Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_004298659.1 C665_RS01920 aspartate aminotransferase family protein
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000310185.1:WP_004298659.1 Length = 391 Score = 191 bits (486), Expect = 3e-53 Identities = 133/399 (33%), Positives = 193/399 (48%), Gaps = 38/399 (9%) Query: 32 ENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA--YQIVPYQGYVT 89 E L+D G+ Y D +GIAV G++HPR+++AIA Q ER HT+ Y+I P Q Sbjct: 19 EGVWLYDETGKRYLDALSGIAVNTLGYKHPRLVKAIADQAERVLHTSNLYRI-PLQEQ-- 75 Query: 90 LAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPGV-----IAFSGAFHGRTL 144 L++RI G+++ +G EA E AIK+AR + G+ I AFHGRT+ Sbjct: 76 LSDRI---AEAAGMDEVFFCNSGCEANEAAIKLARMYGHNKGIELPHIIVMENAFHGRTM 132 Query: 145 LGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAAI 204 ++ TG + GF P P+ +E + K V A+ Sbjct: 133 ATLSATGN-RKAQAGFEPLVQGFIRVPYKD-------------IEAIRKIAEHNHTVVAV 178 Query: 205 IVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPDL 264 ++E +QGEGG A F R LRA+CD G ++I DEVQ G GRTGK F H PD+ Sbjct: 179 MLEMIQGEGGVNVADEAFQRDLRALCDDRGWLMICDEVQCGMGRTGKWFGWQHAGTRPDV 238 Query: 265 ITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCER 324 +T+AK LA G+P+ A PG G T+ GNPLA AA A D I E++L + Sbjct: 239 MTLAKGLASGVPIGACVTSGLAKGLFGPGNHGSTFGGNPLACAAGLATFDAIVEDELMDN 298 Query: 325 SASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALEAG 384 + ++G +R+ + + ++RG G M+ E P + RA E G Sbjct: 299 AVAVGAAIRKGMAEALAGEAGVVDIRGRGLMIGIELDRP---------CGVLMARAAENG 349 Query: 385 LVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 L+L T V+R L LT A +++L + + Sbjct: 350 LLLSV--TSERVVRLLPALTFTTADAQTLVSMLAPMIRD 386 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: 429 Number of extensions: 24 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: 423 Length of database: 391 Length adjustment: 31 Effective length of query: 392 Effective length of database: 360 Effective search space: 141120 Effective search space used: 141120 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