Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_011780514.1 MVAN_RS16610 acetylornithine transaminase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >NCBI__GCF_000015305.1:WP_011780514.1 Length = 390 Score = 213 bits (542), Expect = 8e-60 Identities = 141/415 (33%), Positives = 214/415 (51%), Gaps = 40/415 (9%) Query: 7 DLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAA 66 +L+ R +A + G P+ A VTDV+G+ ++D GGIAV GH HP +I A Sbjct: 3 ELLNRWSAVMMNNYGT-PPLALAGGDGAVVTDVDGKAYLDLLGGIAVNVLGHRHPAVIEA 61 Query: 67 VTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAA 126 VT Q+N L HT + A EP V L E + + K +G+EA E A KI R Sbjct: 62 VTRQMNTLGHTS-NLYATEPGVALAESLVGLLGAP--AKAFFCNSGTEANEAAFKITRL- 117 Query: 127 TGRAGVIAFTGAYHGRTMMTLGLTG---KVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183 TGR V+A GA+HGRTM +L LTG K P+ +PGG+ Y + Sbjct: 118 TGRTKVVAAEGAFHGRTMGSLALTGQPSKRAPFEP----LPGGVTHVPYGD--------- 164 Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243 I + R+ + AA+ +EP+ GEGG V P ++ R + HG LL+ DEVQ Sbjct: 165 -IDELRRVVDDQT-----AAVFLEPIMGEGGVVVPPAGYLVAAREITAAHGALLVLDEVQ 218 Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 TG GRTG F+A + G+ D+ T AK + GG P+ + D + PG G T+ G+P Sbjct: 219 TGVGRTGAFYAHQHDGITPDIVTLAKGLGGGLPIGACLAIGDTADLLTPGLHGSTFGGNP 278 Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFEN 363 + AAALAV++V +E L++R +G+ + G++++ +P++ VR G + + L Sbjct: 279 VCTAAALAVLKVLADEGLVERADVLGKTIAHGVESL--GHPLVDHVRGRGLLRGIVL--T 334 Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIL 418 D+ KP V AR+ G ++ + ++R+ PL + Q++ L+ L Sbjct: 335 ADAAKP-------VETAAREAGFLVNAAAP--AIVRLAPPLVITEAQVETFLSAL 380 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: 460 Number of extensions: 20 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 394 Effective length of database: 359 Effective search space: 141446 Effective search space used: 141446 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 24 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