Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__MR1:201879 Length = 461 Score = 172 bits (435), Expect = 3e-47 Identities = 130/439 (29%), Positives = 206/439 (46%), Gaps = 42/439 (9%) Query: 16 DAAHHLHPFTDSADLAKRGTRV--IERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSI 73 D+AH HP+T R V + A+G + G KL+D + W GYG +I Sbjct: 10 DSAHIWHPYTSMT----RALPVFGVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAI 65 Query: 74 ADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMV 133 A QL L + F THEPAI L K+ ++ + +VF SGS A + ++M Sbjct: 66 LTAMEQQLHQLS-HVMFGGITHEPAIELCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMA 124 Query: 134 RRYWDLKGMP-----SKKTIISRKNAYHGSTVAGASL-GGMGFMHQQGDLPIPGIVHIDQ 187 +YW + +P K+ I++ K YHG T A S+ G MH + +D Sbjct: 125 LQYWQGQDLPLAQKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDA 184 Query: 188 PYW-FGEGR---DMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDS 242 P FGE D++P +IL +AA I EP QGAGG+ Sbjct: 185 PQTPFGESLHQDDLAPMQ-----------RILREQHQDIAAVIIEPIMQGAGGMRFYSSE 233 Query: 243 YWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGV 302 Y ++ + ++YN+L ILDE+ +GFGRTG FA + + PD++ + K +T GYI + Sbjct: 234 YLRGLRALCDEYNVLLILDEIATGFGRTGKLFAYEHTDITPDILCLGKALTGGYISLAAT 293 Query: 303 IVSDRVAD-VLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQD 361 + +D VA + S G F HG T+ G+P+A A A ++ ++ ++ +V +Q Sbjct: 294 LCTDNVAQGISQSPAGVFMHGPTFMGNPLACAAACASLDLINQQEWPAQVAA-IEQQMQR 352 Query: 362 RLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVG 421 L P V VR +G VG +E+ H V + ++ ++ G+ +R Sbjct: 353 ELADAIDIPSVKAVRVLGAVGVLEM----HQAVNTAA-------LQQQFVDLGVWVRPFA 401 Query: 422 DTMIISPPLCITRDEIDEL 440 + + I PP I+ ++ +L Sbjct: 402 NLIYIMPPYVISSAQLSQL 420 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: 523 Number of extensions: 23 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: 461 Length adjustment: 33 Effective length of query: 427 Effective length of database: 428 Effective search space: 182756 Effective search space used: 182756 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