Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate Synpcc7942_2557 Synpcc7942_2557 bidirectional hydrogenase complex protein HoxU
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__SynE:Synpcc7942_2557 Length = 238 Score = 107 bits (266), Expect = 2e-28 Identities = 72/209 (34%), Positives = 99/209 (47%), Gaps = 30/209 (14%) Query: 1 MSEINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWP 60 MS + LQID +E+ A G T+L A+ I IPTLCH + + G CR+C VEV G P Sbjct: 1 MSVVTLQIDDQELAANVGQTVLQVAREASIPIPTLCHLQGVSDVGACRLCV--VEVAGSP 58 Query: 61 KLVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAH---------APDSEELKALAQEY 111 KL C+ V +GLVV+TR+ ++++ R+ ++E A A + EL+ A Sbjct: 59 KLQPACLLTVSEGLVVQTRSPRLERYRRQIVELFFAEGNHVCAICVANGNCELQDAAIAV 118 Query: 112 GADRDRFE----------KHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNREI 155 G D R+ H F CI C CVR C EI+ + RG + I Sbjct: 119 GMDHSRYPYRFPKRDVDLSHRFFGLDHNRCILCTRCVRVCDEIEGAHVWDVAMRGEHCRI 178 Query: 156 ---SFIPEIAAKECWDCKECFPLCPTSAL 181 P A C +C +C CPT AL Sbjct: 179 VAGMDQPWGAVDACTNCGKCIDACPTGAL 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: 169 Number of extensions: 19 Number of successful extensions: 3 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: 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 Sep 17 2021. 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