Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_066329653.1 BLR17_RS09610 aspartate aminotransferase family protein
Query= reanno::Cola:Echvi_3848 (381 letters) >NCBI__GCF_900100165.1:WP_066329653.1 Length = 398 Score = 155 bits (393), Expect = 1e-42 Identities = 126/384 (32%), Positives = 185/384 (48%), Gaps = 32/384 (8%) Query: 17 ASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAF------YSNSVQIP 70 A GS I+D +YLD G + ++GH P + IK+QLD + YS S + Sbjct: 24 AIGSYIYDTNNKKYLDFVAGVSACTLGHQPPRVNQAIKDQLDKYSHVMVYGEYSQSPAVE 83 Query: 71 IQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTSGA 130 K +A+ L + P +L NSG EA E +LKLA TG+ +I+ +HG T G+ Sbjct: 84 YCKLMASLLPE----PLNKTYLVNSGTEAIEGSLKLARRVTGRSQWISCYNAYHGNTMGS 139 Query: 131 VALTDNPKIIAPFNAH-EGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGGIQVPDPA 189 +++ + F V + FN+ +EK T AGV++E IQG G P Sbjct: 140 MSVMGFEERKQAFRPLIPDVDFITFNNEADLEK--ITTKTAGVLLETIQGGAGFIEPQND 197 Query: 190 FLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGFPIGGV 249 +L + + GA LILDE+Q G+ R+GK F Q + + PD++ + KGMG G P+G Sbjct: 198 YLKKVRERCTEVGAMLILDEIQPGFGRTGKLFGFQNYD-IVPDIVAMGKGMGGGMPVGAF 256 Query: 250 LISP---EFKASHGLLG--TTFGGNHLACAAALAVLEVIDEENLITAAAENGKAIMAALE 304 S + + LG TTFGG+ + AA LA L+ I E +L+ A E K + L Sbjct: 257 TASSAMMDLLTENPKLGHITTFGGHPVIAAACLATLKEITETDLMQEALEKEKLFRSLLV 316 Query: 305 KVAGVTEVRGKGLMIGFDLATEAGPVRAALIHEHK-------IFTGSAGGKHTIRLLPPL 357 + EVRGKGLM+ AT L + K +F G A IR+ PPL Sbjct: 317 HPL-IQEVRGKGLMLAAMTATAEITNEVILKCQDKGLILFWLLFEGCA-----IRITPPL 370 Query: 358 NIEPKALTLFLEKLETVLNVKQST 381 I + + + TV++ Q + Sbjct: 371 TISNEEIREGCNIMLTVMDEIQKS 394 Lambda K H 0.318 0.137 0.400 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: 378 Number of extensions: 28 Number of successful extensions: 6 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: 381 Length of database: 398 Length adjustment: 30 Effective length of query: 351 Effective length of database: 368 Effective search space: 129168 Effective search space used: 129168 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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