Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_011385142.1 AMB_RS13895 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000009985.1:WP_011385142.1 Length = 439 Score = 182 bits (463), Expect = 1e-50 Identities = 131/433 (30%), Positives = 204/433 (47%), Gaps = 22/433 (5%) Query: 12 LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71 L+A+DA H HPFT + + + A G I+ A G + LD ++ W G+ Sbjct: 8 LRALDARHVWHPFTQAG--TAQPAILALGARGSTIYAADGREYLDLVSSWWVNLHGHANP 65 Query: 72 SIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLR 131 +IA A Q L F THEPA RLA ++ PG +NRVF++ GS A + L+ Sbjct: 66 AIAQAVADQAGRLEQVI-FADFTHEPAARLAHRVCKRLPGDLNRVFYSDDGSTAVEVALK 124 Query: 132 MVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLG-GMGFMHQQGDLPIPGIVHIDQPYW 190 + +YW G + T I+ + YHG T S G G+ ++ P W Sbjct: 125 LAHQYWRNHGQ-HRSTYIAFEGGYHGDTAGAMSAGHSSGYFGAWKEMLFPVETVPFPATW 183 Query: 191 FGEGRDMSPEAFGIKTAQALEAK--ILELGEDKVAAFIAEPF-QGAGGVIIPPDSYWNEI 247 G+ E K AL+A + D VAA I EP QGA G+ + + ++ Sbjct: 184 NGD------ETVEDKEQAALDALDLLFAANPDHVAAVIIEPLIQGASGMRMCRPDFLRKL 237 Query: 248 KRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDR 307 + + L ILDEV++GFGRTG FA G+ PDLI ++KG+T G++P+ + D Sbjct: 238 EAKVRDNGSLLILDEVMTGFGRTGEIFACVKAGITPDLICLSKGLTGGFLPLSVTVARDG 297 Query: 308 VADVLISD--GGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQT 365 + + + F HG +Y+ +P+ A L +I +LE ++ + + RL Sbjct: 298 IFEAFLGQDLSRAFLHGHSYTANPLGCAAGLTSIDLLESAACQQRIGAIEAIH-RRRLDG 356 Query: 366 LSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI 425 L V R G V A++++ G E G + A +E GL++R +G+ + Sbjct: 357 LKGLSNVAHTRLTGTVAALDVIGGGK-----GYEAGIGPKLKAAFLERGLLLRPLGNVLY 411 Query: 426 ISPPLCITRDEID 438 + PP CIT E++ Sbjct: 412 LLPPYCITDAELE 424 Lambda K H 0.321 0.137 0.408 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: 548 Number of extensions: 30 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: 460 Length of database: 439 Length adjustment: 33 Effective length of query: 427 Effective length of database: 406 Effective search space: 173362 Effective search space used: 173362 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 17 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