Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate CCNA_01250 CCNA_01250 FecCD-family transporter protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Caulo:CCNA_01250 Length = 346 Score = 158 bits (399), Expect = 2e-43 Identities = 119/321 (37%), Positives = 171/321 (53%), Gaps = 14/321 (4%) Query: 5 LVIFITLALAGCALLSLHMGVIPVPW----RALLTDWQAGHEHYYVLMEYRLPRLLLALF 60 L + + LALA A L++ +G +ALL E VL R PR+ +A Sbjct: 24 LCLLMALALALAAALAITLGETAFSLSQYGQALLLPASPPGE---VLWTIRAPRVTVAAL 80 Query: 61 VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVM--VLPLLAFAG 118 VGAAL +AG +QG++RNPLA P +LGV+ + L + AL + L V+ + L A AG Sbjct: 81 VGAALGMAGATLQGLLRNPLADPGVLGVSAVSGLGA--ALAISAGLAVLPGAIELSALAG 138 Query: 119 GM-AGLILLKMLAKTHQPMKLALTGVALSACWASLTDYLMLSRPQDVNNA--LLWLTGSL 175 + AG ++ + A+ +P L L GVALSA +LT + P V A L WL GS+ Sbjct: 139 ALVAGGTVVVVAARFREPEALILFGVALSALGGALTALVFNLSPSPVATAEILAWLMGSV 198 Query: 176 WGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAM 235 RD A+ M + L L L +L LG+ A + + R +A+ + + Sbjct: 199 ENRDLMDALRALVPMAIGALLCLRAGAGLRMLTLGEDAARMSALPMARLRIYAVAGSALL 258 Query: 236 TSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLE 295 T VAA G I F+GL PH++R++ +R+L +AL GALL+V+ADL AR+I E Sbjct: 259 TGAAVAASGVIGFVGLAAPHLVRALVRDDPKRILWPAALAGALLVVLADLAARMIPTEQE 318 Query: 296 LPVGVLTAIIGAPWFVWLLVR 316 L +GV+TA+ GAP F L R Sbjct: 319 LKLGVVTALFGAPVFALLAWR 339 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: 285 Number of extensions: 13 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: 346 Length adjustment: 28 Effective length of query: 290 Effective length of database: 318 Effective search space: 92220 Effective search space used: 92220 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