Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_009545024.1 CCE_RS10775 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000017845.1:WP_009545024.1 Length = 404 Score = 343 bits (879), Expect = 7e-99 Identities = 182/388 (46%), Positives = 239/388 (61%), Gaps = 10/388 (2%) Query: 8 KTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFNIG 67 +T+AEINE+I KAVV EE+ + V+ +G ++A + +DV+ TGTF PM SSG +FN+G Sbjct: 2 RTLAEINEKIIDKKAVVWTVEELKKRVQDIGVDQAFKTVDVICTGTFEPMESSGAIFNLG 61 Query: 68 QQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTE-------DDPLNKVYPGRFKYGG 120 DPP +K + W++ VPAYAG AVD YLGAT + +D N+ + GG Sbjct: 62 HTDPP-IKIRQCWLDGVPAYAGFGAVDLYLGATAMVDYKAIGEMNDSENRPGNVNIERGG 120 Query: 121 GHVIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNL 180 GHVIEDL+ GK + L+A TDCYPR S + IT + +L NPRN YQN+ VN Sbjct: 121 GHVIEDLIAGKPISLKAIGQVTDCYPRASFETNITRKTINQFYLYNPRNLYQNFIVGVNS 180 Query: 181 TSRIIYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQ 240 + R +YTY+GPL+P L N ++ G I+PLFNDP IG+G+RIFLGGG GYV GTQ Sbjct: 181 SDRFLYTYLGPLQPTLGNAVYSNPGAIAPLFNDPDLELIGIGSRIFLGGGVGYVAWEGTQ 240 Query: 241 HVAAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEE 300 H KR P+ PA TL L GD K M+ +++RG F YG SL +GVGIP P+L+ + Sbjct: 241 HFPLQKRLSNRTPIGPAATLALIGDAKTMSPKWVRGCYFNHYGPSLMLGVGIPFPVLDRK 300 Query: 301 IAWFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYP 360 + V D D+ PV D+ P + V+Y LK+G + I GK V P+ S Sbjct: 301 VIEHCAVADKDVVAPVIDF--SIPRRVRPTFGLVSYAQLKTGRMTIEGKSVRVAPLASIA 358 Query: 361 LSLEVANTLKSWIEKGEFLLTEPVELLP 388 LS +VA LKSWIEKGEF LT+PV LP Sbjct: 359 LSRKVAEELKSWIEKGEFTLTDPVAPLP 386 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: 466 Number of extensions: 25 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: 404 Length adjustment: 31 Effective length of query: 359 Effective length of database: 373 Effective search space: 133907 Effective search space used: 133907 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 10 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