Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_015886749.1 NGR_RS03045 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_000018545.1:WP_015886749.1 Length = 458 Score = 325 bits (834), Expect = 1e-93 Identities = 177/440 (40%), Positives = 250/440 (56%), Gaps = 7/440 (1%) Query: 16 LSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELV 75 L R H + P Y+ + G R++ A+G + D+ G +++D AGLWCVN GYG E +V Sbjct: 9 LDRAHLIHPVASYRGHEKLGVRVLASAKGATVTDASGRQLIDGFAGLWCVNAGYGHESIV 68 Query: 76 QAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVR 135 +AATRQMRELP+ +F P + LA +A+ AP ++HVFFT GS+A D+ +R +R Sbjct: 69 EAATRQMRELPYATGYFGLGSEPAIRLASELAERAPGNLDHVFFTLGGSDAVDSTIRFIR 128 Query: 136 HYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG 195 +YW +G+PQ+ I GYHGS+ G L + A H P I Y Y Sbjct: 129 YYWIGRGEPQRDQFISVEQGYHGSSTVGAGLTALPAFHAGFGIPFDWQHKIPSHYAYRNP 188 Query: 196 GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255 P + L +K+ E+G E VAAF AEPIQG+GGV+VPP + +R++ + Sbjct: 189 VGDDPQAIIDASLAALRQKVEEIGPERVAAFYAEPIQGSGGVLVPPKGWMKAMRQLCQEL 248 Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQ 315 ILF+ADEVI GFGRTG F PD M +AKGLTSGY+PMG V + D I + + Sbjct: 249 GILFVADEVITGFGRTGPLFACHEDEIVPDFMTVAKGLTSGYVPMGAVFMGDHIYQTIAD 308 Query: 316 ---GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLV 372 G HG+TYS HPV+AAV LE +++ E + KA L + L DHPLV Sbjct: 309 SAGAGAVGHGYTYSAHPVSAAVGLEVLKLYENELLDNGRKA--GARLMAGLESLKDHPLV 366 Query: 373 GEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMI-ISPPLV 430 G+ RG GM+AA+ELV +K+ + K + + NGL++RA + ++ +PPL Sbjct: 367 GDVRGRGMLAAVELVVDKEKKTPLPAKAEPARRIFDRAWENGLVIRAFANGVLGYAPPLC 426 Query: 431 IDPSQIDELITLARKCLDQT 450 ++ID ++ RK LD+T Sbjct: 427 CTEAEIDGIVERTRKVLDET 446 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: 627 Number of extensions: 29 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: 458 Length adjustment: 33 Effective length of query: 423 Effective length of database: 425 Effective search space: 179775 Effective search space used: 179775 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 Apr 09 2024. 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