Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Pf1N1B4_1339 ABC transporter (iron.B12.siderophore.hemin) , ATP-binding component
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1339 Length = 323 Score = 152 bits (385), Expect = 6e-42 Identities = 87/233 (37%), Positives = 131/233 (56%), Gaps = 3/233 (1%) Query: 18 LNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQLARR 77 L D SL + G+ LIGPNG GK++LL C R P+ G V L + SSR A+R Sbjct: 86 LRDASLHVAAGEFVGLIGPNGSGKTSLLRCAYRFSKPERGEVKLDHYNVWKQSSRWCAQR 145 Query: 78 LSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVRRLT 137 ++++ Q G++V E+V GR P L+ + ED A+ + Sbjct: 146 IAVVLQEFPDAFGLSVDEVVVMGRTPHKGLFDGDTLEDRKLAAHALESVGLKGFEDHAFA 205 Query: 138 ELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGKTVVAVLHD 197 LSGG++QR LA LAQ +++LDEPT +LD +Q++L++L+ L+ +A +HD Sbjct: 206 TLSGGEKQRVILARALAQQPQLLILDEPTNHLDPRYQLELLQLVKRLQI---GTLASIHD 262 Query: 198 LNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPEPVSGRP 250 LN A+ +CD+L V+ +G ++A G P+EV+T LL VF V+A I P+ G P Sbjct: 263 LNLAAAFCDRLYVINHGRIVASGPPKEVLTAQLLHNVFGVDALIDDHPLHGYP 315 Lambda K H 0.320 0.134 0.393 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: 186 Number of extensions: 4 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: 255 Length of database: 323 Length adjustment: 26 Effective length of query: 229 Effective length of database: 297 Effective search space: 68013 Effective search space used: 68013 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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