Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate BWI76_RS07720 BWI76_RS07720 iron-enterobactin transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Koxy:BWI76_RS07720 Length = 264 Score = 231 bits (588), Expect = 1e-65 Identities = 118/250 (47%), Positives = 168/250 (67%), Gaps = 1/250 (0%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 LR + LT++YG + +++++P G TA+IGPNGCGKSTLL SRL+ P SG V+L Sbjct: 8 LRGDQLTLAYGKKTIAESLNVTIPDGHFTAIIGPNGCGKSTLLRTLSRLMTPASGHVYLD 67 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 I +S+++A+R+ LL Q+ TP ITVQELV+ GR P L+ R ED V+ A Sbjct: 68 GEQIQRYASKEVAKRIGLLAQNATTPGDITVQELVARGRYPHQPLFTRWRKEDEEAVSRA 127 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMG 182 M T I LA + + LSGGQRQRA++AMVLAQ T ++LLDEPTT+LDI+HQ+DL+ L+ Sbjct: 128 MKATGITDLARQSVDTLSGGQRQRAWIAMVLAQETAIMLLDEPTTWLDISHQIDLLELLS 187 Query: 183 ELRTQ-GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241 EL Q G T+ AVLHDLNQA RY L+ + G ++A+G P+E+++ L+ ++ + I Sbjct: 188 ELNQQKGYTLAAVLHDLNQACRYATHLIALREGKIVAEGAPKEIVSAELIEKIYGLRCTI 247 Query: 242 HPEPVSGRPM 251 +PV+ P+ Sbjct: 248 IEDPVAHTPL 257 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: 185 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: 255 Length of database: 264 Length adjustment: 24 Effective length of query: 231 Effective length of database: 240 Effective search space: 55440 Effective search space used: 55440 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