Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BWI76_RS11370 BWI76_RS11370 iron-dicitrate transporter subunit FecD
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Koxy:BWI76_RS11370 Length = 317 Score = 428 bits (1100), Expect = e-124 Identities = 210/313 (67%), Positives = 254/313 (81%) Query: 6 VIFITLALAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAAL 65 ++F+ LAL L SL MG IP+PW+ LL+ W A E++YVLM+YRLPR++LAL +GAAL Sbjct: 5 IVFLLLALTLLTLFSLRMGAIPLPWQVLLSGWHADSEYHYVLMQYRLPRVVLALIIGAAL 64 Query: 66 AVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMAGLIL 125 AV+G L+QG+V NPLASPDILG+NH ASLASV AL +PSLP+ LPLLAF GGM+ + + Sbjct: 65 AVSGALVQGVVHNPLASPDILGINHGASLASVAALWFLPSLPLPWLPLLAFIGGMSAMTI 124 Query: 126 LKMLAKTHQPMKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKI 185 LA PM+LALTG+ALSACWAS+TDYL+LSRPQ++NNALLWLTGSLW RD SFV I Sbjct: 125 AIALAGFSHPMRLALTGIALSACWASVTDYLLLSRPQEINNALLWLTGSLWARDGSFVVI 184 Query: 186 AIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGP 245 A+PL+ + LPLS + RDLDLLALG RA TLGV+V +AL LAVA+ S GVA CGP Sbjct: 185 ALPLLAILLPLSFALSRDLDLLALGRDRAGTLGVNVRRLNGYALTLAVALASIGVAVCGP 244 Query: 246 ISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAII 305 I+FI LVVPH++R + GGRHR LLP+SALTG L+L++ADLLAR +HPPLELP GVLTAII Sbjct: 245 IAFISLVVPHLVRRLFGGRHRYLLPLSALTGGLVLLLADLLARTLHPPLELPAGVLTAII 304 Query: 306 GAPWFVWLLVRMR 318 GAPWF+WLLVRMR Sbjct: 305 GAPWFIWLLVRMR 317 Lambda K H 0.330 0.142 0.447 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: 405 Number of extensions: 12 Number of successful extensions: 2 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: 318 Length of database: 317 Length adjustment: 27 Effective length of query: 291 Effective length of database: 290 Effective search space: 84390 Effective search space used: 84390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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