Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate 349652 BT0124 NADH:ubiquinone oxidoreductase subunit (NCBI ptt file)
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__Btheta:349652 Length = 588 Score = 92.4 bits (228), Expect = 2e-23 Identities = 68/212 (32%), Positives = 97/212 (45%), Gaps = 36/212 (16%) Query: 3 EINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHE------KLEPYGGCRICTVEVEV 56 +I LQIDG + EG TIL+AA +GI+IPTLCH + K P CRIC VEV Sbjct: 5 QITLQIDGHFITVPEGSTILEAACKIGINIPTLCHIDLKGTCIKNNP-ASCRICV--VEV 61 Query: 57 RGWPKLVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAPD---------SEELKAL 107 G L C +G+VV+T ++ RKV+ E +L+ P+ + EL+ L Sbjct: 62 AGRRNLAPACATRCTEGMVVKTSTLRVMNARKVVAELILSDHPNDCLTCPKCGNCELQTL 121 Query: 108 AQEYGADRDRFE----------------KHPSFCIHCGLCVRYCAEIKKKNAVGFVDRGS 151 A + F ++ CI C C C +++ A+G + RG Sbjct: 122 ALRFNIREMPFNGGELSPRKREVTSSIVRNMDKCIFCRRCESVCNDVQTVGALGAIRRGF 181 Query: 152 NREI--SFIPEIAAKECWDCKECFPLCPTSAL 181 N I +F + EC C +C +CP AL Sbjct: 182 NTTIAPAFDRMMKDSECTYCGQCVAVCPVGAL 213 Score = 24.6 bits (52), Expect = 0.004 Identities = 12/43 (27%), Positives = 22/43 (51%) Query: 104 LKALAQEYGADRDRFEKHPSFCIHCGLCVRYCAEIKKKNAVGF 146 + LA++Y DRD F+ + + + R A + K+ +GF Sbjct: 367 MPCLAKKYECDRDEFKVNGVPDVDYSISTRELARLIKRANIGF 409 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: 307 Number of extensions: 21 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 218 Length of database: 588 Length adjustment: 29 Effective length of query: 189 Effective length of database: 559 Effective search space: 105651 Effective search space used: 105651 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: 49 (23.5 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