Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BPHYT_RS20235 BPHYT_RS20235 iron ABC transporter
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS20235 Length = 702 Score = 213 bits (541), Expect = 1e-59 Identities = 117/285 (41%), Positives = 168/285 (58%), Gaps = 6/285 (2%) Query: 37 WQAGHEHY----YVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAA 92 W A +H +L++ RLPRL+ AL GA LA +GVL+Q IVRNPLA P++LGV A Sbjct: 407 WLAAFDHRDELARMLLDLRLPRLICALLAGALLAASGVLMQSIVRNPLAGPEVLGVTQGA 466 Query: 93 SLASVGALLLMPSLPVMVLPLLAFAGGMAGLILLKMLAKTHQ--PMKLALTGVALSACWA 150 LA++ AL++ P L + AGG L L +L + H+ P+ +ALTG+ + W Sbjct: 467 GLATLAALVMWPLANHSTLAAASLAGGGITLALTLLLNRRHRYAPLAVALTGIVIGTLWT 526 Query: 151 SLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALG 210 +L+ +L+ + ++WL G +GR W V +P +L LP+ R LDLLALG Sbjct: 527 TLSQWLITQQSVQPARFVVWLVGGTYGRSWGEVTTLLPWCVLALPVFALLARPLDLLALG 586 Query: 211 DARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLP 270 D +A +LG+ + R L +A VAA GP+ FIGL+ PH+ + HR L Sbjct: 587 DDQAASLGLPIGVLRPLVLTVATLAACAAVAAVGPVGFIGLMAPHLASMLGARAHRTRLW 646 Query: 271 VSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLV 315 ++A GAL+LVVAD+ AR + P E+P GVLTA+IGAP+ + LL+ Sbjct: 647 LAAACGALVLVVADIAARTLLAPREIPAGVLTALIGAPYLLALLI 691 Score = 157 bits (396), Expect = 9e-43 Identities = 99/283 (34%), Positives = 145/283 (51%), Gaps = 4/283 (1%) Query: 30 WRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVN 89 W A T A +L + +PR+L AL G LAVAG L Q + RNPLASPD+LG+ Sbjct: 54 WLAAPTGSDAAQLAGILLFDLSVPRILAALVAGGCLAVAGTLFQSLTRNPLASPDLLGIT 113 Query: 90 HAASLASVGALLLMPSLPVMVLPLLAFAG-GMAGLILLKMLAKTHQPMKLALTGVALSAC 148 A L + A+L+ V +PLL G G A + P++L L G Sbjct: 114 GGAQLGLLAAMLVPSLAGVASVPLLFACGLGAAACVAAAAGGWRATPLRLVLAGSVCMLL 173 Query: 149 WASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208 +++LT ++ Q + LW +GSL+ + +KIA ++L L R LD LA Sbjct: 174 FSALTTLILAFFEQSIVGVSLWASGSLYQPGAAGLKIAASWLVLPLIALPFVIRPLDPLA 233 Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRR- 267 LGD A GV V TR A+++AV S V+ GP+S++GL+ P+++R + G + R Sbjct: 234 LGDDAAAAAGVRVDATRLAAMVVAVGFASVAVSVAGPLSYVGLIAPNLLRQMRGAKASRL 293 Query: 268 --LLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAP 308 L+P+SAL G L++V D + + L GV A +G P Sbjct: 294 AALVPLSALVGGALVLVTDSAVQALDLDATLSTGVAIAFVGTP 336 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: 605 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 318 Length of database: 702 Length adjustment: 33 Effective length of query: 285 Effective length of database: 669 Effective search space: 190665 Effective search space used: 190665 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: 51 (24.3 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