Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate 3609807 Dshi_3190 5-aminolevulinic acid synthase (RefSeq)
Query= SwissProt::O75600 (419 letters) >FitnessBrowser__Dino:3609807 Length = 407 Score = 241 bits (614), Expect = 4e-68 Identities = 138/348 (39%), Positives = 199/348 (57%), Gaps = 6/348 (1%) Query: 64 SGGILNFCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKNLEAKIARFH 123 SG + +C+N+YLG+ HP+V+ A AL+ GAG R I GT H LEA++A H Sbjct: 44 SGPVTIWCSNDYLGMGQHPDVLAAMHGALDRSGAGAGGTRNISGTTHDHVALEAELADLH 103 Query: 124 QREDAILYPSCYDANAGLFEAL--LTPEDAVLSDELNHASIIDGIRLCKAHKYRYRHLDM 181 +E A+L+ S Y +N L + P+ +LSD LNHAS+I+GIR +A + + H DM Sbjct: 104 GKEAALLFTSGYVSNWAALGTLGAMLPDCLILSDALNHASMIEGIRHSRADRVIWTHNDM 163 Query: 182 ADLEAKLQEAQKHRLRLVATDGAFSMDGDIAPLQEICCLASRYGALVFMDECHATGFLGP 241 ADLEAKL R +++A + +SMDGDIAP+ EIC LA RY A+ ++DE HA G GP Sbjct: 164 ADLEAKLAAQPLERPKIIAFESVYSMDGDIAPIAEICDLADRYNAMTYLDEVHAVGLYGP 223 Query: 242 TGRGTDELLGVMDQVTIINSTLGKALGGASGGYTTGPGPLVSLLRQRARPYLFSNSLPPA 301 G G E G+M+++T+I TLGKA G GGY L +R A ++F+ +LPP Sbjct: 224 RGGGVAEREGLMERITVIEGTLGKAF-GVVGGYIAASADLCDFVRSFASGFIFTTALPPH 282 Query: 302 VVGCASKALDLLMGSNTIVQSMAAKTQRFRSKMEAAGFT-ISGASHPICPVMLGDARLAS 360 V A ++ L S+ + + R++ +A G + SH I P+M+GD Sbjct: 283 VAAGACASVRHLKQSSIERRIQQERVAELRARFDAIGLPHVPNPSH-IIPLMVGDPVKCK 341 Query: 361 RMADDMLKR-GIFVIGFSYPVVPKGKARIRVQISAVHSEEDIDRCVEA 407 ++D +L GI++ +YP VPKG R+R+ S VH D+DR A Sbjct: 342 FISDTLLDEFGIYIQPINYPTVPKGTERLRITPSPVHDPADLDRLCTA 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: 380 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: 407 Length adjustment: 31 Effective length of query: 388 Effective length of database: 376 Effective search space: 145888 Effective search space used: 145888 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