Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS15580 Length = 394 Score = 161 bits (408), Expect = 3e-44 Identities = 126/406 (31%), Positives = 196/406 (48%), Gaps = 45/406 (11%) Query: 30 HAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLTHTCFQVLAYEPYVE 89 H K S + D G+ ++DF G AV + GH + +I A+ +Q L + +P + Sbjct: 24 HGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEALNKQSQLLINPS-PAFYNQPMAQ 82 Query: 90 LCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIARA-----ATGRAGVIAFTGAYHGRTM 144 L + D K +G+EA E +IK+AR G +I F ++HGRT+ Sbjct: 83 LAGLLTQHSCFD---KVFFANSGAEANEGAIKLARKWGKKFKDGAFEIITFDHSFHGRTL 139 Query: 145 MTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD--SIASIERIFKNDAEPRDIA 202 T+ +GK PG + +Y ++ G D IAS+E++ Sbjct: 140 ATMSASGK-----------PG--WDTIYAPQVPGFPKADLNDIASVEKLINAKT-----V 181 Query: 203 AIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAA 262 A+++EP+QGEGG A +EFM++LR L +H +LLI DEVQ+G GR GT FA E + Sbjct: 182 AVMLEPIQGEGGVIPATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEP 241 Query: 263 DLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLL 322 D+ T K I GG PLA + KAE + G GGTY G+P+ A +V+ L Sbjct: 242 DIMTLGKGIGGGVPLAALLAKAE-IAVFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFL 300 Query: 323 DRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAKVVAKAR 382 + +A GE L L + + GE R G + A+ L ++ + ++V KAR Sbjct: 301 EGLRARGEYLRAKLLELSEERGFEGE-RGEGLLRALLLGKDIGN---------QIVEKAR 350 Query: 383 D---KGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEECFSEL 425 D GL+L + N+LR + L +E++D+ + ++ L Sbjct: 351 DMQPDGLLLNAARP--NLLRFMPALNVTNEEIDQMMTMLRSILDTL 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: 388 Number of extensions: 30 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: 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