Align Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component) (characterized)
to candidate WP_007473583.1 CMTB2_RS02115 4Fe-4S dicluster domain-containing protein
Query= reanno::Miya:8499492 (147 letters) >NCBI__GCF_000170735.1:WP_007473583.1 Length = 545 Score = 53.1 bits (126), Expect = 6e-12 Identities = 20/45 (44%), Positives = 29/45 (64%) Query: 95 CGMCTAICPTSALAMDIEARVVVFDKDRCTACGLCTRVCPVGAMN 139 CG C +CPT+A+ D E++ ++F C CG C VCPVGA++ Sbjct: 207 CGNCADVCPTNAILKDDESKELIFSHIDCDGCGGCVSVCPVGALD 251 Score = 42.4 bits (98), Expect = 1e-08 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 1/57 (1%) Query: 88 DEDSCMHCGMCTAICPTSALAMDIEARVVVFDKDRCTACGLCTRVCPVGAMNVEVEN 144 D+ C C C +C A D E ++FD CT CG C CP + V +N Sbjct: 416 DDKKCTLCMSCATVCNAGAFIAD-EKGALIFDATYCTDCGYCEVACPEKCIEVIYDN 471 Score = 28.1 bits (61), Expect = 2e-04 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 13/86 (15%) Query: 35 DLTVNILKAQITPRKEGYLTLE--ISGGEDNCLKGIAYLREQDVTVTDV--SQRISRDED 90 D T N +I R+ G + ++ E+ C +L+E DV + I +D++ Sbjct: 165 DPTKNKKAIEIIKRRVGIYEYKNFVNYNENICQYKHRFLKETCGNCADVCPTNAILKDDE 224 Query: 91 S---------CMHCGMCTAICPTSAL 107 S C CG C ++CP AL Sbjct: 225 SKELIFSHIDCDGCGGCVSVCPVGAL 250 Score = 26.2 bits (56), Expect = 8e-04 Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 1/32 (3%) Query: 116 VVFDKDRCTACGLCTRVCPVGAMNVEVENGGL 147 V D +CT C C VC GA + E G L Sbjct: 413 VKIDDKKCTLCMSCATVCNAGAF-IADEKGAL 443 Score = 23.1 bits (48), Expect = 0.007 Identities = 8/30 (26%), Positives = 11/30 (36%) Query: 78 VTDVSQRISRDEDSCMHCGMCTAICPTSAL 107 + D + D C CG C CP + Sbjct: 436 IADEKGALIFDATYCTDCGYCEVACPEKCI 465 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: 231 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 5 Number of HSP's successfully gapped: 5 Length of query: 147 Length of database: 545 Length adjustment: 25 Effective length of query: 122 Effective length of database: 520 Effective search space: 63440 Effective search space used: 63440 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 Jul 25 2024. The underlying query database was built on Jul 25 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