Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Pf1N1B4_2867 Hemin ABC transporter, permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2867 Length = 345 Score = 164 bits (415), Expect = 3e-45 Identities = 109/287 (37%), Positives = 160/287 (55%), Gaps = 17/287 (5%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALL---- 101 +L + RLPR LL L VG LA++GV +QG+ RNPLA P ++GV+ A+L + A++ Sbjct: 61 ILGQIRLPRTLLGLAVGGVLALSGVAMQGLFRNPLADPGLVGVSSGAALGAAIAIVGGSV 120 Query: 102 ---LMPSLPVMVLPLLAFAGGMAGLILLKMLAKTHQPMKLA---LTGVALSACWASLTD- 154 L S +L L AF GG+ L+ L + + +A L G+AL+A S Sbjct: 121 FGGLPESFGPYLLSLCAFLGGLGVTALVYRLGRRNGQTNVATMLLAGIALTALAGSAVGL 180 Query: 155 YLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRD---LDLLALGD 211 + L+ + W GSL G +S + PL+++ ++L R L+ L LG+ Sbjct: 181 FTYLADDATLRTLTFWNLGSLNGASYSRLW---PLLLVSTGVALWLPRRAKALNALLLGE 237 Query: 212 ARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPV 271 + A LG+ V + + VAA G I F+GLVVPH++R + G HR LLP Sbjct: 238 SEAGHLGIDVEGLKRELVFCTALGVGAAVAAAGMIGFVGLVVPHLVRLLAGPDHRVLLPA 297 Query: 272 SALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 S L GA LL+ ADL+AR+ P ELP+G++TA IGAP+F++LL+R R Sbjct: 298 SVLAGASLLLFADLVARLALAPAELPIGIVTAFIGAPFFLYLLLRGR 344 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: 291 Number of extensions: 9 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: 345 Length adjustment: 28 Effective length of query: 290 Effective length of database: 317 Effective search space: 91930 Effective search space used: 91930 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