Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate Ac3H11_4342 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4342 Length = 454 Score = 262 bits (670), Expect = 1e-74 Identities = 158/444 (35%), Positives = 241/444 (54%), Gaps = 24/444 (5%) Query: 19 DHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAA 78 D H PFT + K R+I +G Y D++G KI D ++GLWC +G+GR+++ +A Sbjct: 24 DAHWMPFTGNRNFKAK-PRMIVSGQGAYYTDADGRKIFDGLSGLWCSGLGHGRKDVAEAI 82 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 + L Y+ FQ HP LA + ++ P G+++VFFTGSGSE+ DT L+M R YW Sbjct: 83 GKAAATLD-YSPAFQFGHPASFALANKLKELTPAGLDYVFFTGSGSESADTSLKMARAYW 141 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGM---KALHEQGDFPIPGIVHIAQPYWYGEG 195 KGQ K +IGR GYHG G+S+GG+ + QG + H P + Sbjct: 142 RAKGQASKTRLIGREKGYHGVNYGGISVGGIVGNRKTFGQG-IEADHLPHTQPPAGTFQK 200 Query: 196 GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255 G ++ G A++L I N+AA I EP G+ GV++PP Y +IREI + Sbjct: 201 G--MAEDGGRALADKLLDVIALHDASNIAAVIVEPFSGSAGVVIPPKGYLERIREICTQN 258 Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEV-LN 314 +IL I DEVI GFGR G W G++ +G PD++ AK +T+G P+GGV+ EI + ++ Sbjct: 259 NILLIFDEVITGFGRCGAWTGAEAFGVTPDILNFAKQVTNGAQPLGGVIATKEIYDTFIS 318 Query: 315 QGG-----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADH 369 QGG EF HG+TYS HPVA A + IL++E + +VKA AP+ + L Sbjct: 319 QGGPEYMLEFPHGYTYSAHPVACAAGNAVLDILQKEDMPGRVKA-LAPHFENAVHGLKGA 377 Query: 370 PLVGEARGVGMVAALEL--VKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISP 427 V + R G+ A + + + ++ + + + M C+ G +R GDT+ ++P Sbjct: 378 KHVADIRNYGLAAGITISALPSEPAKRPYE---IAM----KCWEKGFYVRYGGDTIQLAP 430 Query: 428 PLVIDPSQIDELITLARKCLDQTA 451 P + ++ID +++ L +TA Sbjct: 431 PFISTSAEIDRMVSALGDALHETA 454 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: 649 Number of extensions: 41 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: 454 Length adjustment: 33 Effective length of query: 423 Effective length of database: 421 Effective search space: 178083 Effective search space used: 178083 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