Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate 3610165 Dshi_3546 5-aminolevulinic acid synthase (RefSeq)
Query= SwissProt::O75600 (419 letters) >FitnessBrowser__Dino:3610165 Length = 404 Score = 236 bits (602), Expect = 9e-67 Identities = 144/361 (39%), Positives = 203/361 (56%), Gaps = 10/361 (2%) Query: 54 QGPHIRVDGVSGG--ILNFCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSI 111 Q P + G G I +C+N+YLG+ HP+V++ + + + GAG R I GT Sbjct: 32 QHPKAQCHGEDGKRQITVWCSNDYLGMGQHPKVVERMQEVIGQCGAGAGGTRNISGTNHH 91 Query: 112 HKNLEAKIARFHQREDAILYPSCYDANAGLFEAL--LTPEDAVLSDELNHASIIDGIRLC 169 H+ LE ++A H +EDA+L+ S Y +N L + +LSDELNHAS+I+G+R Sbjct: 92 HRLLEDELADLHGKEDALLFTSGYVSNWAALSTLGARLRDCVILSDELNHASMIEGMRHS 151 Query: 170 KAHKYRYRHLDMADLEAKLQEAQKHRLRLVATDGAFSMDGDIAPLQEICCLASRYGALVF 229 +A ++H D ADLEAKL + ++VA + +SMDGDIAP+ EIC +A +YGA+ + Sbjct: 152 RAKVVIWKHNDPADLEAKLAALPANCPKIVAFESVYSMDGDIAPIAEICDVAEKYGAMTY 211 Query: 230 MDECHATGFLGPTGRGTDELLGVMDQVTIINSTLGKALGGASGGYTTGPGPLVSLLRQRA 289 +DE HA G GP G G E GVMD+VT+I TLGKA G GGY TG L +R A Sbjct: 212 LDEVHAVGMYGPRGAGIAERDGVMDRVTLIEGTLGKAF-GVVGGYITGSKTLCDFIRSFA 270 Query: 290 RPYLFSNSLPPAVVGCASKALDLLMGSNTIVQSMAAKTQRFRSKMEAAGFT-ISGASHPI 348 ++F+ +LPPAV A ++ L S+ + + R ++ AG I SH I Sbjct: 271 SGFIFTTALPPAVAAAAQTSIRHLKESSAERDLQKVRVAQLRQMLDRAGIPHIDNPSH-I 329 Query: 349 CPVMLGDARLASRMADDML--KRGIFVIGFSYPVVPKGKARIRVQISAVHSEEDIDRCVE 406 PVM+ D + RM D L + GI+V +YP VPKG R+R S HS +D+ V Sbjct: 330 IPVMIKDP-VKCRMLSDYLMDEFGIYVQPINYPTVPKGTERLRFTPSPNHSVDDLRHLVS 388 Query: 407 A 407 A Sbjct: 389 A 389 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: 391 Number of extensions: 18 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