Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_012384241.1 BIND_RS06310 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_000019845.1:WP_012384241.1 Length = 444 Score = 262 bits (669), Expect = 2e-74 Identities = 160/433 (36%), Positives = 234/433 (54%), Gaps = 20/433 (4%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT + +K RI+ A+ ++ + ++G ILD AGLWC N G+ R+++VQA Q Sbjct: 19 PFTANRAF-KKSPRIVASAKDMHYYTADGKPILDGTAGLWCCNAGHSRDKIVQAIQAQAA 77 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 EL F F Q HP V LA IA +AP ++HVFF SGSEA DT L++ Y +GQ Sbjct: 78 ELDFAPPF-QFGHPKVFALAARIAALAPGDLDHVFFGNSGSEAVDTALKIALAYHNIQGQ 136 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPD-E 202 + +IGR YHG G ++GG+ + + G+ H+ Y E + E Sbjct: 137 GSRVRLIGRERAYHGVGFGGGAVGGIPGNRKAFGALLAGVDHLPTTYNRAEQAFTKGEPE 196 Query: 203 FGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIAD 262 +G A++LEK + +AA I EP+ G+ GV+ PP Y K+R I KY IL I D Sbjct: 197 WGGHLADELEKLVALHDASTIAAVIVEPMSGSTGVLPPPKGYLQKLRAICDKYGILLIFD 256 Query: 263 EVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG----E 318 EVICG+GR G F ++ YG PD++ AKG+TSG +PMGGV++R I E +G E Sbjct: 257 EVICGYGRLGYAFAAERYGVVPDMITFAKGITSGTVPMGGVLIRKPIYEAFMKGPELAVE 316 Query: 319 FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGV 378 HG+TYSGHP+A A L + + +EE + E+ + + P L P + + R V Sbjct: 317 LTHGYTYSGHPLACAAGLATLDLYKEEGLFERAR-KLEPVWADAVHGLKSLPNILDIRTV 375 Query: 379 GMVAALEL--VKNKKTRERF--TDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPS 434 G+ AA++L + + + F DK L L+ R GD++I++PPL+I Sbjct: 376 GLTAAIDLAPIADAPGKRAFGVMDKAFHEL--------DLLTRIAGDSIILTPPLIISEG 427 Query: 435 QIDELITLARKCL 447 QI E++ K + Sbjct: 428 QIGEIVEKTGKAI 440 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: 587 Number of extensions: 28 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: 444 Length adjustment: 33 Effective length of query: 423 Effective length of database: 411 Effective search space: 173853 Effective search space used: 173853 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 24 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