Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 468 bits (1205), Expect = e-136 Identities = 234/423 (55%), Positives = 294/423 (69%), Gaps = 1/423 (0%) Query: 4 TNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63 +NA+L AR+ A+ RG G +P++ E A NA + DVEG+ +IDF GIAV NTGH HPK+ Sbjct: 2 SNAELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKV 61 Query: 64 IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123 +AAV QL+ +HTC V YE V L E++N PG KK + VTTG+EAVEN VKIA Sbjct: 62 VAAVKAQLDNFSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIA 121 Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183 RA TGR GVIAF G +HGRT +T+ LTGK+ PY G G IF A YP HGVS+ D Sbjct: 122 RAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKD 181 Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243 S+ +IE +FK D P D+AAI++EPVQGEGGFY AP EF++ LRALCDQHGI+L+ DE+Q Sbjct: 182 SLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQ 241 Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 TG GRTG F+ E GV DL T AK IAGGFPLA V GK+E MDA PGGLGGTY GSP Sbjct: 242 TGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSP 301 Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYP-VIGDVRALGAMIAVELFE 362 + C AALAV+EV +EE L++R +G+ L A++++YP +IG+VR GAMIA+EL Sbjct: 302 VGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVI 361 Query: 363 NGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECF 422 +GD +PN A ++A A GL+LL+CG YGNV+R L LT DE + +GLA + F Sbjct: 362 DGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLF 421 Query: 423 SEL 425 L Sbjct: 422 ESL 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: 564 Number of extensions: 18 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: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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