Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate AZOBR_RS03625 AZOBR_RS03625 5-aminolevulinate synthase
Query= SwissProt::O75600 (419 letters) >FitnessBrowser__azobra:AZOBR_RS03625 Length = 404 Score = 235 bits (599), Expect = 2e-66 Identities = 131/345 (37%), Positives = 197/345 (57%), Gaps = 4/345 (1%) Query: 70 FCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKNLEAKIARFHQREDAI 129 +C+N+YLG+ +P V++A A++ GAG R I GT H LE ++A HQ+E A+ Sbjct: 51 WCSNDYLGMGQNPVVLKAMHDAIDGVGAGAGGTRNISGTNIYHVLLERELADLHQKEAAL 110 Query: 130 LYPSCYDANAGLFEAL--LTPEDAVLSDELNHASIIDGIRLCKAHKYRYRHLDMADLEAK 187 L+ S Y +N L L P +LSD LNH S+I GIR A K+ +RH D L+ Sbjct: 111 LFTSGYVSNDATLGTLGKLLPNCVILSDALNHNSMITGIRNSGAEKHIFRHNDPKHLDEL 170 Query: 188 LQEAQKHRLRLVATDGAFSMDGDIAPLQEICCLASRYGALVFMDECHATGFLGPTGRGTD 247 L + R ++VA + +SMDGD+AP+ ++C +A ++GA+ ++DE HA G GP G G Sbjct: 171 LSQIAPDRPKVVAFESVYSMDGDVAPIHDLCDVADKHGAMTYLDEVHAVGMYGPRGGGVA 230 Query: 248 ELLGVMDQVTIINSTLGKALGGASGGYTTGPGPLVSLLRQRARPYLFSNSLPPAVVGCAS 307 E G MD++TII TLGKA G GGY TG LV +R A ++FS SL P + A Sbjct: 231 ERDGAMDRLTIIEGTLGKAF-GVQGGYITGSTALVDCIRSFAAGFIFSTSLSPVLAAGAL 289 Query: 308 KALDLLMGSNTIVQSMAAKTQRFRSKMEAAGFTISGASHPICPVMLGDARLASRMADDML 367 ++ L S T + + M AG + ++ I PVM+GDA R +D+++ Sbjct: 290 ASIRYLKTSQTERDQHQERAATLKRLMAEAGLPVMPSASHIVPVMVGDAHRCKRASDELM 349 Query: 368 KR-GIFVIGFSYPVVPKGKARIRVQISAVHSEEDIDRCVEAFVEV 411 +R I+V +YP VP+G R+R + +HS+ ++ R V+A ++V Sbjct: 350 ERHDIYVQPINYPTVPRGGERLRFTPTPLHSDAEMARLVDALLDV 394 Lambda K H 0.322 0.137 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: 375 Number of extensions: 23 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: 419 Length of database: 404 Length adjustment: 31 Effective length of query: 388 Effective length of database: 373 Effective search space: 144724 Effective search space used: 144724 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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