Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 3607150 Dshi_0572 transport system permease protein (RefSeq)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Dino:3607150 Length = 360 Score = 212 bits (539), Expect = 1e-59 Identities = 129/332 (38%), Positives = 194/332 (58%), Gaps = 20/332 (6%) Query: 5 LVIFITLALAGCALLSLHMGVIPVPWRALLTDW------QAGHEHYYVLMEYRLPRLLLA 58 L +++ + L + SL +G RA + DW AG + +L + RLPRL L Sbjct: 26 LHLWLWIFLLAVSAFSLGIGAAGAQVRAAVADWIRTGTLDAGAQ--VILFDIRLPRLALG 83 Query: 59 LFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVM--------V 110 L VGAALAVAG ++QG+ RNPLA P I+GV+ A L ++ A++L +LP + Sbjct: 84 LLVGAALAVAGAVMQGLFRNPLADPGIVGVSAGAGLGAILAIVLGAALPAFFIDALGNYL 143 Query: 111 LPLLAFAGGMAGLILLKMLAKTHQPMKLA---LTGVALSACWASLTDYLM-LSRPQDVNN 166 +PL AFAGG ILL ++ +A L G+AL+A +L+ L+ ++ + + + Sbjct: 144 IPLAAFAGGWGSTILLYKVSTRRGRTSVATMLLAGIALAALTGALSGILVYIADDRQLRD 203 Query: 167 ALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRF 226 W GSL G W+ V IA PL+ + + R L+ +ALG+A A +GV++ + Sbjct: 204 LTFWGLGSLAGATWTKVLIAGPLIAVAFLSAPLLARGLNGMALGEAAAAHMGVALERLKT 263 Query: 227 WALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLL 286 A+L+ + T VA G I F+G+VVPH++R G HR LLP +AL GA LLV+AD + Sbjct: 264 GAILIVASATGAAVAVSGGIGFVGIVVPHLLRIAVGPDHRTLLPNAALLGASLLVLADCI 323 Query: 287 ARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 +R I P ELP+G++TA++GAP F+W+L+R R Sbjct: 324 SRTIIAPAELPIGIVTAVLGAPVFLWILLRAR 355 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: 286 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: 360 Length adjustment: 28 Effective length of query: 290 Effective length of database: 332 Effective search space: 96280 Effective search space used: 96280 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