Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_013404169.1 CALHY_RS11790 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000166355.1:WP_013404169.1 Length = 358 Score = 143 bits (361), Expect = 5e-39 Identities = 101/288 (35%), Positives = 154/288 (53%), Gaps = 18/288 (6%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASL-ASVGALLL-- 102 ++ + RL R++ A+ G LA+ G IQ + NPLASP LG++ A+ A++G ++L Sbjct: 68 IVFDIRLVRVVAAILAGIGLAIGGAAIQSLFHNPLASPFTLGISQGAAFGAAIGIIVLGG 127 Query: 103 -----MPSLPVMVLP-----LLAFAGGMAGLILLKMLA--KTHQPMKLALTGVALSACWA 150 S V +L AF G M ++ LA K P + L+GVALS+ ++ Sbjct: 128 GVASSAASDSVTILHPSRVVACAFLGSMLSTAVVLALAQIKRFSPEAVVLSGVALSSLFS 187 Query: 151 SLTDYLMLSRPQDVNNALL--WLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208 + T + DV A L W G + W VKI +IL L+ + + +A Sbjct: 188 AATTIIQYFA-SDVKIAALVFWTFGDIGRATWDDVKIMAVFVILAWLYFLANSWNYNAIA 246 Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRL 268 G+ A +LGV+V RF+ +L++ +TS V+ G I FI LV PH+ R G R L Sbjct: 247 SGEDVAKSLGVNVEKARFFGILVSSFITSVIVSFLGIIGFICLVAPHIARRFIGNDQRFL 306 Query: 269 LPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 S L GA LL+++D +AR+I P+ LPVG +T+ +GAP F++LL+R Sbjct: 307 TLASGLVGAFLLLLSDTVARLIVSPVVLPVGAVTSFLGAPLFMYLLIR 354 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: 212 Number of extensions: 5 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: 358 Length adjustment: 28 Effective length of query: 290 Effective length of database: 330 Effective search space: 95700 Effective search space used: 95700 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 24 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