Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Echvi_3111 Echvi_3111 ABC-type Fe3+-siderophore transport system, permease component
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Cola:Echvi_3111 Length = 357 Score = 183 bits (465), Expect = 5e-51 Identities = 109/290 (37%), Positives = 165/290 (56%), Gaps = 14/290 (4%) Query: 42 EHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALL 101 E VL R PR++L + VG +LAVAG +QG+ RNPL P I+GV+ ++L +V ++ Sbjct: 64 EKMAVLWAIRFPRVVLGVLVGGSLAVAGACLQGLFRNPLVEPAIIGVSSGSALFAVIVIV 123 Query: 102 LMPSLP--------VMVLPLLAFAGGMAGLILLKMLA----KTHQPMKLALTGVALSACW 149 S+ LPL AF GG+ L LA KT + L L GVA++A Sbjct: 124 FSSSIGWQLQSVFGAFALPLAAFTGGLLNTFLAYRLASKAGKTDISI-LILAGVAINALS 182 Query: 150 ASLTDYLML-SRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208 A+L ++ + N W GSL G WS V I + L + LSF R L+ LA Sbjct: 183 AALIGLVIYYGDDHAIRNFTFWSLGSLGGASWSKVYIVGVFIFLSTVVMLSFPRSLNALA 242 Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRL 268 +G+A A +G++V + L + GV+ G I F+GLVVPH++R + G HR L Sbjct: 243 VGEAEAYHMGINVQRVKHLLLFFSALAVGAGVSVTGAIGFVGLVVPHLVRMLLGADHRIL 302 Query: 269 LPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 LP++ L GA+L++VAD+++R++ P EL +G++TA+IGAP+F+ +L+ + Sbjct: 303 LPMAFLFGAILMLVADVVSRLVVAPAELSIGIITALIGAPFFISILMNFK 352 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: 269 Number of extensions: 8 Number of successful extensions: 2 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: 357 Length adjustment: 28 Effective length of query: 290 Effective length of database: 329 Effective search space: 95410 Effective search space used: 95410 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