Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BWI76_RS14455 BWI76_RS14455 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Koxy:BWI76_RS14455 Length = 447 Score = 226 bits (577), Expect = 9e-64 Identities = 138/425 (32%), Positives = 225/425 (52%), Gaps = 15/425 (3%) Query: 38 IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97 + A+G YI D+ G + LDA G +G+ +++ A RQ+ L + + F T+ Sbjct: 15 VAVSAQGAYITDASGQRYLDACGGAAVSCLGHAHPDVLAAMHRQIDRLAYAHTSFFTSDT 74 Query: 98 PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157 V +LA+ + AP +N+ +F GSEA +T L++ R Y+ GQP + + I R YH Sbjct: 75 -VEQLAEQLVRTAPGSLNYAYFVSGGSEAVETALKLARQYFVEIGQPDRTLFIARKQSYH 133 Query: 158 GSTVAGVSLGGMKALHEQGDFPIPGIVHIA--QPYWYGEGGDMSPDEFGVWAAEQLEKKI 215 G+T+ +++GG + Q + +V ++ Y E G+ S ++ +LE I Sbjct: 134 GNTLGALAVGGNEWRRRQFAPLLMDVVRVSACNEYRDREAGE-SQQQYTERLLGELEAAI 192 Query: 216 LEVGEENVAAFIAEPIQGAG-GVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEW 274 L+ G E + FIAE + GA G + P Y +R + KY IL+IADEV+CG GRTG Sbjct: 193 LDAGPEKIIGFIAETVVGATTGAMPPTPGYLQGVRRLCDKYGILYIADEVMCGMGRTGTL 252 Query: 275 FGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG-GEFYHGFTYSGHPVAAA 333 + G PD++ IAKGL GY P+G V+ ++IV L G G F HG TY HP AAA Sbjct: 253 HAFEQDGVVPDIVTIAKGLGGGYQPIGAVLASEQIVAALQAGSGMFQHGHTYICHPTAAA 312 Query: 334 VALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKKTR 393 AL +++ ++++E+V+ + A Q L P VG+ RG G+ A +ELV +K+ + Sbjct: 313 AALAVQQVIERDRLLEQVQQQGAYLQQALHDVLGGLPYVGDTRGRGLFAGVELVCDKERK 372 Query: 394 ERFTD-KGVGMLCREHCFRNGLIMRAV--------GDTMIISPPLVIDPSQIDELITLAR 444 F + + C +GL++ + GD ++I+PP ++ S++D ++ Sbjct: 373 TAFDPLLKLHAAIKAQCMGHGLLVYPMGGTIDGQRGDHILIAPPFIVSRSELDFVVDTLH 432 Query: 445 KCLDQ 449 K + + Sbjct: 433 KVISE 437 Lambda K H 0.320 0.138 0.425 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: 552 Number of extensions: 34 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: 456 Length of database: 447 Length adjustment: 33 Effective length of query: 423 Effective length of database: 414 Effective search space: 175122 Effective search space used: 175122 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