Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= BRENDA::Q3UEG6 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 182 bits (463), Expect = 2e-50 Identities = 132/416 (31%), Positives = 207/416 (49%), Gaps = 36/416 (8%) Query: 95 LFDSEGNRYLDFFSGIVTVSVGHCHPKVSAVAKKQIDRLWHTS-SVFFHSPMHEYAEKLS 153 L+D EG R++DF +GI ++ GH HPK+ + Q+D+ HT+ + ++ E AE+++ Sbjct: 38 LWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPYASYVELAERIN 97 Query: 154 ALLPE--PLKVIFLVNSGSEANDLAMVMARAHSNHTDIISFRGAYHGCSPYTLGLTN-VG 210 L P P K F ++G+EA + A+ +ARAH+ +I+F G +HG + + LT V Sbjct: 98 RLTPGNYPKKTAFF-STGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMMGMALTGKVA 156 Query: 211 IYKMEVPGGIGCQSTMCPDVFRGPW-GGIHCRDSPVQTVRDCSCAPDCCQAKERYIEQFK 269 YK+ G G DVF P+ +H S E +E K Sbjct: 157 PYKL----GFG---PFPGDVFHAPYPSALHGITS------------------EDALEAVK 191 Query: 270 DTLNTSV-ATSIAGFFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCIADEVQTGFGRL 328 + + A +A EP+QG G P +F++ AL E G + IADEVQ+G+GR Sbjct: 192 GLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRT 251 Query: 329 GSHFWGFQTHDVLPDIVTMAKGIGNGFPMAAVVTTPEIAKSLAKRLLHFSTFGGNPLACA 388 G F + +DVLPD++TMAK + G P++AV EI + A L T+ GNPLA A Sbjct: 252 GKLF-AMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLG-GTYAGNPLAIA 309 Query: 389 IGSAVLEVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEMVQDKISR 448 AVL+V+EEE L Q +G + +LR + +VRG G MV +E + Sbjct: 310 SALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADPATGK 369 Query: 449 QPLPKTEVNQIHEDCKDMGLLVGRGGNFSQTFRIVPPMCVTKMEVDFAYEVFRAAL 504 T+ ++ + + GLL+ G++ R + P+ + +D A + A+ Sbjct: 370 PDAEYTK--KVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAKAI 423 Lambda K H 0.323 0.137 0.424 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: 518 Number of extensions: 27 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: 513 Length of database: 426 Length adjustment: 33 Effective length of query: 480 Effective length of database: 393 Effective search space: 188640 Effective search space used: 188640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 51 (24.3 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