Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate WP_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= CharProtDB::CH_002469 (406 letters) >NCBI__GCF_002869505.1:WP_084199387.1 Length = 467 Score = 186 bits (472), Expect = 1e-51 Identities = 135/409 (33%), Positives = 195/409 (47%), Gaps = 36/409 (8%) Query: 20 PAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYT 79 PA FI R EG +WD G +YIDF G A N LG+ HPE+ EA++E ++ Sbjct: 42 PAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQRQYGFQWEHPL 101 Query: 80 NEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFH 139 P+ ++ + R F SG EA E+A+ LA RY IV+F + FH Sbjct: 102 RIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLALCHTQRRY------IVSFTSCFH 155 Query: 140 GRTLFT--VSA--GGQPAYSQDFA------------PLPADIRHAAYNDIN--------S 175 G L T VSA Y + +A +PA + A Y + + Sbjct: 156 GEGLGTKMVSAYNSDNNLYMEGWAGGVLKAPFPYSEEIPAGMDQAQYTEYCLWYIETHLT 215 Query: 176 ASALIDDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGEL 235 + ++ A++VEP EGG S AF+QGLR +C++ + LLI DEV TG+GRTG + Sbjct: 216 EYVVPAENIAAILVEPGLAEGGNWIPSKAFMQGLRRICDKFDWLLIADEVLTGLGRTGTM 275 Query: 236 YAYMHYGVTPDLLTTAKALGGGF-PVGALLATEECARVMTVGTHGTTYGGNPLASAVAGK 294 +A H+ V PD+L K L GG P + A +E T G+T+ G P A A K Sbjct: 276 WAVEHFDVVPDILVAGKNLSGGIEPCAGVAARDEILGDNPRATAGSTFAGTPGGCAAALK 335 Query: 295 VLELINTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNA-----DYAG 349 LE+ +L + ++R++ RY + S+VRGLGLL+G A + Sbjct: 336 TLEIYERDAVLTHTQHLAGVAMQRMSDWESRYEIVSQVRGLGLLLGVSFRAGREDIEDFH 395 Query: 350 QAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACE 398 A+ + E K G+ + VR PALN++E+ + GL R A E Sbjct: 396 IARSVRDEMLKRGLWAICDNEPQVRMYPALNMAEDVLLEGLSRMEEAIE 444 Lambda K H 0.319 0.136 0.407 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: 468 Number of extensions: 22 Number of successful extensions: 3 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: 467 Length adjustment: 32 Effective length of query: 374 Effective length of database: 435 Effective search space: 162690 Effective search space used: 162690 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 24 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