Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_900115975.1:WP_092481894.1 Length = 453 Score = 207 bits (527), Expect = 5e-58 Identities = 140/398 (35%), Positives = 210/398 (52%), Gaps = 29/398 (7%) Query: 34 STVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYEPY-VELCE 92 ST D+ G+E ID GG + N GH HPKV+ AV +QL + + ++L +P L + Sbjct: 69 STFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQRQALHSQELL--DPLRAFLAK 126 Query: 93 KINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTMMTLGLTGK 152 + + PGD + V +G+E+VE +K A+ TGR I+ T +HG+++ +L T K Sbjct: 127 LLGSITPGDL-QYAFFVNSGTESVEAGIKFAKMYTGRRSFISTTRAFHGKSLGSLSATAK 185 Query: 153 VVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDA-EPRDIAAIILEPVQG 211 V + L+PG H + +A A VE + ++ A D+AA+I+EPVQG Sbjct: 186 GVFRKPFLPLIPG----------FHHVPYGNAEA-VEMMLESCAFVGEDVAAVIVEPVQG 234 Query: 212 EGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSI 271 EGG + P++ + +LR LCD++G LLI DEVQTG GRTG FA E V PD+ AK+ Sbjct: 235 EGGVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHSNVVPDILCLAKAF 294 Query: 272 AGG-FPLAGVCGKAEYMDAIA--PGGLGGTYAGSPIACAAALAVIEVFEEEKLLDRSKAV 328 GG P+ + + + P T+ G+P+ CAAA+A I V EE L RS Sbjct: 295 GGGIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINVLLEENLPQRSAES 354 Query: 329 GERLTAGLREIQKKYP-IIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVAKAR-EKGLI 386 G + LRE+ +KYP ++ +VRG G MI +E F +G VAK +G++ Sbjct: 355 GVYMLGKLRELAEKYPAVVQEVRGKGLMIGIEFFND--------ELGYEVAKGLFARGVL 406 Query: 387 LLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424 + +RI PLT D+ + ++ AE+ Sbjct: 407 VAGTLINAKSIRIEPPLTISREQQDQVIERLDNTLAEV 444 Lambda K H 0.320 0.138 0.395 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: 503 Number of extensions: 29 Number of successful extensions: 4 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: 425 Length of database: 453 Length adjustment: 32 Effective length of query: 393 Effective length of database: 421 Effective search space: 165453 Effective search space used: 165453 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