Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >MicrobesOnline__882:208056 Length = 542 Score = 178 bits (451), Expect = 4e-49 Identities = 147/429 (34%), Positives = 211/429 (49%), Gaps = 69/429 (16%) Query: 15 VFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFRVAGQ 74 + + +G +L TDG R+LD + + NV GH +P++ EA+ Q ++ H S L + G Sbjct: 86 IIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAH-STLLGLGGT 144 Query: 75 ES--LAKRLTEATFADT--VFFTNSGAEAWECGAKLIRKYHYE--KGDKARTRIITFEQA 128 S LA RLT A VF+++SG+ A E K+ +YH + +GD RTR++ F A Sbjct: 145 PSIELAARLTAIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFSNA 204 Query: 129 FHGRTLAAVSAAQQEKLIKGFGPLLDG-------------FDLVP-------FGDLEAVR 168 +HG T+ +VS +GPLL DL P G++E + Sbjct: 205 YHGDTIGSVSLGGMSLFHGIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVERLM 264 Query: 169 NAVTDETAGICLEP-IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLF 227 E + +EP +QG G+ +LRGLR++CD HG+ + DE+ G G+TG +F Sbjct: 265 RHHGHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTGTMF 324 Query: 228 AHEWAGITPDVMAVAKGIGGGF-PLGACLATEKAASGMTAG-------THGSTYGGNPLA 279 A E G+ PD++ +AKGI GG+ PL A L TE G G HG TY GN LA Sbjct: 325 ACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGHTYTGNALA 384 Query: 280 TAVGNAVLDKVLEPGFLDHVQ-RIGGLLQDRLAGLVAE-NPAVFKG-VRGKGLMLGLACG 336 A A LD E L+ ++ RI +RLA L+A N G +R G+M G+ Sbjct: 385 CAAALASLDVFEEERTLETLRPRI-----ERLATLLAPLNDLPHVGDIRRVGVMTGI--- 436 Query: 337 PAVGD----------------VVVALRANGLLSVPAGDNVVRLLPPLNIGEAEVEEAV-- 378 V D V + R G++ P GD V+ L+PPL+I E E+E V Sbjct: 437 ELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPLGD-VMVLMPPLSITETELETLVHT 495 Query: 379 ---AILAKT 384 AI+A T Sbjct: 496 VRGAIIAVT 504 Lambda K H 0.321 0.139 0.414 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: 571 Number of extensions: 40 Number of successful extensions: 7 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: 389 Length of database: 542 Length adjustment: 33 Effective length of query: 356 Effective length of database: 509 Effective search space: 181204 Effective search space used: 181204 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 Apr 09 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