Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_022947828.1 H035_RS0104615 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000421465.1:WP_022947828.1 Length = 463 Score = 238 bits (608), Expect = 2e-67 Identities = 150/398 (37%), Positives = 218/398 (54%), Gaps = 33/398 (8%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQ-PLHSQELLDPLRAMLAKTLA 134 L D + E++D L GFG+F +G +P + SA++ L P Q + L +LA+ L Sbjct: 49 LYDQEDNEYLDLLSGFGVFALGRNHPTIQSALREVLDLDLPDLVQMDVSILSGLLAEKLV 108 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKS 194 +TP L FFCNSG E+VEAA+K A+ Y + R + + AFHG +LGALS + Sbjct: 109 QVTPEPLTKLFFCNSGAEAVEAAIKFAR-YTTGRSRILYC--EHAFHGLTLGALSLNGEE 165 Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYL 254 FR+ F PLLP +PF ++EA+ AL E AA I+EPIQG+G V LP YL Sbjct: 166 VFRQGFGPLLPDCDAIPFNDLEALERALKE-----QPTAAFIVEPIQGKG-VNLPDDDYL 219 Query: 255 TAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIA 314 T +LC ++GAL I DE+Q G+GRTG+++A EH V+PD+L +AKAL GG +P+GA Sbjct: 220 TEAARLCRKYGALFIADEIQAGLGRTGRLWAIEHWGVEPDMLLMAKALSGGFVPVGAVAM 279 Query: 315 TEEVFSVLF---DNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 T V +F D +H +TF N A AA LAT++V+ E+ L A A ++G+ L+ G Sbjct: 280 TAHVMDKVFNRMDRAVVHGSTFSKNNPAMAAGLATLSVIEEEKLLANAARQGEALIGGLN 339 Query: 372 QLAREYPDLVQEARGKGMLMAIEF-------------VDNEIGYNFASEMF------RQR 412 L +Y + Q RGKG+++A+EF + S+M R R Sbjct: 340 ALTDKY-EFFQAVRGKGLMLALEFGKPRSLKLKTAWSLLETANKGLFSQMVTIPLFKRHR 398 Query: 413 VLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALA 450 +L + ++ PPL + + E ++ A LA Sbjct: 399 ILSQVAGHGMNVVKFLPPLVIGAKDVEWIVSAMDDVLA 436 Lambda K H 0.320 0.135 0.393 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: 485 Number of extensions: 27 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 459 Length of database: 463 Length adjustment: 33 Effective length of query: 426 Effective length of database: 430 Effective search space: 183180 Effective search space used: 183180 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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