Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Ac3H11_3353 Iron(III) dicitrate transport system permease protein FecD (TC 3.A.1.14.1)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3353 Length = 364 Score = 149 bits (375), Expect = 1e-40 Identities = 99/295 (33%), Positives = 153/295 (51%), Gaps = 7/295 (2%) Query: 31 RALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNH 90 R L T +L E RLP ++A+ VGA+L +AG +Q + NPLASP LGV+ Sbjct: 67 RGLFTPGALPQAQQVILWEVRLPYAVMAVLVGASLGLAGAEMQTALNNPLASPFTLGVSA 126 Query: 91 AA----SLASVGALLLMPSLPVMVLPLLAFAGGMAGLILLKMLAKTHQPM--KLALTGVA 144 AA S A V L+ + +PL AF G L+++LA + L G+A Sbjct: 127 AAAVGASAAVVSGFTLLAWGENLAVPLCAFVGAACATALIQLLAWRQGATVDTVVLFGIA 186 Query: 145 LSACWASLTDYLM-LSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRD 203 L + +L L ++ + + W GSL W+ + I ++ L L S Sbjct: 187 LLLSFEALLWLLQFIADSNALQQIVFWTMGSLSRATWTKIGIVGTVLSLCLLWSARQAWA 246 Query: 204 LDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGG 263 L L G+ +A + G++V R LL + +T ++ G I F+GLV PH+ R + G Sbjct: 247 LTALRAGEDQARSFGIAVERLRLVTLLRVSLLAATALSFVGTIGFVGLVGPHIARMLLGE 306 Query: 264 RHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 HR LP SAL GAL+L +A +L++ + P + LP+G++TA++G P F+ L++R R Sbjct: 307 DHRYYLPGSALAGALMLSLASILSKALVPGVVLPIGIITALVGVPLFMTLVLRQR 361 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: 300 Number of extensions: 14 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: 364 Length adjustment: 28 Effective length of query: 290 Effective length of database: 336 Effective search space: 97440 Effective search space used: 97440 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