Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_900115975.1:WP_092481894.1 Length = 453 Score = 198 bits (504), Expect = 2e-55 Identities = 136/404 (33%), Positives = 205/404 (50%), Gaps = 32/404 (7%) Query: 10 FDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAG 69 F E+ V + + GS D GKE+ID GG + +GH HP+++KA+ +Q Sbjct: 48 FLEYRKSVSTDYTSVEWKDSGSTFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQ 107 Query: 70 KFWHTGNGYTNEPVLRLAKQLIDATFADR--VFFCNSGAEANEAALKLARKYAHDRFGSE 127 + + LAK L T D FF NSG E+ EA +K A+ Y R Sbjct: 108 RQALHSQELLDPLRAFLAKLLGSITPGDLQYAFFVNSGTESVEAGIKFAKMYTGRR---- 163 Query: 128 KSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAK------ALID 181 ++ AFHG++L ++SA + + + F PL P H Y + ++ + A + Sbjct: 164 --SFISTTRAFHGKSLGSLSATAKGVFRKPFLPLIPGFHHVPYGNAEAVEMMLESCAFVG 221 Query: 182 DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHY 241 ++ AVIVEP+QGEGGV+ D+L LRELCD + ALLI DEVQTG+GRTG+++A H Sbjct: 222 EDVAAVIVEPVQGEGGVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHS 281 Query: 242 GVTPDLLSTAKALGGG-FPIGALLASERCASVMTVG--THGTTYGGNPLACAVAGEVFAT 298 V PD+L AKA GGG PIGA +A + + H TT+GGNP+ CA A Sbjct: 282 NVVPDILCLAKAFGGGIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINV 341 Query: 299 INTREVLNGVKQRHQWFCERLNAINARY-GLFKEIRGLGLLIGCVLKDEYAGKAKAISNQ 357 + + + + +L + +Y + +E+RG GL+IG ++ G A Sbjct: 342 LLEENLPQRSAESGVYMLGKLRELAEKYPAVVQEVRGKGLMIGIEFFNDELGYEVA---- 397 Query: 358 AAEEGLM---ILIAG----ANVVRFAPALIISEDEVNSGLDRFE 394 +GL +L+AG A +R P L IS ++ + ++R + Sbjct: 398 ---KGLFARGVLVAGTLINAKSIRIEPPLTISREQQDQVIERLD 438 Lambda K H 0.321 0.137 0.412 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: 463 Number of extensions: 26 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: 406 Length of database: 453 Length adjustment: 32 Effective length of query: 374 Effective length of database: 421 Effective search space: 157454 Effective search space used: 157454 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