Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate SMc03104 SMc03104 5-aminolevulinate synthase
Query= SwissProt::O75600 (419 letters) >FitnessBrowser__Smeli:SMc03104 Length = 405 Score = 231 bits (588), Expect = 4e-65 Identities = 139/392 (35%), Positives = 209/392 (53%), Gaps = 10/392 (2%) Query: 24 LAQLRGILEGELEGIRGAGTWKSERVITSRQGPHIRV-----DGVSGGILNFCANNYLGL 78 + + EL+G+ G ++ + +G + DG + +C+N+YLG+ Sbjct: 1 MMDFESFFKNELDGLHQEGRYRVFADLARHRGSFPKATRYTADGAQE-VTVWCSNDYLGM 59 Query: 79 SSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKNLEAKIARFHQREDAILYPSCYDAN 138 P V +A A++E GAG R I GT H LE ++A H +E A+L+ S Y +N Sbjct: 60 GQCPIVTEAMKNAIDECGAGAGGTRNISGTNHYHVLLERELADLHGKESALLFTSGYVSN 119 Query: 139 AGLFEALLT--PEDAVLSDELNHASIIDGIRLCKAHKYRYRHLDMADLEAKLQEAQKHRL 196 L + P V SD NHAS+I+GIR K + ++H +ADLEAKL A Sbjct: 120 WAALGTLCSKIPGVIVFSDAGNHASMIEGIRHSKCERVIFKHNSVADLEAKLAAADPRAP 179 Query: 197 RLVATDGAFSMDGDIAPLQEICCLASRYGALVFMDECHATGFLGPTGRGTDELLGVMDQV 256 +++A + +SMDGDIAP++E C LA +YGA+ ++DE HA G GP G G E G+M ++ Sbjct: 180 KIIAFESVYSMDGDIAPIREFCDLADKYGAMTYLDEVHAVGMYGPRGGGIAEREGLMHRL 239 Query: 257 TIINSTLGKALGGASGGYTTGPGPLVSLLRQRARPYLFSNSLPPAVVGCASKALDLLMGS 316 T+I TLGKA G GGY TG L +R A ++F+ +LPPA+ A ++ L S Sbjct: 240 TVIEGTLGKAF-GVMGGYITGSAALCDFIRSFASGFIFTTALPPALAAGALASIRHLKES 298 Query: 317 NTIVQSMAAKTQRFRSKMEAAGFTISGASHPICPVMLGDARLASRMADDMLKR-GIFVIG 375 + + +R RS ++ G I PV++GDA ++D +L GI+V Sbjct: 299 QVERFAHQERVRRLRSLLDQRGIPHMVNPSHIVPVIVGDAAKCKWISDLLLDNFGIYVQP 358 Query: 376 FSYPVVPKGKARIRVQISAVHSEEDIDRCVEA 407 +YP VPK R+R+ + +HS+ DID V A Sbjct: 359 INYPTVPKKTERLRITPTPMHSDADIDHLVSA 390 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: 383 Number of extensions: 22 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: 405 Length adjustment: 31 Effective length of query: 388 Effective length of database: 374 Effective search space: 145112 Effective search space used: 145112 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