Align Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component) (characterized)
to candidate 209435 DVU0498 iron-sulfur cluster-binding protein, putative
Query= reanno::Miya:8499492 (147 letters) >MicrobesOnline__882:209435 Length = 501 Score = 43.1 bits (100), Expect = 6e-09 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 6/80 (7%) Query: 72 REQDVTVTDVSQRISRDEDSCMHCGMCTA-----ICPTSALAMDIEAR-VVVFDKDRCTA 125 R +D+ +T + + RD HC C I T + + + + D D CT Sbjct: 286 RSRDLGLTLSTDNVRRDAGFICHCCGCCCNLMRGIKVTGHTGILVTSNWLATCDADACTG 345 Query: 126 CGLCTRVCPVGAMNVEVENG 145 CGLC R CPV A++V ++G Sbjct: 346 CGLCVRACPVDALHVVRKDG 365 Score = 40.8 bits (94), Expect = 3e-08 Identities = 37/157 (23%), Positives = 56/157 (35%), Gaps = 35/157 (22%) Query: 17 FPPEISGKPIVSDLVRRYDLTVNILKAQITPRKEGYLTLEISGGEDNCLKGIAYLREQDV 76 F I ++ L R DL + + + R++ G N ++GI + Sbjct: 271 FARRIDRAEMLDILARSRDLGLTLSTDNV--RRDAGFICHCCGCCCNLMRGIKVTGHTGI 328 Query: 77 TVTDVSQRISRDEDSCMHCGMCTAICPTSALAM---------------------DIEA-- 113 VT + + D D+C CG+C CP AL + D EA Sbjct: 329 LVTS-NWLATCDADACTGCGLCVRACPVDALHVVRKDGQRTASNETVDARGDVPDDEAAS 387 Query: 114 ---------RVVVFDKDRCTACGLCTRVCPVGAMNVE 141 R + D C CG+C CP GA+ +E Sbjct: 388 STARRGKARRRLEVDTSVCLGCGVCALRCPTGALRLE 424 Lambda K H 0.321 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: 194 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 147 Length of database: 501 Length adjustment: 25 Effective length of query: 122 Effective length of database: 476 Effective search space: 58072 Effective search space used: 58072 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: 47 (22.7 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