Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO356_28705 AO356_28705 hypothetical protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28705 Length = 449 Score = 293 bits (750), Expect = 8e-84 Identities = 166/418 (39%), Positives = 235/418 (56%), Gaps = 13/418 (3%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 P + N II + +G YI D EG+++LD + GLW VNVG+ R + A Q+ Sbjct: 15 PMSSSAPANRSKTLIIARGDGNYITDIEGHRMLDGVGGLWNVNVGHNRPSVKAAIAAQLD 74 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADV-APEGMNHVFFTGSGSEANDTVLRMVRHYWATKG 142 EL +Y F AHP V +LA+ + + A E M V F+ GS+A +T L+M R YW G Sbjct: 75 ELAYYQTFDGIAHPRVFDLAERLTSMFAQENMARVLFSSGGSDAVETALKMARQYWIASG 134 Query: 143 QPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM-SPD 201 +P + + NGYHG V G S+GG H + G + P+ Y D P+ Sbjct: 135 EPGRTRFLSLRNGYHGVHVGGTSVGGNGVYHYNHGPLLAGCHLLDTPWLYRNPWDCRDPE 194 Query: 202 EFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIA 261 E QLE +I +G + +AA IAEP+QGAGGVIVPP YW ++RE+ ++ IL IA Sbjct: 195 ELTAHCIRQLEDQIALLGPQTIAALIAEPVQGAGGVIVPPAHYWKRLREVCDRHGILLIA 254 Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEF-- 319 DEV+ GFGRTG GS+ +G APD++ +AKG+T+GYIPMG V I + + G F Sbjct: 255 DEVVTGFGRTGCMLGSRGWGVAPDVLCLAKGITAGYIPMGATVFNQRIADAIENGPGFSS 314 Query: 320 --YHGFTYSGHPVAAAVALENIRILREEKI---IEKVKAETAPYLQKRWQELADHPLVGE 374 HG+TYSGHP A A AL + I+ E + KV A+ LQ + A +VGE Sbjct: 315 VIMHGYTYSGHPTACAAALAVLDIVEAEDLPGNAGKVGAQLLEQLQPLTERYA---VVGE 371 Query: 375 ARGVGMVAALELVKNKKTRERFTD-KGVGMLCREHCFRNGLIMRAVGDTMIISPPLVI 431 RG G++ A++LV +K TRE G+ E R G+++R +G+ +++SPPL + Sbjct: 372 VRGKGLMIAVDLVADKVTREPLDPANGLASRIAEQARRAGVLVRPIGNKIVMSPPLTL 429 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: 562 Number of extensions: 25 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: 449 Length adjustment: 33 Effective length of query: 423 Effective length of database: 416 Effective search space: 175968 Effective search space used: 175968 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