Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_007473232.1 CMTB2_RS01220 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::A0A140N9B6 (406 letters) >NCBI__GCF_000170735.1:WP_007473232.1 Length = 420 Score = 133 bits (334), Expect = 1e-35 Identities = 105/352 (29%), Positives = 171/352 (48%), Gaps = 23/352 (6%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNE 81 PFI +GEG+ ++D +G +Y+D+ GH + + A+ E K G + Sbjct: 30 PFIE-KGEGAYIFDIEGNKYLDYIQSWGPLIFGHCDKDTQNAIIEAVKK--GVSFGAPTK 86 Query: 82 PVLRLAKKLIDA-TFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHG 140 + LAK++++ + + F NSG EA +A++LAR + + K I+ F+ +HG Sbjct: 87 VEVELAKEVLELFPHLNLIRFVNSGTEATMSAIRLARGY------TGKDDIIKFEGCYHG 140 Query: 141 RT-LFTVSAG-GQPAYSQDFAP-LPADI-RH---AAYNDINSASALIDDSTCA-VIVEPI 192 + VSAG G + +P +PAD +H A YNDI S ++ VI+EPI Sbjct: 141 HSDSLLVSAGSGAATFGVPSSPGVPADFTKHTLLAKYNDIESVKKCFENGDVGCVIIEPI 200 Query: 193 QGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAK 252 G +VP FL LRE+CN + A+LIFDEV +G R ++ YG+ D++T K Sbjct: 201 AGNMSLVPGEKEFLGELREICNHYGAVLIFDEVMSGF-RASLRGSFDIYGIKADIVTFGK 259 Query: 253 ALGGGFPVGALLATEE-CARVMTVGT--HGTTYGGNPLA-SAVAGKVLELINTPEMLNGV 308 +GGG PVGA +E ++ VG T GNP+A SA + +L PE+ + Sbjct: 260 VIGGGMPVGAFAGKKEIMEKLSPVGPVYQAGTLSGNPVAMSAGLTVIKKLKENPEIYKEL 319 Query: 309 KQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK 360 + + +E + I+ + +G + G N ++++ K Sbjct: 320 EDKAKKLMEGFSEISKENNIDFNYNVIGSMFGFFFNKKLPKNFDEVNESDTK 371 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: 416 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: 420 Length adjustment: 31 Effective length of query: 375 Effective length of database: 389 Effective search space: 145875 Effective search space used: 145875 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