Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate AO356_16425 AO356_16425 ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16425 Length = 338 Score = 174 bits (441), Expect = 3e-48 Identities = 111/329 (33%), Positives = 180/329 (54%), Gaps = 16/329 (4%) Query: 3 IALVIFITLALAGCAL--LSLHMGVIPVPWRALLTD-WQAGHE----HYYVLMEYRLPRL 55 +AL + +AG A+ S+ V+ ++ L W AG+ ++ YRL R Sbjct: 10 LALAALLLAVIAGVAIGETSIEPSVV---FQVLANKLWAAGYALDPIDEGIVWNYRLTRA 66 Query: 56 LLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLA 115 L+A GA LA GV++Q ++RNPLA P +LG++ AS +V LL ++ L + A Sbjct: 67 LVAAACGAGLATCGVILQSLLRNPLADPYLLGISAGASTGAVLVALLGIGAGLISLSVGA 126 Query: 116 FAGGMAGLILLKMLAKTHQPM----KLALTGVALSACWASLTDYLML--SRPQDVNNALL 169 FAG +A ++ +LA+ + ++ L G+A S + +LT +L+ + + + Sbjct: 127 FAGAVAAFAVVVLLARASRSPAGTGQIILAGIAGSQLFNALTAFLITKSASSEQARGIMF 186 Query: 170 WLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWAL 229 WL G+L G W V +++P+ ++ L + L R LD G A +LG+ V +F + Sbjct: 187 WLLGNLSGVRWPSVWLSVPVALIGLAVCLWHRRALDAFTFGADSAASLGIPVRRVQFLLI 246 Query: 230 LLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARI 289 A +T+ V+ G I F+GLV+PH +R + G RH RLLP SAL GA+ L+ AD+ +R Sbjct: 247 SCAALVTAVMVSIVGSIGFVGLVIPHAVRLLLGTRHARLLPASALGGAVFLIAADVFSRT 306 Query: 290 IHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 + +PVGV+TA++GAP F +L+ R Sbjct: 307 LIKGQVIPVGVITALVGAPVFALILIGRR 335 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: 274 Number of extensions: 13 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: 338 Length adjustment: 28 Effective length of query: 290 Effective length of database: 310 Effective search space: 89900 Effective search space used: 89900 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