Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate GFF3533 PS417_18095 iron-dicitrate transporter subunit FecD
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__WCS417:GFF3533 Length = 322 Score = 268 bits (684), Expect = 2e-76 Identities = 139/303 (45%), Positives = 199/303 (65%), Gaps = 3/303 (0%) Query: 18 LLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVR 77 L+SL G + + A+L A + + +RLPR L+A+ G A +AG ++QG++R Sbjct: 20 LISLSAGTVWLTPDAVLDRLLAHDALDFDVWNHRLPRSLIAILAGCAFGLAGAIVQGVIR 79 Query: 78 NPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMAGLILLKML--AKTHQP 135 NPLASP+ILGV A LA A++ P +P+ LPL+A GG G +LL + + Sbjct: 80 NPLASPEILGVTQGAGLALTVAIISWPHMPIAWLPLVACLGGAGGALLLALYNAGVSFSG 139 Query: 136 MKLALTGVALSACWASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLP 195 ++ AL+GVA++ +S+T++L+LS P D+N ALL LTGSLW R+W V + +P ++L +P Sbjct: 140 VRFALSGVAIAVTLSSVTEFLILSHPLDINTALLALTGSLWSRNWHHVALVLPFLVL-IP 198 Query: 196 LSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPH 255 + L + L+L+ALGD A +LG ++ TR+ A+ AV +TS GV GPI FIGLV PH Sbjct: 199 VGLCLAKPLNLIALGDEAAHSLGTALGRTRWLAMACAVVLTSLGVGVIGPIGFIGLVAPH 258 Query: 256 MMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLV 315 M R + GG H+ LLP + LTGALLLV+AD L R + P E+P GVLTA+IGAP+F+WLL Sbjct: 259 MARRLVGGHHQYLLPAAMLTGALLLVLADTLGRTLIAPSEIPAGVLTAVIGAPYFLWLLA 318 Query: 316 RMR 318 R + Sbjct: 319 RFK 321 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: 353 Number of extensions: 14 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: 322 Length adjustment: 28 Effective length of query: 290 Effective length of database: 294 Effective search space: 85260 Effective search space used: 85260 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