Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 202 bits (514), Expect = 2e-56 Identities = 144/424 (33%), Positives = 215/424 (50%), Gaps = 51/424 (12%) Query: 19 APAAFIP--VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHT 74 AP A +P VRG+G + D G YID GG AV+ LGH+HPR+++A+ Q + + HT Sbjct: 8 APRASLPIAVRGDGIEIVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHT 67 Query: 75 GNGYTNEPVLRLAKQLIDATFAD--RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIV 132 + +T EP LA LI+A + V+F + G+EA EAALKLAR+Y ++ E+ + Sbjct: 68 -SFFTTEPAEALADLLIEAAPRNLGHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFI 126 Query: 133 AFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQH-----------AIYNDLDSAKALID 181 A + ++HG TL ++ GG + F P+ + H A D A+ L D Sbjct: 127 ARRQSYHGNTLGALAIGGNAWRREPFLPILIEAHHVTPCFAYREQQAGETDEAFAQRLAD 186 Query: 182 D-----------NTCAVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGV 229 + + A + E + G G VP ++ R +R +CD + LLI DEV +G+ Sbjct: 187 ELEAKILELGAQSVAAFVAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGM 246 Query: 230 GRTGELYAYMHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGG 284 GRTG L+A GV+PD+L+ AK LG G+ PIGA L S + + G+ HG TY G Sbjct: 247 GRTGHLFACEEDGVSPDILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTYIG 306 Query: 285 NPLACAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLK 344 + ACA A EV I ++L+ VK R + RL A + ++RG GL G L Sbjct: 307 HATACAAALEVQKVIAEEQLLDNVKARGEQLRARLREWQANHPFIGDVRGRGLFTGVELV 366 Query: 345 DEYAGKA---------KAISNQAAEEGLMILIAGANV-------VRFAPALIISEDEVNS 388 + A K I ++A + GLM+ G V V AP I + ++++ Sbjct: 367 QDRASKTAFDPKHKLHAIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQIDT 426 Query: 389 GLDR 392 ++R Sbjct: 427 IVER 430 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: 431 Number of extensions: 20 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: 406 Length of database: 447 Length adjustment: 32 Effective length of query: 374 Effective length of database: 415 Effective search space: 155210 Effective search space used: 155210 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