Align Probable gamma-aminobutyrate transaminase 4; OsGABA-T; EC 2.6.1.96 (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q6ZH29 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 261 bits (668), Expect = 3e-74 Identities = 156/431 (36%), Positives = 240/431 (55%), Gaps = 17/431 (3%) Query: 48 SPPLVIERSEGCYVYDVNGTKYLDALAGLLSTALGGSEPRLVKAATEQLNKLPFYHSFWN 107 S P+ + R +G + D GT+Y+DA G + LG S PR+++A Q+ +LP+ H+ + Sbjct: 12 SLPIAV-RGDGIEIVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSF- 69 Query: 108 HTTRPSLDLAKELISMFTAREMGKVFFTNSGSEANDSQVKIVWYYNNALGRPKKKNIISR 167 TT P+ LA LI R +G V+F + GSEA ++ +K+ Y G+P++++ I+R Sbjct: 70 FTTEPAEALADLLIEA-APRNLGHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIAR 128 Query: 168 TQSYHGTTFISASLSGLPTLHQDFDLPGRFVLHTDCPHY-WRFHLPGETEEEFATRLADN 226 QSYHG T + ++ G + F LP H P + +R GET+E FA RLAD Sbjct: 129 RQSYHGNTLGALAIGGNAWRREPF-LPILIEAHHVTPCFAYREQQAGETDEAFAQRLADE 187 Query: 227 LENLILKQGPETIAAFIAEPVIGA-GGVILPPKTYFEKIQAVVKKYDILFIVDEVITGFG 285 LE IL+ G +++AAF+AE V+GA G + P + YF KI+AV KY +L I+DEV++G G Sbjct: 188 LEAKILELGAQSVAAFVAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGMG 247 Query: 286 RLGTMFGSDLYNIKPDLVSLAKALSSAYAPIGAILVSPEISDVIHSHSNKLGTFAHGFTY 345 R G +F + + PD++++AK L + Y PIGA LVS EI + I S G F HG TY Sbjct: 248 RTGHLFACEEDGVSPDILAIAKGLGAGYQPIGATLVSNEIFNTIVGGS---GFFQHGHTY 304 Query: 346 SGHPVSCAVALEALKIYRERDIPGHVTHVAQRFQEGIKAFAAGSPIVGETRGVGLLIATE 405 GH +CA ALE K+ E + +V ++ + ++ + A P +G+ RG GL E Sbjct: 305 IGHATACAAALEVQKVIAEEQLLDNVKARGEQLRARLREWQANHPFIGDVRGRGLFTGVE 364 Query: 406 FTDNKSPYELFPFEWGVGEIFGQECKKRGMMVKVLGNL--------IAMSPPLIITREEI 457 +++ F + + I E KRG+MV +G + ++PP I T +I Sbjct: 365 LVQDRASKTAFDPKHKLHAIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQI 424 Query: 458 DKLVSIYGEAL 468 D +V +A+ Sbjct: 425 DTIVERLADAI 435 Lambda K H 0.318 0.136 0.403 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: 509 Number of extensions: 32 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: 483 Length of database: 447 Length adjustment: 33 Effective length of query: 450 Effective length of database: 414 Effective search space: 186300 Effective search space used: 186300 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 (21.7 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