Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 3607140 Dshi_0562 transport system permease protein (RefSeq)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Dino:3607140 Length = 348 Score = 190 bits (482), Expect = 5e-53 Identities = 112/296 (37%), Positives = 169/296 (57%), Gaps = 10/296 (3%) Query: 43 LLPGH-TP---TLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGIN 98 +LPG TP T A+V +RLPR+L+A ++GA LAL G LQ++T NP+A P LLGI+ Sbjct: 55 ILPGLLTPDWTTGQAAIVWEIRLPRALLAAMVGAGLALVGASLQSVTRNPLADPHLLGIS 114 Query: 99 SGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIA 158 SGAA A+ + L G + A G ++ L++ F ++L+LAG+A Sbjct: 115 SGAAFG-AILALLHTGLFLGLLTVPLLAFAGALAATLLVLGVTSFAQATGADRLVLAGVA 173 Query: 159 LSAFCMGLTRITLLLAEDHA-YGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLAN- 216 +S M I + + + A + + +W+ GG+ A+W + L P V+ + LAN Sbjct: 174 VSFIVMSCANILIFIGDPRATHTVVFWMLGGLGLAQWDQL--LFPAVILVGCGLWFLANA 231 Query: 217 -QLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWA 275 +LN + + D TA TLG+ + R RL + ++ LL G V+ +G + F+GL++PH+ R Sbjct: 232 SRLNAMTIGDETASTLGIPIARFRLSVFVVGALLTGCMVAFSGIIGFVGLMIPHIVRMLV 291 Query: 276 GFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 G D VLP S L+GA ++ AD+ AR + P D+P G V LIG FVWL+RRR Sbjct: 292 GGDYARVLPASALVGAIFLVWADIAARTVMAPEDIPIGIVTGLIGGAFFVWLLRRR 347 Lambda K H 0.327 0.140 0.436 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: 377 Number of extensions: 24 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: 332 Length of database: 348 Length adjustment: 28 Effective length of query: 304 Effective length of database: 320 Effective search space: 97280 Effective search space used: 97280 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 (21.7 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