Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__SynE:Synpcc7942_0031 Length = 424 Score = 145 bits (365), Expect = 3e-39 Identities = 123/416 (29%), Positives = 195/416 (46%), Gaps = 26/416 (6%) Query: 25 PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84 P+ S K A +T +GRE ID V GH H +I+ A+ +Q L H F ++ Sbjct: 20 PLKVVSGKGARLTLADGRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSH 79 Query: 85 EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA-----RAATGRAGVIAFTGAY 139 EP L ++ K+ + + GS AVE A+K+A R+ ++AF GAY Sbjct: 80 EPAERLAMEL-CKILPEKLTRVFFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAY 138 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHG-VSIDDSIASIERIFKNDAEP 198 HG T + + G+ ++A + + YP G +++ A+ + Sbjct: 139 HGDTFGAMSV-GERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAAAIAAVEQALAA 197 Query: 199 RDIAAIIIEP-VQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQ 257 D+AA+IIEP VQG GG +A +F+++L A G LLIADEV TG GRTG +FA ++ Sbjct: 198 GDVAAVIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQR 257 Query: 258 MGVAADLTTFAKSIAGGF-PLAGVCGKAEYMDAIAPGG------LGGTYAGSPIACAAAL 310 G+ DL +K + GGF PL+ D G G +Y +P+ CAAA+ Sbjct: 258 AGIQPDLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAAI 317 Query: 311 AVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELF-ENGDSHKP 369 A +E+ + + + + + + GL+ + ++P + R G + A +L + G P Sbjct: 318 ASLELLLDSEAI--VQGLEDAHLPGLELL-AQHPKVTRPRLTGGIAACDLVSDRGGYLDP 374 Query: 370 NAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECFSEL 425 V Q A +GL+L GNVL +L P +L A + + E+ Sbjct: 375 IGLRVRQA---AIARGLLL---RPLGNVLYLLPPYCLTPTELQDIYAAIADLLDEI 424 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: 464 Number of extensions: 18 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: 424 Length adjustment: 32 Effective length of query: 393 Effective length of database: 392 Effective search space: 154056 Effective search space used: 154056 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: 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