Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_241479666.1 D471_RS0120295 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000341125.1:WP_241479666.1 Length = 341 Score = 191 bits (485), Expect = 2e-53 Identities = 130/332 (39%), Positives = 185/332 (55%), Gaps = 21/332 (6%) Query: 5 LVIFITLALAGCALLSLHMGVIPVP--------WRALLTDWQAGHEHY--YVLMEYRLPR 54 L+ +T AL AL+S +G PVP A+ D + VL + RLPR Sbjct: 6 LLTGLTAALVAVALVSAGLGAYPVPVDQVAASLLHAIGLDLGTPPDRIGQTVLWDVRLPR 65 Query: 55 LLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVM---VL 111 + LA+ VGAAL VAG ++QGI NPLA P ++GV+ A++ ++ L++ L V + Sbjct: 66 VTLAVAVGAALGVAGAMMQGIFGNPLAEPGVIGVSSGAAVGAI--LVIFSGLTVFGHWTI 123 Query: 112 PLLAFAGGMAGLILLKMLAKTH---QPMKLALTGVALSACWASLTDYLMLSRPQD--VNN 166 +F G+A + + + A++H + + L LTGVA++A A LM + QD + Sbjct: 124 IASSFVFGLATTLFVYVFARSHGRTEVVTLLLTGVAVNAV-AGAAIGLMTNFSQDAQIQT 182 Query: 167 ALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRF 226 W GS+ W+ V P ++L L + + R LDLLALG+ A LGV V R Sbjct: 183 ITFWQLGSVSTATWAKVAAITPCLLLGLAVIPLYARRLDLLALGEGPARHLGVDVERMRL 242 Query: 227 WALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLL 286 + +TS VA G ++FIGLVVPH++R +TG HR LLP SAL G LLL+ ADLL Sbjct: 243 VVIAALALLTSAAVAFAGIVAFIGLVVPHIVRMVTGPGHRILLPSSALGGGLLLMSADLL 302 Query: 287 ARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 AR P E+P+GV+TA +G P+F +LL R R Sbjct: 303 ARTAAAPAEIPLGVVTAALGGPFFFFLLHRTR 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: 278 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: 341 Length adjustment: 28 Effective length of query: 290 Effective length of database: 313 Effective search space: 90770 Effective search space used: 90770 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 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