Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 14737 b0600 putative aminotransferase (NCBI)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Keio:14737 Length = 386 Score = 171 bits (432), Expect = 4e-47 Identities = 116/366 (31%), Positives = 182/366 (49%), Gaps = 7/366 (1%) Query: 22 YRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAER 81 + ++ + Q + + LS G PDFD P + + + G YA + G +ALR+ IA++ Sbjct: 20 FTQMSALAQQHQAINLSQGFPDFDGPRYLQERLAHHVAQGANQYAPMTGVQALREAIAQK 79 Query: 82 HRRRSGQAVDAEQ-VVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARV 140 R G DA+ + V AGA ALYA + L+ GDEVI +P Y +Y G V Sbjct: 80 TERLYGYQPDADSDITVTAGATEALYAAITALVRNGDEVICFDPSYDSYAPAIALSGGIV 139 Query: 141 VPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLW 200 + ++ + FRV +E AAL++ RTR + LN+PHNPS +A + AL + H+++ Sbjct: 140 KRMALQPPH-FRVDWQEFAALLSERTRLVILNTPHNPSATVWQQADFAALWQAIAGHEIF 198 Query: 201 MISDEVYSELLFDGE-HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHL 259 +ISDEVY + F + H S + P + +R ++S K++ MTGW+VG+ V PA + A + Sbjct: 199 VISDEVYEHINFSQQGHASVLAHPQLRERAVAVSSFGKTYHMTGWKVGYCVAPAPISAEI 258 Query: 260 ENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPD 319 + + + Q A L A A+ + YR++RD+++ L +S L L + Sbjct: 259 RKVHQYLTFSVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNALNES-RLEILPCE 317 Query: 320 GGMFVMVDIRPTG-LSAQAFADRLLDRHGVSVLAGEAFGPSAAGH--IRLGLVLGAEPLR 376 G F++VD L F L HGV+ + F H IRL L Sbjct: 318 GTYFLLVDYSAVSTLDDVEFCQWLTQEHGVAAIPLSVFCADPFPHKLIRLCFAKKESTLL 377 Query: 377 EACRRI 382 A R+ Sbjct: 378 AAAERL 383 Lambda K H 0.322 0.136 0.411 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: 383 Number of extensions: 16 Number of successful extensions: 4 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: 393 Length of database: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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 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