Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 8501786 DvMF_2502 glutamate-1-semialdehyde aminotransferase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__Miya:8501786 Length = 425 Score = 150 bits (378), Expect = 9e-41 Identities = 122/407 (29%), Positives = 188/407 (46%), Gaps = 34/407 (8%) Query: 1 MSKTNADLMARRTAAVPRGVGQ---------IHPIFAESAKNATVTDVEGREFIDFAGGI 51 M + +L R +P GV P+F AK + +T V+G F+D+ Sbjct: 1 MDHRSKELFERAQQLIPGGVNSPVRACLGVDSDPLFVAHAKGSHLTTVDGTSFVDYVQSW 60 Query: 52 AVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTT 111 + GH HP + +A+ +++ T E V L E + +PG + +V + Sbjct: 61 GPMLLGHAHPVVASAIHAAVDRGTS---YGAPCEDEVVLAEAVIDALPG--VEMVRMVNS 115 Query: 112 GSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPG--GIFR 169 G+EA +A+++AR TGR V+ F G YHG L G V + +PG G+ Sbjct: 116 GTEATMSALRLARGVTGRNKVVKFVGCYHGHADAFLASAGSGVATLS----IPGTPGVPE 171 Query: 170 ALYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRAL 229 A + L ++ + + ++ +F +DIAAII+EPV G G + F++ LR L Sbjct: 172 ATVRDTL--LAPYNDLTAVAELFT--LHGKDIAAIIVEPVAGNMGLVLPMNGFLQGLRDL 227 Query: 230 CDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDA 289 C +HG LLI DEV TG R A ++ + DLTT K I GG P+ G+A+ M Sbjct: 228 CTEHGALLIFDEVITGF-RVNYGGAQKRFDITPDLTTLGKIIGGGLPVGAYGGRADLMRR 286 Query: 290 IAPGG---LGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVI 346 IAP G GT +G+P+A AA +A + ++ D +A L L+AI V Sbjct: 287 IAPCGEVYQAGTLSGNPLAMAAGIATLAELKKSD-YDALEARVAALATELQAILAAKGVP 345 Query: 347 GDVRALGAMIAV-----ELFENGDSHKPNAAAVAQVVAKARDKGLIL 388 V + +M V + + + NAA + RDKG+ L Sbjct: 346 VRVNTIASMFTVFFTDQPVTDFASAKTANAALYTSYYKQMRDKGIYL 392 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: 426 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: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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