Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate RR42_RS26850 RR42_RS26850 hypothetical protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Cup4G11:RR42_RS26850 Length = 447 Score = 221 bits (562), Expect = 5e-62 Identities = 137/417 (32%), Positives = 215/417 (51%), Gaps = 17/417 (4%) Query: 38 IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97 + +G+ + DS G +DA G +G+G +++A +Q L + + F T Sbjct: 15 VAVAGKGIELVDSNGKHYIDASGGAAVSCLGHGHPRVIEAIKQQADSLAYAHTSFFTTEV 74 Query: 98 PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157 ELA+ +A AP +NHV+F GSEA + L++ R Y+ GQ Q++ I R YH Sbjct: 75 SE-ELARTLAQAAPGDLNHVYFVSGGSEAVEAALKLARQYFVEIGQTQRRHFIARRQSYH 133 Query: 158 GSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYG--EGGDMSPDEFGVWAAEQLEKKI 215 G+T+ +++GG E + H+A Y Y E G+ + ++ A++LE KI Sbjct: 134 GNTLGALAIGGNAWRREPFLPLLVPAHHVAPCYAYRDQEAGE-TDQQYAQRLADELEAKI 192 Query: 216 LEVGEENVAAFIAEPIQGAGGVIVPPDT-YWPKIREILAKYDILFIADEVICGFGRTGEW 274 LE+G +VAAF+AE + GA VPP Y ++R + KY +L I DE++ G GRTG Sbjct: 193 LELGPHSVAAFVAETVVGATAGAVPPVADYLRRVRAVCDKYGVLLILDEIMSGMGRTGYL 252 Query: 275 FGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVE-VLNQGGEFYHGFTYSGHPVAAA 333 F + G PD++ IAKGL +GY P+G ++ I + V+ G F HG TY GH A A Sbjct: 253 FACEEDGVVPDIVTIAKGLAAGYQPIGAMISSSRIYDAVVGGSGFFQHGHTYIGHATACA 312 Query: 334 VALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKKTR 393 AL R + E+ ++E V A + + L DHP VG+ RG G+ +E V ++T+ Sbjct: 313 AALAVQRTIAEDCLLENVLARGGQLRARLRETLGDHPNVGDIRGRGLFVGVEFVAERETK 372 Query: 394 ERFTDKGVGMLCR--EHCFRNGLIMRAV--------GDTMIISPPLVIDPSQIDELI 440 D + M R +NGL++ + GD ++ +PP + ID ++ Sbjct: 373 ATL-DPALKMHARLKSTAMQNGLLIYPMGGTVDGMRGDHVLFAPPFICSAQDIDRIV 428 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: 517 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: 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