Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate WP_009544984.1 CCE_RS10970 bidirectional hydrogenase complex protein HoxU
Query= uniprot:Q39TW6 (218 letters) >NCBI__GCF_000017845.1:WP_009544984.1 Length = 238 Score = 103 bits (256), Expect = 4e-27 Identities = 69/207 (33%), Positives = 97/207 (46%), Gaps = 36/207 (17%) Query: 6 LQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWPKLVAG 65 L I+ + + A+E TIL+AAK GI IPTLCH + + G CR+C VE+E G KL Sbjct: 6 LIINNQLLTASEDQTILEAAKDAGIDIPTLCHLDGVSDVGACRLCLVEIE--GSSKLQPA 63 Query: 66 CIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAH---------APDSEELKALAQEYGADRD 116 C+ V++G+V++T EK+ R++ +E + A + +L+ +A G D Sbjct: 64 CVTQVQEGMVIQTETEKLQTYRRMAVELLFAEGNHVCAVCVVNGNCQLQDVAVRVGMDHS 123 Query: 117 RFE----------KHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNREISFI-- 158 RF HP F CI C CVR C EI+ + RG SFI Sbjct: 124 RFPYQFPQRKVDLSHPQFGMDHNRCILCTRCVRVCDEIEGAHVWDVASRGGQ---SFIVS 180 Query: 159 ----PEIAAKECWDCKECFPLCPTSAL 181 P C C +C CPT A+ Sbjct: 181 GINQPWGDVNACTSCGKCVDACPTGAI 207 Lambda K H 0.320 0.137 0.432 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: 161 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 218 Length of database: 238 Length adjustment: 23 Effective length of query: 195 Effective length of database: 215 Effective search space: 41925 Effective search space used: 41925 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 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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