Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_017596976.1 D471_RS0101440 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000341125.1:WP_017596976.1 Length = 356 Score = 201 bits (510), Expect = 3e-56 Identities = 117/277 (42%), Positives = 165/277 (59%), Gaps = 13/277 (4%) Query: 45 YVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMP 104 +++ R PR+ A+FVGA LAVAG ++Q +VRNP+A P ILG++ S ASVGA+LLM Sbjct: 69 FIVWRLRAPRVFQAVFVGAGLAVAGAVVQALVRNPVADPHILGLS---SGASVGAVLLMT 125 Query: 105 SLP-----VMVLPLLAFAGGMAGLILLKMLAKTH---QPMKLALTGVALSACWASLTDYL 156 +L + LPL AFAG + +L+ +A+T +P++L L GVA+ +T +L Sbjct: 126 TLGSAALGALALPLAAFAGALVAGLLVFAVARTRGTLEPLRLILVGVAIGQLLGGVTSFL 185 Query: 157 MLSRPQD--VNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARA 214 +L + L WL GSL G WS + ++ L + L++L LG A Sbjct: 186 VLRKQSGDAQQQVLFWLLGSLSGARWSSALVCAAAVLALSALLTARAGSLNVLVLGSEGA 245 Query: 215 TTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSAL 274 +LGV +R A +T T VA G I F+GLVVP++ R + G HRR+LPV AL Sbjct: 246 ASLGVDADRSRERLFAAAALLTGTTVAVAGAIGFVGLVVPNLARLLVGADHRRVLPVCAL 305 Query: 275 TGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFV 311 +GAL+LV ADL AR + P ELP+GVLTA++G P+FV Sbjct: 306 SGALMLVWADLAARTVLRPTELPIGVLTAVVGVPFFV 342 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: 281 Number of extensions: 15 Number of successful extensions: 4 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: 356 Length adjustment: 28 Effective length of query: 290 Effective length of database: 328 Effective search space: 95120 Effective search space used: 95120 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