Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate BPHYT_RS00155 BPHYT_RS00155 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS00155 Length = 384 Score = 171 bits (432), Expect = 4e-47 Identities = 122/369 (33%), Positives = 194/369 (52%), Gaps = 12/369 (3%) Query: 22 YRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAER 81 + + ++ + L LS G P+F A ++ ++ AG+ YA + G ALR+ +A++ Sbjct: 19 FTVIGQLAAQHDALNLSQGAPNFAPDAKLIDGVAQAMRAGHNQYAPMAGIAALREALADK 78 Query: 82 HRRRSGQAVD-AEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARV 140 G D A +V V+A A LY+ + L++PGDEVI EP + +Y + GA Sbjct: 79 VATLYGVRYDPASEVTVIASASEGLYSTISALVHPGDEVIYFEPSFDSYGPIVRLQGATP 138 Query: 141 VPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLW 200 VP+ + S + FRV +EVAA ITP+TR + N+PHNP+ A E L + D+ Sbjct: 139 VPIKL-SLDDFRVNWDEVAAAITPKTRMIITNTPHNPTATVFSEADVERLKAVTRNTDIV 197 Query: 201 MISDEVYSELLFDG-EHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHL 259 +++DEVY ++FDG +H S A +A+R+ ++S KS+ +TGWRVG+ + PAAL + Sbjct: 198 ILADEVYEHVVFDGAKHQSMACHSELAERSVIVSSFGKSYHVTGWRVGYCLAPAALMDEI 257 Query: 260 ENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPD 319 + M++ + +Q A AL A + Y+++RDL+ E L DS L P Sbjct: 258 RKVHQFMVFSADTPMQYAFVDAL-ANRESYLGLSAFYQKKRDLLAEALRDS--RFELLPS 314 Query: 320 GGMFVMVDIRPTGLSAQAFAD---RLLDRHGVSVLAGEAF--GPSAAGHIRLGLVLGAEP 374 G F M+ R G S ++ +D RL+ V+ + AF + +G IRL Sbjct: 315 EGSFFML-ARFRGFSDESDSDFVLRLIRDARVATIPLSAFYTDGTDSGLIRLSFSKDDAT 373 Query: 375 LREACRRIA 383 L E RR++ Sbjct: 374 LIEGARRLS 382 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: 352 Number of extensions: 25 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: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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