Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_110803747.1 C8J30_RS00315 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_003217355.1:WP_110803747.1 Length = 459 Score = 232 bits (591), Expect = 2e-65 Identities = 143/435 (32%), Positives = 227/435 (52%), Gaps = 26/435 (5%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78 HHL + +K R+ + +G+ +WD+ G + LDA +G +W VN+GYGR ++ +A Sbjct: 23 HHL---SQHKPYETTDPRVFVEGKGMRLWDATGREFLDATSGGVWTVNLGYGRADIARAV 79 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 Q+ LP+Y T P A+A+ P G+ V+++ SGSEAN+ V +MVR Sbjct: 80 QEQLLRLPYYAGAAGTV--PGARYAEALIAKMP-GLARVYYSNSGSEANEKVYKMVRQIS 136 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQ-GDFPIPGIVHIAQPYWYGEGGD 197 +K ++ R YHG+T+A ++ G EQ G FP G V + Y D Sbjct: 137 HRHHGGRKGKILFRERDYHGTTIAALATSGQAQRAEQYGPFP-DGFVSVPHCLEYRAQWD 195 Query: 198 MSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDI 257 +S +G AA+ +E+ IL G +++ + EPI GGVIVPP YW K+ I KY+I Sbjct: 196 VS--NYGERAADAIEEVILREGPDSIGCLVLEPITAGGGVIVPPAGYWEKVSHICRKYNI 253 Query: 258 LFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG 317 L DEV+CG GRTG WFG Q+YG PD + +AKG+ SGY + V + + E+ Sbjct: 254 LLHLDEVVCGLGRTGAWFGYQHYGIQPDFVTMAKGVASGYAAISCTVTTEAVFELFKDTP 313 Query: 318 -----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELAD-HPL 371 F T+ G A ALE +RI+ +E ++E L ++LA+ H + Sbjct: 314 TDPLCHFRDISTFGGCTAGPAAALETLRIIEDEGLLENT-TRMGERLLANLRDLAERHTV 372 Query: 372 VGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRA-------VGDTMI 424 +G+ RG G+ ELV +++T+E + V + + C G+++ A + T+ Sbjct: 373 IGDVRGKGLFCGAELVADRRTKEPLAEAKVQAVVAD-CAAQGVLIGATNRSIPGLNTTLC 431 Query: 425 ISPPLVIDPSQIDEL 439 ++P L+ ++ID + Sbjct: 432 LAPALIASEAEIDRI 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: 574 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 456 Length of database: 459 Length adjustment: 33 Effective length of query: 423 Effective length of database: 426 Effective search space: 180198 Effective search space used: 180198 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 24 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