Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 194 bits (492), Expect = 5e-54 Identities = 139/411 (33%), Positives = 200/411 (48%), Gaps = 50/411 (12%) Query: 25 PIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84 P+ + A + + +GR F+D A GIAV GH HP ++ A+T+Q L H L + Sbjct: 13 PLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHV--SNLYH 70 Query: 85 EPYVE-LCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATGRAGVIAFTG 137 P + L +++ V FA +G+E+ E AVK+AR R ++ F+G Sbjct: 71 IPQQQALADRL---VEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSG 127 Query: 138 AYHGRTMMTLGLTGKVVPYSAGMG-LMPGGIFRALYPNELHGVSIDDSIASIERIFKNDA 196 ++HGR+ + G +AG G ++PG F+ L +L GV+ DA Sbjct: 128 SFHGRSSAGISAAGSE-KMTAGFGPMLPG--FKHLMFGDLDGVT--------------DA 170 Query: 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256 AAI+IEPVQGEGG P +K LR +CD+HG+LLI DEVQ G GRTG FA E Sbjct: 171 ITDQTAAILIEPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHE 230 Query: 257 QMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF 316 G+T D+ AK I GGFPL V E + G G TY G+P+ CA AVM+ Sbjct: 231 WAGITPDIMMVAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHV 290 Query: 317 EEEHLLDRCKAVGERLVTGLKAIQAKYPVIGE-VRALGAMIAVELFENGDSHKPNAAAVA 375 + L L L+ + A +P + E VR G M+ ++ AA Sbjct: 291 TDPEFLAEVSRKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKC----------VAANT 340 Query: 376 QVVAKARDKGLILLSCGTYGNVLRVLVPLTSPD-------AQLDKGLAIIE 419 VVA + ++ + NV+R+L PLT D A+LD+ ++E Sbjct: 341 DVVAAGYEAEVVTVPAA--DNVVRLLPPLTLTDEDIAEAFARLDQAATLVE 389 Lambda K H 0.320 0.137 0.394 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: 419 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 394 Length adjustment: 31 Effective length of query: 394 Effective length of database: 363 Effective search space: 143022 Effective search space used: 143022 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: 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