Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Ac3H11_3353 Iron(III) dicitrate transport system permease protein FecD (TC 3.A.1.14.1)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3353 Length = 364 Score = 147 bits (372), Expect = 3e-40 Identities = 113/335 (33%), Positives = 173/335 (51%), Gaps = 26/335 (7%) Query: 13 LPVAALIIIFWLSLFCYSAIPVSG---ADATRALL-PGHTPTLPEALVQNLRLPRSLVAV 68 L +AAL+ + S+ A+ S AD R L PG P + ++ +RLP +++AV Sbjct: 36 LLLAALLAVLCASVVADIALGPSTFAFADVLRGLFTPGALPQAQQVILWEVRLPYAVMAV 95 Query: 69 LIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIA-GYSLS----- 122 L+GASL LAG +QT +NP+ASP LG+++ AA+ + T +A G +L+ Sbjct: 96 LVGASLGLAGAEMQTALNNPLASPFTLGVSAAAAVGASAAVVSGFTLLAWGENLAVPLCA 155 Query: 123 FI-AACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYG- 180 F+ AAC + LL G + ++L GIAL L + +A+ +A Sbjct: 156 FVGAACATALIQLLAWRQGATV------DTVVLFGIALLLSFEALLWLLQFIADSNALQQ 209 Query: 181 IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQ----LNLLNLSDSTAHTLGVNLT 236 I +W G +S A W + +V T + + LL + + L L + A + G+ + Sbjct: 210 IVFWTMGSLSRATWTKIG----IVGTVLSLCLLWSARQAWALTALRAGEDQARSFGIAVE 265 Query: 237 RLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLL 296 RLRLV + V LL +S G + F+GL+ PH+AR G D R LP S L GA ++ L Sbjct: 266 RLRLVTLLRVSLLAATALSFVGTIGFVGLVGPHIARMLLGEDHRYYLPGSALAGALMLSL 325 Query: 297 ADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 A +L++AL LP G + AL+G P F+ LV R+ Sbjct: 326 ASILSKALVPGVVLPIGIITALVGVPLFMTLVLRQ 360 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: 311 Number of extensions: 15 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: 332 Length of database: 364 Length adjustment: 29 Effective length of query: 303 Effective length of database: 335 Effective search space: 101505 Effective search space used: 101505 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