Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate SM_b20057 SM_b20057 ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Smeli:SM_b20057 Length = 347 Score = 184 bits (468), Expect = 2e-51 Identities = 112/328 (34%), Positives = 178/328 (54%), Gaps = 18/328 (5%) Query: 4 ALVIFITLALAGCALLSLHMGVIPVPWRALLTD-----WQAGHE----HYYVLMEYRLPR 54 ALVI G A+ G +P++ + W AG+ ++ YRL R Sbjct: 22 ALVILFAALWMGAAI-----GETAIPFKTVAQTVANRLWNAGYPLAPIDEGIIWSYRLSR 76 Query: 55 LLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLL 114 ++A GA+LA++G ++Q ++RNPLA P ILG++ AS +V +L ++ LPL Sbjct: 77 AVVAASCGASLALSGAVLQSLLRNPLADPYILGISAGASTGAVSVAILGVGAGMLTLPLG 136 Query: 115 AFAGGMAGLILLKMLAKT--HQPMKLALTGVALSACWASLTDYLML--SRPQDVNNALLW 170 AF G + +L+ +LA + L GVA S + +LT +++ + + + W Sbjct: 137 AFIGALVAFVLVSLLAVKAGRGTAAIILAGVAGSQLFNALTSFIVTKAATAEQARGIMFW 196 Query: 171 LTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALL 230 L G+L G W +A+P +L L + L R LD G A +LG+SV T F + Sbjct: 197 LLGNLSGVRWPDAWLAVPATLLGLVVCLWHARPLDAFTFGSESAASLGISVRRTYFALVG 256 Query: 231 LAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARII 290 ++ MT+ V+ G I F+GLV+PH R + G RH LLP +AL GA+ +++AD+L+R++ Sbjct: 257 VSAMMTAVMVSIVGSIGFVGLVIPHAARMLVGVRHGVLLPAAALIGAVFMILADILSRVL 316 Query: 291 HPPLELPVGVLTAIIGAPWFVWLLVRMR 318 P LP+GV+TA++GAP F +L + R Sbjct: 317 IPGQVLPIGVITALVGAPAFALILGQRR 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: 292 Number of extensions: 14 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: 347 Length adjustment: 28 Effective length of query: 290 Effective length of database: 319 Effective search space: 92510 Effective search space used: 92510 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