Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 6938540 Sama_2643 putative aminotransferase (RefSeq)
Query= BRENDA::B1XNF8 (418 letters) >FitnessBrowser__SB2B:6938540 Length = 460 Score = 176 bits (445), Expect = 2e-48 Identities = 129/418 (30%), Positives = 216/418 (51%), Gaps = 44/418 (10%) Query: 35 IAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHISNLYYIPEQG 94 I + EG +WD +G LD +AG+ +G+ ++ A AQ+Q L +N + + Sbjct: 38 IERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEP 97 Query: 95 ALAQWIVEHSCA----DKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVILSAKSSFH 150 A+ S A ++VFF SG+EAN+ +++VR+Y + + I+S K+++H Sbjct: 98 AIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRY-WDLKGMPSKKTIISRKNAYH 156 Query: 151 GRTLATITATGQPKYQKHFD-PLPDGFAYV--PY---------------NDIRALEEAIT 192 G T+A + G + D P+P G ++ PY +ALE I Sbjct: 157 GSTVAGASLGGMGFMHQQGDLPIP-GIVHIDQPYWFGEGRDMSPEAFGIKTAQALEAKIL 215 Query: 193 DIDEGNRRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKY 252 ++ G +VAA + E QG GGV Y+ ++RI ++ IL +LDEV G GRTG + Sbjct: 216 EL--GEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFILDEVISGFGRTGNW 273 Query: 253 WGYENLGIEPDIFTSAKGLAGG-IPIGAMMCKDSCA---VFNPGE--HASTFGGNPFSCA 306 + + LG++PD+ T AKG+ G IP+G ++ D A + + GE H T+ G+P + A Sbjct: 274 FAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAA 333 Query: 307 AALAVVETLEQENLLENVNA-RGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKAD--- 362 AL + LE+E L++ V G L+ L+TL+ +P +VRG G++ +E+ AD Sbjct: 334 VALENIRILEEERLVDKVRTDTGPYLQDRLQTLS-AHPLVGEVRGMGMVGAIELVADKHS 392 Query: 363 -----LELTSIEVVK-AAMEKGLLLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 E+++ + + A +E GL++ G ++ PPL ++ EI+E I Q L+ Sbjct: 393 MVRFGSEISAGMLCREACIESGLVMRAVGDTMI-ISPPLCITRDEIDELIFKASQALS 449 Lambda K H 0.319 0.136 0.406 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: 439 Number of extensions: 28 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: 418 Length of database: 460 Length adjustment: 32 Effective length of query: 386 Effective length of database: 428 Effective search space: 165208 Effective search space used: 165208 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 09 2024. The underlying query database was built on Apr 09 2024.
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