Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BPHYT_RS04855 BPHYT_RS04855 iron ABC transporter
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS04855 Length = 350 Score = 167 bits (424), Expect = 3e-46 Identities = 116/333 (34%), Positives = 173/333 (51%), Gaps = 29/333 (8%) Query: 9 ITLALAGCALL----SLHMGVIPVPWRALLTDWQAGHEHYY--------VLMEYRLPRLL 56 I LALAG AL SL +G + + +L H ++ RLPR + Sbjct: 23 IWLALAGIALAVLMASLALGSVTLAPMRVLAALMPSHAPASGSSDLAAEIVRTLRLPRAV 82 Query: 57 LALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAF 116 GA LA+AG L+Q ++RNPLA P +LGV+ A AS + ++ ++ AF Sbjct: 83 AGFACGALLALAGALLQVLLRNPLAEPYVLGVSGGA--ASFALIAMIAGCAWWIVDASAF 140 Query: 117 AGGMAGLILLKMLAKTH----QPM----KLALTGVALSACWASLTDYLMLSRPQD-VNNA 167 AG ++L+ LA+ +P +L LTG ++A W +L L+ P + + Sbjct: 141 AGAFVSILLVLGLARRELWRGEPQDTSPRLLLTGAVIAAGWGALITLLLNLAPDNRLRGM 200 Query: 168 LLWLTGSLWG--RDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTR 225 L WLTG L G W+ + + +++ +P + L++L GDA A LGV+V R Sbjct: 201 LFWLTGDLNGGAMPWTALAALVIVLVAIVPAAPR----LNVLLRGDAAAQALGVAVMPLR 256 Query: 226 FWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADL 285 L+A + V G I F+GLVVPHM+R G R LLP +AL G + ++ ADL Sbjct: 257 LRVYLVASLAAAAAVTTAGTIGFVGLVVPHMLRLAFGNDQRMLLPAAALGGGVAVMGADL 316 Query: 286 LARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 +AR + P +LPVGV+T+IIG P F+W+L+ R Sbjct: 317 IARTVIAPAQLPVGVITSIIGVPVFLWMLLHRR 349 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: 310 Number of extensions: 18 Number of successful extensions: 5 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: 318 Length of database: 350 Length adjustment: 28 Effective length of query: 290 Effective length of database: 322 Effective search space: 93380 Effective search space used: 93380 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