Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate H281DRAFT_05493 H281DRAFT_05493 4-aminobutyrate---pyruvate transaminase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Burk376:H281DRAFT_05493 Length = 462 Score = 345 bits (884), Expect = 2e-99 Identities = 178/435 (40%), Positives = 261/435 (60%), Gaps = 7/435 (1%) Query: 21 HLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATR 80 HL T+ +G ++ + +G+ ++D G + +++M+GLWC +G+ L AATR Sbjct: 19 HLHSQTNLPVHQHRGPLVMCRGDGICVYDETGKEYIESMSGLWCAALGFSDRRLAAAATR 78 Query: 81 QMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWAT 140 Q+ LP+Y+ F V LA+ +A + P +FF SGSEANDT+ ++ Y Sbjct: 79 QLETLPYYHTFNHRVPDVVARLAERVAAIVPLEDPKIFFASSGSEANDTMTKIAWSYHRA 138 Query: 141 KGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG-GDMS 199 G+P+++ +I G+HGSTV G SL G+ +H P+ GI+H+ P++Y G + + Sbjct: 139 LGKPERRKMIAHKKGFHGSTVMGASLSGLPHMHAAFGLPVEGILHVECPHFYRNGRSNET 198 Query: 200 PDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILF 259 EF +LE I G +AAFI+EPI GAGGVIVPP Y+P ++++L K+ IL Sbjct: 199 EAEFVARLVAELEALIAREGAGTIAAFISEPILGAGGVIVPPAGYFPAVQKVLRKHGILM 258 Query: 260 IADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLN----Q 315 ++DE+ICGFGRTG+WFG+Q G PD+M AK L+SGY+P+ VV+ EI L + Sbjct: 259 LSDEIICGFGRTGDWFGAQGAGFVPDMMSCAKTLSSGYVPISAVVISGEIYSALQSESAR 318 Query: 316 GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEA 375 G F HGFTYSGHPVAAAVALE + I +E E+ + E YL R LA HPLVGE Sbjct: 319 SGPFGHGFTYSGHPVAAAVALEAVTIYQEMNAPERTQ-ELGAYLHDRLASLAGHPLVGEI 377 Query: 376 RGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPS 434 RG G++A +ELV +K TR F ++ VG +GLI+R +GD + +SPP ++ Sbjct: 378 RGRGLIAGIELVSDKDTRAPFRSEAHVGATVEARARAHGLILRNMGDVIALSPPFIVTRD 437 Query: 435 QIDELITLARKCLDQ 449 +ID ++ + LD+ Sbjct: 438 EIDLIVQKLTRALDE 452 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: 575 Number of extensions: 29 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: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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