Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000015985.1:WP_011842390.1 Length = 442 Score = 253 bits (645), Expect = 1e-71 Identities = 160/431 (37%), Positives = 234/431 (54%), Gaps = 21/431 (4%) Query: 37 VIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPF-YNNFFQCTH 95 V EG YI DA+G + LD G +G+ ++ A + QL L F + FF T Sbjct: 16 VAAEGEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGFF--TS 73 Query: 96 EPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAY 155 EPA RLA ++A+ AP + RV+ GSEA + L++ R+Y+ G P + +I+R+ +Y Sbjct: 74 EPAERLADRLAAAAPEGIERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIARRQSY 133 Query: 156 HGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWF-GEGRDMSPEAFGIKTAQALEAKI 214 HG+T+ + GG + Q + H+ Y + G D S EA+G++ A LEA+I Sbjct: 134 HGNTLGALAAGGNEWRRAQFAPLLVETSHVSPCYEYRGRAEDESLEAYGLRVADELEAEI 193 Query: 215 LELGEDKVAAFIAEPFQGAGGVIIPP-DSYWNEIKRILEKYNILFILDEVISGFGRTGNW 273 LG + V AF+AEP GA +P Y I+ I +++ +L ILDEV+ G GRTG+ Sbjct: 194 QRLGPETVMAFVAEPVVGATAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGRTGHL 253 Query: 274 FAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAA 333 FA G+ PD+ITIAKG+ +GY P+G ++V R+ D + + G F HG TY GH +AAA Sbjct: 254 FACAEDGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHAMAAA 313 Query: 334 VALENIRILEEERLVDKVRTDTGPYLQDRLQ-TLSAHPLVGEVRGMGMVGAIELVADKHS 392 A + +E L+ VR G L+ LQ L HP VG++RG G+ IELVAD+ + Sbjct: 314 AANAVLDEIEGRDLLQAVRRQ-GARLEGLLQERLGQHPHVGDIRGRGLFRGIELVADRET 372 Query: 393 M----------VRFGSEISAGMLCREACIESGLVMRAV-GDTMIISPPLCITRDEIDELI 441 R +E AG L C G + V GD ++++PP I+ E++EL+ Sbjct: 373 KEPFDPARKLHARIKAEAFAGGL---ICYPMGGTLDGVRGDHILLAPPFIISNAELEELV 429 Query: 442 FKASQALSLTL 452 K S AL L Sbjct: 430 DKLSGALDRAL 440 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: 545 Number of extensions: 31 Number of successful extensions: 6 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: 442 Length adjustment: 33 Effective length of query: 427 Effective length of database: 409 Effective search space: 174643 Effective search space used: 174643 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 Apr 10 2024. 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