Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate SM_b20058 SM_b20058 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Smeli:SM_b20058 Length = 266 Score = 192 bits (487), Expect = 8e-54 Identities = 106/244 (43%), Positives = 149/244 (61%), Gaps = 3/244 (1%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60 MTL ++ S G ++L DVSL++ TG+ +IGPNG GK++L++ S + P+ G V Sbjct: 1 MTLSASGVSWSAGGVEILKDVSLTVETGEFLGIIGPNGSGKTSLMSLISGIRKPKRGEVL 60 Query: 61 LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120 L PI L R +A+RL+L+ Q T E IT ++ V GR P+L S ED+A V Sbjct: 61 LDGCPIGTLGRRTVAQRLALVEQQAETGERITARQAVELGRTPYLGPLSPWSPEDDAIVG 120 Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180 A+ + HLA R LSGG+RQR +A LAQ + ++LLDEPT +LDI HQ+ L+ L Sbjct: 121 AALANVDMAHLADRLWHTLSGGERQRLHIARALAQQSKILLLDEPTNHLDIGHQISLLDL 180 Query: 181 MGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAE 240 +R Q TVVA LHDLN A+ +CD++ VM G ++A G P EV+T +R VF +E E Sbjct: 181 ---VRRQDLTVVAALHDLNHAAMFCDRIAVMQAGRLVALGRPREVLTVERIRAVFGIEVE 237 Query: 241 IHPE 244 + E Sbjct: 238 VEHE 241 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: 168 Number of extensions: 6 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: 266 Length adjustment: 24 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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