Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate N515DRAFT_2515 N515DRAFT_2515 iron complex transport system permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Dyella79:N515DRAFT_2515 Length = 352 Score = 188 bits (478), Expect = 1e-52 Identities = 117/322 (36%), Positives = 174/322 (54%), Gaps = 16/322 (4%) Query: 13 LAGCALLSLHMGVIPVPWRALL------TDWQAGHEHYYVLMEYRLPRLLLALFVGAALA 66 LA A+ + +G +P+ +L D V++ RLPR+L+A VGAALA Sbjct: 26 LAAAAIGGMAVGAMPLSAAQVLGALLRWLDGAPAQGQDAVVLTLRLPRVLMASLVGAALA 85 Query: 67 VAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLL--------AFAG 118 +G +QG+ RNPL P ++GV+ A+L ++G ++L + + PLL AFAG Sbjct: 86 CSGATMQGLFRNPLVEPGLVGVSAGAALGAIGMIVLGGAATATLPPLLGSFGIAAAAFAG 145 Query: 119 GMAGLILLKMLAKTHQPMK-LALTGVALSA-CWASLTDYLMLSRPQDVNNALLWLTGSLW 176 G+ +L+ + H + L L GVA++A A + ++ Q + + W GS Sbjct: 146 GLLATLLVYLFGSRHPGVATLLLAGVAINAIAMAGVGVLTYVANEQQLRDLTFWTLGSFG 205 Query: 177 GRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMT 236 G W+ + PLM+L L + L+ L LG+ A+ LG R + L T Sbjct: 206 GTSWARLGAVAPLMLLPLLWLPAHAGALNALLLGEREASLLGFEPRRLRRRLVALVALAT 265 Query: 237 STGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLEL 296 VA CG I F+GL+VPH++R G HR LLP SAL GA L++ AD +AR+ P EL Sbjct: 266 GAAVAMCGVIGFVGLLVPHVLRLAWGPDHRLLLPGSALAGASLMIGADAVARVAVAPAEL 325 Query: 297 PVGVLTAIIGAPWFVWLLVRMR 318 PVGV+TA++G P+F+WLL R+R Sbjct: 326 PVGVITALLGGPFFLWLLSRLR 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: 323 Number of extensions: 16 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: 352 Length adjustment: 28 Effective length of query: 290 Effective length of database: 324 Effective search space: 93960 Effective search space used: 93960 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