Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 202769 SO3674 hemin ABC transporter, permease protein (NCBI ptt file)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__MR1:202769 Length = 338 Score = 195 bits (495), Expect = 1e-54 Identities = 120/287 (41%), Positives = 173/287 (60%), Gaps = 11/287 (3%) Query: 39 AGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVG 98 A HE V+ RLPR LLAL VGA LA G ++QG+ RNPLA P I+GV+ A+L + Sbjct: 52 APHEQL-VVSNVRLPRTLLALTVGAILAQCGAVMQGLFRNPLADPGIIGVSSGAALGAAI 110 Query: 99 ALLLMPSLPVMVLPLLAFAGGMAGLILLKMLAKTH---QPMKLALTGVALSA-CWASLTD 154 ++L P + +++ L AF G+A +++ LA + L L+GVA++A A + Sbjct: 111 CIVLFPDVGSLMISLGAFLCGLATTLIVYRLASNGLGTSVVLLLLSGVAIAALAGAGIGV 170 Query: 155 YLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRD---LDLLALGD 211 L+ + + LW GS+ G W +V + + +++L LS F RD L+ L LG+ Sbjct: 171 LTYLANDMALRDLTLWQMGSIAGAQWQYVGLCLLVLVL---LSWRFQRDAMALNALLLGE 227 Query: 212 ARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPV 271 A A LG++V + +LL VAA G I FIGLVVPH++R I G H+RLLP+ Sbjct: 228 AEARHLGINVDRLKLRLILLCALGVGVSVAATGIIGFIGLVVPHLVRMILGPDHKRLLPM 287 Query: 272 SALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 SAL GA LL +AD+ AR PP ELPV ++TA+IGAP+F++LL++ R Sbjct: 288 SALLGAALLALADIGARTFLPPAELPVSLVTALIGAPFFIFLLLQQR 334 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: 287 Number of extensions: 12 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: 318 Length of database: 338 Length adjustment: 28 Effective length of query: 290 Effective length of database: 310 Effective search space: 89900 Effective search space used: 89900 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: 49 (23.5 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