Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 167 bits (424), Expect = 4e-46 Identities = 134/408 (32%), Positives = 200/408 (49%), Gaps = 42/408 (10%) Query: 26 IFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYE 85 +F E K + +TD G+ ++DF G AV GH + +I A+ +Q KL + E Sbjct: 21 VFTEG-KGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPS-PAFYNE 78 Query: 86 PYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA-----ATGRAGVIAFTGAYH 140 P + L ++ D K +G+EA E A+K+AR G +I ++H Sbjct: 79 PMLRLARQLTDASCFD---KVFFANSGAEANEGAIKLARKWGRKHKNGAFEIITMDHSFH 135 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRD 200 GRT+ T+ +GK + +PG +P ++D +AS+E++ + Sbjct: 136 GRTLATMSASGKAGWDTIFAPQVPG------FPK----ADLND-LASVEKLINDKT---- 180 Query: 201 IAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260 AI++EPVQGEGG A +EFM+ LR L DQH +L I DEVQTG GR GT FA E GV Sbjct: 181 -VAIMLEPVQGEGGVIPASREFMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGV 239 Query: 261 AADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEH 320 D+ T K I GG PLA + KAE + + G GGTY G+P+ A AV+ Sbjct: 240 EPDIMTLGKGIGGGVPLAALLCKAE-VASFEAGDQGGTYNGNPVMTAVGSAVISQLTAPG 298 Query: 321 LLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFENGDSHKPNAAAVAQVVAK 380 L + G L L A+ ++ +G R G + A+ L N Q+V + Sbjct: 299 FLQSVQDKGAYLREQLLALTSEFG-LGGERGEGLLRALVL---------NKDIGPQLVEE 348 Query: 381 ARD---KGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECFSEL 425 ARD +GL+L S N+LR + L E++D+ +++L +L Sbjct: 349 ARDMQPQGLLLNS--PRPNLLRFMPALNVTIEEIDQMISMLRTLLKKL 394 Lambda K H 0.320 0.137 0.395 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: 397 Number of extensions: 25 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: 425 Length of database: 395 Length adjustment: 31 Effective length of query: 394 Effective length of database: 364 Effective search space: 143416 Effective search space used: 143416 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