Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Pf6N2E2_1633 Iron(III) dicitrate transport system permease protein FecD (TC 3.A.1.14.1)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1633 Length = 349 Score = 210 bits (534), Expect = 5e-59 Identities = 129/321 (40%), Positives = 193/321 (60%), Gaps = 7/321 (2%) Query: 3 IALVIFITLALAGCALLSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVG 62 + +V + LAL + S + V V W+ALL Q +L E RLPR+LLA+ G Sbjct: 29 LLMVAVVALALYALTVGSYSLSVAQV-WQALLAPEQVNSTMRNLLWELRLPRVLLAVLAG 87 Query: 63 AALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSL-PVMVLPLLAFAGGMA 121 AA+++AG+L+Q + RNPLA+P ++GV AS+ + ++L P+L P+ PL A AGG+A Sbjct: 88 AAMSLAGLLMQSLTRNPLAAPGLVGVESGASVTMLLIIVLWPALLPLEFYPLAALAGGLA 147 Query: 122 GLILLKMLAKTH--QPMKLALTGVALSACWASLTDYLMLSRPQD-VNNALLWLTGSLWGR 178 + +L+ P++L L GV L+A +++ D L+ D V +AL+WL GSL Sbjct: 148 VAFFVALLSWRQGISPLRLILVGVGLTAMLSAVADLLITYGNIDQVESALMWLGGSLHRA 207 Query: 179 DWSFVKIAIPLMILFLPLSLSFC-RDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTS 237 W V ++ L +L + L FC R L+LL LG+ A + G++V LL +V +T+ Sbjct: 208 SWPQVH-SLGLWLLVAGVPLLFCHRQLNLLQLGEKVALSRGLNVTWIMVSLLLCSVMLTA 266 Query: 238 TGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELP 297 VA G ++F+GLV PH+ R + G RH L+P+SAL GALL++ D L R + PPL+LP Sbjct: 267 AAVANVGTMTFVGLVAPHLARQMAGDRHGALIPLSALVGALLVLAGDTLGRGLLPPLQLP 326 Query: 298 VGVLTAIIGAPWFVWLLVRMR 318 G++ AIIGAP+ + LL R R Sbjct: 327 AGLVVAIIGAPYLIVLLARQR 347 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: 303 Number of extensions: 12 Number of successful extensions: 3 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: 349 Length adjustment: 28 Effective length of query: 290 Effective length of database: 321 Effective search space: 93090 Effective search space used: 93090 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