Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_084544820.1 H566_RS0102945 aspartate aminotransferase family protein
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000482785.1:WP_084544820.1 Length = 387 Score = 203 bits (517), Expect = 6e-57 Identities = 132/392 (33%), Positives = 202/392 (51%), Gaps = 35/392 (8%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYVT 89 R E LWD +GR Y D AGIAV GH HP+++ A+ Q+ + HT+ I +G Sbjct: 13 RGEGVWLWDEQGRKYLDGLAGIAVNGLGHAHPKLVAALTDQIGKLIHTS-NIYGVRGQED 71 Query: 90 LAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPG-----VIAFSGAFHGRTL 144 LA+ I A G+ + ++GAEA ENAIK+AR + + G + A+HGRT+ Sbjct: 72 LADAICAR---SGMEEVFFCSSGAEANENAIKLARFYGYKQGKDFIKTVVMENAWHGRTI 128 Query: 145 LGMALTGKVAPYKIGFGPFPSDIY-HAPFPSALHGVSTERALQALEGLFKTDIDPARVAA 203 +A T K GF P + + P + L A+ + +T+ + + + Sbjct: 129 ATLAATDSPKARK-GFEPMQDECFVRVPHNN----------LAAIIEVAETNPE---INS 174 Query: 204 IIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPD 263 +++E +QGEGG A ++++GLR +CD+ G +LI DEVQ G GRTG F H +EPD Sbjct: 175 VMLEVLQGEGGINLASVEYLQGLRKLCDERGWLLILDEVQCGVGRTGTWFGYQHAGIEPD 234 Query: 264 LITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCE 323 IT+AK L G+P+ A++ R + PG G T+ GNPLA+ A + +EE+ L + Sbjct: 235 AITLAKGLGSGVPIGALAVRGSAAKLIGPGNFGTTFGGNPLAMRAGTCTLQTLEEDGLLQ 294 Query: 324 RSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALEA 383 + +G +R A + + ++RG G M+ E P + TRALEA Sbjct: 295 HAVVIGDHIRAGFRAALEGVAGVTDIRGQGLMIGIELDRP---------CGVIVTRALEA 345 Query: 384 GLVLLTCGTYGNVIRFLYPLTIPQAQFDAALA 415 G ++ T V+R L PL + A+ D +A Sbjct: 346 GFLINV--TRDKVVRLLPPLIMTTAEADLLVA 375 Lambda K H 0.321 0.136 0.400 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: 388 Number of extensions: 25 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: 423 Length of database: 387 Length adjustment: 31 Effective length of query: 392 Effective length of database: 356 Effective search space: 139552 Effective search space used: 139552 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 (21.9 bits) S2: 50 (23.9 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