Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BPHYT_RS27170 BPHYT_RS27170 hypothetical protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__BFirm:BPHYT_RS27170 Length = 442 Score = 255 bits (651), Expect = 2e-72 Identities = 151/443 (34%), Positives = 241/443 (54%), Gaps = 17/443 (3%) Query: 26 TDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMREL 85 T + +L ++ + +G+ I DS G + +DA G +G+ + ++ A RQ ++L Sbjct: 3 TVFHRLPKQSLPVAVAGDGIEIIDSTGKRYIDASGGAAVSCLGHSNQRVIDAIKRQAQQL 62 Query: 86 PF-YNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQP 144 P+ + FF TA P ELA + AP+G+ HV+F GSEA + L++ R Y+ KG+P Sbjct: 63 PYAHTSFFTTA--PAEELADRLVASAPQGLEHVYFVSGGSEAIEAALKLARQYFVEKGEP 120 Query: 145 QKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP-YWYGEG-GDMSPDE 202 Q++ I R YHG+T+ +++GG A + PI H P Y Y E D + + Sbjct: 121 QRRHFIARRQSYHGNTLGALAIGG-NAWRREPFLPILIEAHHVSPCYAYREQRADETEEA 179 Query: 203 FGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPP-DTYWPKIREILAKYDILFIA 261 F A++LE+KILE+G + VAAF+AE + GA VPP Y+ KIR + +Y +L I Sbjct: 180 FAQRLADELEQKILELGADTVAAFVAETVVGATAGAVPPVREYFRKIRAVCDRYGVLLIL 239 Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG-GEFY 320 DE++ G GRTG + + G APD++ IAKGL +GY P+G +V D I + + G G F Sbjct: 240 DEIMSGMGRTGHLYACEEDGVAPDILTIAKGLGAGYQPIGATLVSDRIYQAIVGGSGFFQ 299 Query: 321 HGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGM 380 HG TY GH A A ALE R++ E+K++ V A + + A HP +G+ RG G+ Sbjct: 300 HGHTYIGHATACAAALEVQRVIEEDKLLPNVLARGEQLRGQLREHYAQHPHIGDVRGRGL 359 Query: 381 VAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIM--------RAVGDTMIISPPLVI 431 +ELV+++ + F + + + R F GL++ +GD ++++PP + Sbjct: 360 FVGVELVRDRAGKTPFDARLKLHAVIRREAFARGLMVYPMGGTVDGQIGDHVLLAPPFIC 419 Query: 432 DPSQIDELITLARKCLDQTAAAV 454 IDE+++ + AA+ Sbjct: 420 TERDIDEIVSRFTDAVGGALAAI 442 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: 545 Number of extensions: 30 Number of successful extensions: 6 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: 442 Length adjustment: 33 Effective length of query: 423 Effective length of database: 409 Effective search space: 173007 Effective search space used: 173007 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