Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate N515DRAFT_2515 N515DRAFT_2515 iron complex transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Dyella79:N515DRAFT_2515 Length = 352 Score = 171 bits (432), Expect = 3e-47 Identities = 114/312 (36%), Positives = 167/312 (53%), Gaps = 16/312 (5%) Query: 31 AIPVSGADATRALL---PGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHN 87 A+P+S A ALL G +A+V LRLPR L+A L+GA+LA +G +Q L N Sbjct: 38 AMPLSAAQVLGALLRWLDGAPAQGQDAVVLTLRLPRVLMASLVGAALACSGATMQGLFRN 97 Query: 88 PMASPSLLGINSGAALAM--------ALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTA 139 P+ P L+G+++GAAL A T+ L P + + ++ A GG ++ LLV Sbjct: 98 PLVEPGLVGVSAGAALGAIGMIVLGGAATATLPPL-LGSFGIAAAAFAGGLLATLLVYLF 156 Query: 140 GGGFRHTHDRNKLILAGIALSAFCM-GLTRITLLLAEDHAYGIFYWLAGGVSHARWQDVW 198 G RH L+LAG+A++A M G+ +T + E + +W G W + Sbjct: 157 GS--RHPGVAT-LLLAGVAINAIAMAGVGVLTYVANEQQLRDLTFWTLGSFGGTSWARLG 213 Query: 199 QLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAG 258 + P+++ + + A LN L L + A LG RLR + LV L GA V++ G Sbjct: 214 AVAPLMLLPLLWLPAHAGALNALLLGEREASLLGFEPRRLRRRLVALVALATGAAVAMCG 273 Query: 259 PVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLAL 318 + F+GLLVPH+ R G D R +LP S L GA+LM+ AD +AR P +LP G + AL Sbjct: 274 VIGFVGLLVPHVLRLAWGPDHRLLLPGSALAGASLMIGADAVARVAVAPAELPVGVITAL 333 Query: 319 IGSPCFVWLVRR 330 +G P F+WL+ R Sbjct: 334 LGGPFFLWLLSR 345 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: 374 Number of extensions: 17 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: 332 Length of database: 352 Length adjustment: 29 Effective length of query: 303 Effective length of database: 323 Effective search space: 97869 Effective search space used: 97869 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