Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_042119995.1 RHE_RS27835 iron chelate uptake ABC transporter family permease subunit
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000092045.1:WP_042119995.1 Length = 346 Score = 181 bits (460), Expect = 2e-50 Identities = 112/328 (34%), Positives = 174/328 (53%), Gaps = 13/328 (3%) Query: 4 ALVIFITLALAGCALLSLHMGVIPVPWRALLT------DWQA---GHEHYYVLMEYRLPR 54 AL++ +A +S+ +G +P+P + W A H V+ +YRL R Sbjct: 16 ALLLASLCLIAVVVGVSVGIGDLPIPLATTFSAVTNRLGWTAVELNRIHETVIWDYRLSR 75 Query: 55 LLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLL 114 L+A F GA LA++G ++Q ++RNPLA P +LG++ AS +V ++L + L Sbjct: 76 ALVAAFCGAGLALSGAIMQSLLRNPLAEPYVLGISAGASTGAVAIVILGVGAGAVSLSAG 135 Query: 115 AFAGGMAGLILLKMLAKTHQ--PMKLALTGVALSACWASLTDYLMLS--RPQDVNNALLW 170 AFAG A + +L+ + + L GVA S + + T Y++ + Q + + W Sbjct: 136 AFAGAFAAFFFVALLSNGTRGGADRTILAGVAASQLFNASTSYIVTTSANAQQARDVMFW 195 Query: 171 LTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALL 230 L GS G W + ++ L L + R LD A GD A++LGV+V R Sbjct: 196 LLGSFSGVRWPEFALVSVVVSFGLAACLLYARVLDAFAFGDEAASSLGVNVSRARMALFA 255 Query: 231 LAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARII 290 L MT+T V+ G I F+GLVVPH+ R + G H RLLP A+ GA+ +V+AD+ AR + Sbjct: 256 LTAMMTATIVSMVGSIGFVGLVVPHVARFVVGPLHIRLLPACAIAGAIFMVLADIAARAL 315 Query: 291 HPPLELPVGVLTAIIGAPWFVWLLVRMR 318 P LP+GV+TA++G P+F +L R + Sbjct: 316 IPNQILPIGVVTALVGVPFFSIILYRFQ 343 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: 250 Number of extensions: 8 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: 346 Length adjustment: 28 Effective length of query: 290 Effective length of database: 318 Effective search space: 92220 Effective search space used: 92220 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 Apr 09 2024. 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