Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012473666.1 CPHAMN1_RS01040 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::A0A140N9B6 (406 letters) >NCBI__GCF_000020545.1:WP_012473666.1 Length = 431 Score = 140 bits (352), Expect = 9e-38 Identities = 104/323 (32%), Positives = 148/323 (45%), Gaps = 26/323 (8%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81 P +G+G+ + D G Y+D+ G LG HP + A+ +K T G E Sbjct: 36 PIFMAKGQGAYMTDVDGNTYLDYVGSWGPFILGSMHPRITAAIENTLTKIG-TSFGTPIE 94 Query: 82 PVLRLAKKLIDATFA-DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHG 140 + +A+ L + + V NSG EA +A++LAR + + + I+ F+ +HG Sbjct: 95 MEIEIAELLTQIVPSIEMVRMVNSGTEATMSAVRLARGY------TGRDKIIKFEGCYHG 148 Query: 141 R-TLFTVSAG------GQPAYSQDFAPLPADIRHAAYNDINSASALID---DSTCAVIVE 190 F + AG G P D +A YNDI S L+ DS A+I+E Sbjct: 149 HGDSFLIKAGSGALTLGAPDSPGVTKGTANDTLNAKYNDIESVRVLVKENKDSIAAIIIE 208 Query: 191 PIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTT 250 P+ G GV+PA FLQ LR+LC +LIFDEV G R A YG+TPDL T Sbjct: 209 PVAGNTGVIPAKTDFLQALRDLCTEEGIVLIFDEVMCGF-RVALGGAQERYGITPDLTTM 267 Query: 251 AKALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLASAVAGKVLELINT----PE 303 K +GGG PVGA E RV +G T GNPLA + L+++ PE Sbjct: 268 GKIIGGGLPVGAFGGKREIMQRVAPIGDVYQAGTLSGNPLALTAGLETLKILRDDNPYPE 327 Query: 304 MLNGVKQRHDWFVERLNTINHRY 326 + + F + +N + Y Sbjct: 328 LERKAAFLEEGFRDNMNKLGLSY 350 Score = 23.9 bits (50), Expect = 0.010 Identities = 13/44 (29%), Positives = 20/44 (45%) Query: 319 LNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAG 362 L RYG+ ++ +G +IG L G ++I Q A G Sbjct: 251 LGGAQERYGITPDLTTMGKIIGGGLPVGAFGGKREIMQRVAPIG 294 Lambda K H 0.319 0.135 0.406 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: 402 Number of extensions: 19 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: 2 Length of query: 406 Length of database: 431 Length adjustment: 32 Effective length of query: 374 Effective length of database: 399 Effective search space: 149226 Effective search space used: 149226 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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