Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >NCBI__GCF_900115975.1:WP_207545101.1 Length = 434 Score = 407 bits (1045), Expect = e-118 Identities = 203/438 (46%), Positives = 286/438 (65%), Gaps = 19/438 (4%) Query: 1 MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 M+KTNA+L+AR+ + RG+ +F E A+ AT+ DVEG+E+IDF GGI LN GH Sbjct: 1 MAKTNAELVARKHQLIARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCP 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 ++ A+ Q KL HTCF V YEPY++L EK+ PG+F K+ + V +G+E VENAV Sbjct: 61 APVVEAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIF------------ 168 KIAR+ R G+I+F A+HGRT+MT+ LT KV PY G G ++ Sbjct: 121 KIARSYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTY 180 Query: 169 RALYPN-ELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLR 227 R+ YP LH + +R+F + P +IAA+IIEPVQGEGGF V P EF+ LR Sbjct: 181 RSTYPECGLH------CLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLR 234 Query: 228 ALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYM 287 +CD+HGI+LIADEVQTG GRTG FA E G+ DL T AKSIA G PL+ V GKA+ M Sbjct: 235 KICDKHGIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIM 294 Query: 288 DAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIG 347 +A PG +GGTY+G+P++CAA LA ++ ++++L++R +G++ + A+Q+KYP+IG Sbjct: 295 NAPNPGEIGGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIG 354 Query: 348 DVRALGAMIAVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAP 407 DVR LGAM A+EL ++ ++ +P A V+ D G+I++ G + NV+R L+PL Sbjct: 355 DVRGLGAMNAMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVIT 414 Query: 408 DEQLDKGLAILEECFSEL 425 DEQL+KGL +LE+ + + Sbjct: 415 DEQLEKGLDVLEQAVASV 432 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: 533 Number of extensions: 23 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 393 Effective length of database: 402 Effective search space: 157986 Effective search space used: 157986 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 Apr 09 2024. 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