Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 351627 BT2099 Fe3+ ABC transporter, permease (NCBI ptt file)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Btheta:351627 Length = 312 Score = 137 bits (346), Expect = 3e-37 Identities = 98/302 (32%), Positives = 159/302 (52%), Gaps = 18/302 (5%) Query: 26 IPVP--WRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASP 83 IP+P W A+LT + +L+ R R+++A +G AL+V+G+ +Q + +NPLA P Sbjct: 8 IPIPKVW-AVLTGGECDEMTRNILLSIRFIRVVVAGLIGIALSVSGLQMQTVFQNPLADP 66 Query: 84 DILGVNHAASLASVGALLLMPSLPVMVLPLLAFAG----GMAG--LILLKMLA---KTHQ 134 +LGV+ A L +L P L PLL AG G G +ILL + K Sbjct: 67 YLLGVSSGAGLGVALFILGAPLLGWADFPLLQSAGIVGSGWIGTAVILLGVAIISRKVKN 126 Query: 135 PMKLALTGVALSACWASLTDYLM-LSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILF 193 + + + GV + ++ L LS + + LW GSL + I IP++ + Sbjct: 127 ILGVLIMGVMIGYVAGAIIQILQYLSSAEQLKMFTLWSMGSLSHITAGQLSIMIPVVCIG 186 Query: 194 LPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVV 253 L LS++ + L+LL LG+ A T+G+S+ +R + +T T A CGP+ FIGL V Sbjct: 187 LLLSVACIKSLNLLLLGENYARTMGMSIKRSRTLVFISTALLTGTVTAFCGPVGFIGLAV 246 Query: 254 PHMMRSI-TGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVW 312 PH+ R + HR L+P + LTG + +++ D++A+ LPV +TA++G P +W Sbjct: 247 PHITRLLFDNADHRILMPGTMLTGLIAMLICDIIAK----KFLLPVNCITALLGVPVILW 302 Query: 313 LL 314 ++ Sbjct: 303 VI 304 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: 273 Number of extensions: 13 Number of successful extensions: 4 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: 312 Length adjustment: 27 Effective length of query: 291 Effective length of database: 285 Effective search space: 82935 Effective search space used: 82935 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 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