Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AZOBR_RS22505 AZOBR_RS22505 omega amino acid--pyruvate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__azobra:AZOBR_RS22505 Length = 436 Score = 280 bits (715), Expect = 9e-80 Identities = 161/441 (36%), Positives = 233/441 (52%), Gaps = 19/441 (4%) Query: 19 DHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAA 78 D H PFT ++ + R+I +AEG + WD+EG KI D+++GLWC G+ R E+ +A Sbjct: 7 DAHWMPFTANREF-KANPRLIARAEGAWYWDAEGRKIYDSLSGLWCCGAGHSRREISEAV 65 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 RQ+ EL Y+ FQ HP +LA +A + P G++HVFF SGSEA DT L+M R YW Sbjct: 66 ARQIAELD-YSPAFQFGHPAAFKLAHKLASMTPAGLDHVFFVNSGSEATDTSLKMARAYW 124 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM 198 KGQP K +IGR GYHG G+SLGG+ + + H+ Sbjct: 125 RLKGQPAKTKLIGRSKGYHGVNFGGISLGGIGGNRKLFGSGVEAD-HLPHTLLPQNAFTK 183 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 E G A+ LE+ + N+AA I EP+ G+ GV+ PP Y ++R + K++IL Sbjct: 184 GLPEQGAELADALEELVALHDASNIAAVIVEPLAGSAGVLPPPKGYLQRLRALCDKHNIL 243 Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG- 317 I DEVI GFGR G FG+ +G PD+M +AKGLT+G +PMG VV EI + G Sbjct: 244 LIFDEVITGFGRMGAAFGADAFGVVPDIMNVAKGLTNGAVPMGAVVANHEIYQTFMDNGG 303 Query: 318 -----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLV 372 EF HG+TYS HPVA A L + + +K+ EK A+ AP+ + L V Sbjct: 304 ADYMVEFPHGYTYSAHPVACAAGLAALELFERDKLAEKA-ADLAPHFETVLHGLKGLRHV 362 Query: 373 GEARGVGMVAALEL--VKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLV 430 + R G+ A+++ + + R + + M C++ G +R GDT+ P + Sbjct: 363 TDIRNYGLAGAVQIAALPGEPARRPYE---IAM----KCWKAGFYVRFGGDTLQFGPHFI 415 Query: 431 IDPSQIDELITLARKCLDQTA 451 + +D L+ + TA Sbjct: 416 SEREDLDRLMNAVSDAIQATA 436 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: 566 Number of extensions: 36 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: 436 Length adjustment: 32 Effective length of query: 424 Effective length of database: 404 Effective search space: 171296 Effective search space used: 171296 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