Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate SM_b20423 SM_b20423 hypothetical protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Smeli:SM_b20423 Length = 458 Score = 334 bits (857), Expect = 3e-96 Identities = 184/446 (41%), Positives = 261/446 (58%), Gaps = 12/446 (2%) Query: 9 KTREWQALSRDHHLPPFTDYKQ--LNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66 ++ E A RDH P T E R+I EGVYI D G + LDA AGL+CVN Sbjct: 4 RSNELTAWDRDHFFHPSTHMGMHARGETPTRVIGGGEGVYITDISGKRSLDAFAGLYCVN 63 Query: 67 VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126 VGYGR+++ A Q + L +Y+ + + L+K I D APEGM+ V+F SGS+A Sbjct: 64 VGYGRQKIADAIAEQAKNLAYYHAYVGHGTEASIRLSKMIIDRAPEGMSRVYFGLSGSDA 123 Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186 N+T ++++ +Y G+P+KK +I RW GYHGS V SL G+ H D P I+H Sbjct: 124 NETNIKLIWYYNNILGRPEKKKIISRWRGYHGSGVMTGSLTGLHLFHNAFDLPRAPILHT 183 Query: 187 AQPYWYGE-GGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYW 245 PY++ MS ++F + A++LE+ IL G + VAAFI EPI G GG++ PP YW Sbjct: 184 EAPYYFRRPDRSMSEEQFSQYCADKLEEMILAEGPDTVAAFIGEPILGTGGIVPPPKGYW 243 Query: 246 PKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVV 305 KI+ +L KYDIL +ADEV+ GFGR G FGS +YG PDL+ IAKGLTS Y P+ G +V Sbjct: 244 EKIQAVLQKYDILLVADEVVTGFGRLGTMFGSDHYGIKPDLITIAKGLTSAYAPLSGTIV 303 Query: 306 RDEIVEVLNQG----GEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQK 361 D++ +VL +G G HG+TYS HP+ AA + N+ ++ E I+E + A + + Sbjct: 304 SDKLWQVLVKGSDELGAIGHGWTYSAHPICAAAGIANLELIDELGIVENAGSTGAYFRAE 363 Query: 362 RWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDKG--VGMLCREHCFRNGLIMRAV 419 + + DH VGE RG G++AA+E V+++ R F D G VG G+I RA+ Sbjct: 364 LQKAVGDHRHVGEVRGDGLMAAIEFVEDRDDR-AFFDPGRKVGPQVAAALLERGVIGRAM 422 Query: 420 --GDTMIISPPLVIDPSQIDELITLA 443 GD + +PPL + + D ++ A Sbjct: 423 PQGDILGFAPPLCLTRDEADIVVKAA 448 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: 646 Number of extensions: 33 Number of successful extensions: 4 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: 458 Length adjustment: 33 Effective length of query: 423 Effective length of database: 425 Effective search space: 179775 Effective search space used: 179775 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