Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate HSERO_RS21915 HSERO_RS21915 iron-siderophore ABC transporter permease
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__HerbieS:HSERO_RS21915 Length = 364 Score = 138 bits (348), Expect = 2e-37 Identities = 108/327 (33%), Positives = 161/327 (49%), Gaps = 15/327 (4%) Query: 15 VAALIIIFWLSLFCYSAIPVSGA--DATRALLPGHTPTLPEAL---VQNLRLPRSLVAVL 69 VA L++I + + P A D LL H P L V RLP +++A+L Sbjct: 39 VALLVLIIGAVVLDIATGPAGIAVQDLLATLL--HADAAPAGLRVVVWEFRLPTAVMALL 96 Query: 70 IGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALS---PTPIAGYSLSFIAA 126 +G L L G +QT+ NP+ASP LGI++ AA AL + P AG ++S A Sbjct: 97 VGMCLGLGGGEMQTVLDNPLASPYTLGISAAAAFGAALAITFNWRFPALPAGMTVS-ACA 155 Query: 127 CGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAY-GIFYWL 185 C ++ +LV+ +R +IL GIAL L + +A + A GI +W Sbjct: 156 CAAALASVLVLERVARWRGGSTLG-VILFGIALVYSFQALIMLLQFVASEEALQGIVFWT 214 Query: 186 AGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINML 245 G ++ A W V L P L A +L L L + A + G+++ RLR++ + Sbjct: 215 MGSLARASWTTVAILGLAFALVAPFSLRDAWKLTALRLGEERAASFGIDMPRLRMLSLLR 274 Query: 246 VLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALA 305 + +L VS G + F+GL+ PH+AR G D R LP S + G ++ LA V ++ L Sbjct: 275 ISVLAALSVSFVGTIGFVGLVAPHIARLLLGEDHRYYLPGSAMAGGLIISLASVASKTL- 333 Query: 306 FPGDL-PAGAVLALIGSPCFVWLVRRR 331 PG L P G V +L+G P F+ +V RR Sbjct: 334 LPGVLIPVGIVTSLVGIPLFLIIVLRR 360 Lambda K H 0.327 0.140 0.436 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: 309 Number of extensions: 12 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: 332 Length of database: 364 Length adjustment: 29 Effective length of query: 303 Effective length of database: 335 Effective search space: 101505 Effective search space used: 101505 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 (21.7 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