Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_013402813.1 CALHY_RS04480 iron ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >NCBI__GCF_000166355.1:WP_013402813.1 Length = 336 Score = 199 bits (505), Expect = 1e-55 Identities = 114/325 (35%), Positives = 196/325 (60%), Gaps = 16/325 (4%) Query: 5 LVIFITLALAGCALLSLHMGVIPVP----WRALLT-----DWQAGHEHYYVLMEYRLPRL 55 ++I + L L ++S+ +G + +P +ALL+ A ++ + RLPR+ Sbjct: 4 VLIILALLLLTVFIISIGVGSVFIPPLRVLKALLSLIGISFGPANDMDLTIVGQIRLPRI 63 Query: 56 LLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLL-MPSLPVMVLPLL 114 ++A+ VG +L++AG L+QG+ RNP+A P I+G + ASL ++ + + ++ + LPLL Sbjct: 64 IIAMIVGMSLSIAGALVQGLYRNPMADPGIIGTSSGASLGAIVCIAFSLNTINIFYLPLL 123 Query: 115 AFAGGMAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLMLSRPQ-DVNNALLW 170 AFAG + L+ L+ + L L G+A+S +S+ ++ + Q V+ + W Sbjct: 124 AFAGALLISFLVYRLSTKNNKTPITNLILIGIAVSTFVSSINSLILSNINQYQVSEYIFW 183 Query: 171 LTGSLWGRDWSFVKIA-IPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWAL 229 + GSL GR W VKI+ +PL IL L SL F + +++L LG+ + T+GV+ + L Sbjct: 184 MLGSLDGRSWVHVKISFVPLCILIL-CSLLFAKRINILILGEEESFTIGVNPEKLKKTLL 242 Query: 230 LLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARI 289 L +T V+ GPISF+GL+VPHM+R I G +RRL+P S L+G + L++ D +AR+ Sbjct: 243 FLVSLITGIAVSVSGPISFVGLIVPHMLRLIVGSDYRRLIPASILSGGIFLIMCDTIARV 302 Query: 290 IHPPLELPVGVLTAIIGAPWFVWLL 314 + P+E+ VG++T+++G P+F++LL Sbjct: 303 LFSPVEVKVGIITSLVGVPYFLYLL 327 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: 244 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: 336 Length adjustment: 28 Effective length of query: 290 Effective length of database: 308 Effective search space: 89320 Effective search space used: 89320 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: 48 (23.1 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