Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate Synpcc7942_0414 Synpcc7942_0414 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >FitnessBrowser__SynE:Synpcc7942_0414 Length = 390 Score = 335 bits (858), Expect = 2e-96 Identities = 179/382 (46%), Positives = 230/382 (60%), Gaps = 11/382 (2%) Query: 8 KTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFNIG 67 +TIAEINE+I+ G+AVV A E+ +G A+++DV+TTGTF PM +SG + N+G Sbjct: 2 RTIAEINEKIQAGRAVVWTATEVKARAPELGIAAIAQQVDVITTGTFEPMEASGAILNLG 61 Query: 68 QQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGHVIEDL 127 Q DPP +K + W+NDV AY+G A D LGA+E +ED +YGGG VI DL Sbjct: 62 QTDPP-IKIRQCWLNDVRAYSGFGAADLLLGASEESEDPEA--------EYGGGQVIADL 112 Query: 128 VRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTSRIIYT 187 + G+ V LRA GTDCYPR+S + I + +L NPRN YQN+ VN +YT Sbjct: 113 IAGQKVRLRAIGQGTDCYPRRSFETTIDRDSINQFYLFNPRNLYQNFIVGVNGGDETLYT 172 Query: 188 YMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHVAAPKR 247 Y+GPL PNL N +A G I+PLFNDP +IG+GTRIFLGGG GY+ GTQH KR Sbjct: 173 YLGPLLPNLGNAVYANPGAIAPLFNDPDLVSIGIGTRIFLGGGVGYIAWEGTQHFPLQKR 232 Query: 248 TERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIAWFTGV 307 P+ PA TL L GD K M ++RG F YG SL +GVGIP+ + E + V Sbjct: 233 LPNRTPVGPAATLALIGDAKQMLPDWVRGCYFQNYGASLMLGVGIPLAVTTEAVVAACAV 292 Query: 308 DDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLSLEVAN 367 D I PV D+ P + V+Y LKSG + + G+++ T P+ S S +VA Sbjct: 293 TDDQIVAPVVDF--SIPRRVRPTFGLVSYAKLKSGSIMLEGQRIRTAPLASLYRSQQVAE 350 Query: 368 TLKSWIEKGEFLLTEPVELLPS 389 LK WIE GEFLLTEPV LPS Sbjct: 351 LLKQWIEAGEFLLTEPVASLPS 372 Lambda K H 0.318 0.137 0.409 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: 420 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: 390 Length of database: 390 Length adjustment: 31 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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