG+P+ A +A + ++ +L ERA ++G F + L A+ I EVR G M+ Sbjct: 297 YGGSPVGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIA 356 Query: 341 LEL---------KEKAAPYIARLEKEHRVLALQAG--PTVIRFLPPLVIEKE 381 +EL I H ++ L G VIRFLP L I E Sbjct: 357 MELVIDGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDE 408 Lambda K H 0.319 0.137 0.403 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: 424 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: 395 Length of database: 426 Length adjustment: 31 Effective length of query: 364 Effective length of database: 395 Effective search space: 143780 Effective search space used: 143780 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 (21.7 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