Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 197 bits (500), Expect = 7e-55 Identities = 152/428 (35%), Positives = 216/428 (50%), Gaps = 57/428 (13%) Query: 26 VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83 V G+G L D GK Y+D +GG AV+ LGH+ ++ A+ EQ GK F HTG T+EP Sbjct: 17 VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGF-LTSEPA 75 Query: 84 LRLAKQLIDATFAD--RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141 LA LI D RV+F + G+EA EAA+KLAR+Y +R + + ++A + ++HG Sbjct: 76 EALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGN 135 Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHA---------------------IYNDLDSAKALI 180 TL ++AGG Q FAPL I H + N+L++ + Sbjct: 136 TLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRL 195 Query: 181 DDNTC-AVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238 T A + EP+ G G VPA + + +RE+CD + LLI DEV G+GRTG L+A Sbjct: 196 GPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFAC 255 Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293 GV PD+L AK LG G+ PIGA+L S + + G+ HG TY G+P+A A Sbjct: 256 EADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGL 315 Query: 294 EVFATINTREVLNGVKQRHQWFCERLN-AINARYGLFK---EIRGLGLLIGCVLK----- 344 V + R G+ QR E L+ A+ AR+G ++RG GL G L Sbjct: 316 AVVRALLDR----GLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRES 371 Query: 345 ----DEYAGKAKAISNQAAEEGLMIL-IAG------ANVVRFAPALIISEDEVNSGLDRF 393 D G A + A E GL+ +AG + + AP I+SED++ D+ Sbjct: 372 KTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKL 431 Query: 394 ELACKRFL 401 E+A + L Sbjct: 432 EVALDQVL 439 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: 478 Number of extensions: 25 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: 440 Length adjustment: 32 Effective length of query: 374 Effective length of database: 408 Effective search space: 152592 Effective search space used: 152592 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: 50 (23.9 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