Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Ac3H11_227 Hemin ABC transporter, permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_227 Length = 360 Score = 173 bits (438), Expect = 7e-48 Identities = 119/329 (36%), Positives = 177/329 (53%), Gaps = 15/329 (4%) Query: 16 AALIIIFWLSLFCYSAIPVSGADATRALLP--GHTPTL---PEALVQ-NLRLPRSLVAVL 69 AAL+ + ++ A ++ A + LL G P+ PE LV N+RLPR L+ V Sbjct: 28 AALVGLSFVWASTRGAYAIAPAQLWQVLLQAVGAAPSAEQAPEYLVFINIRLPRLLMGVA 87 Query: 70 IGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALS-------PTPIAGYSLS 122 GA L LAG L+Q L NP+A P L+G++SGAALA A+T L P + ++L Sbjct: 88 AGAGLGLAGALMQGLFRNPLADPGLVGVSSGAALAAAVTIVLGMHWLPDMPRTLGSWALV 147 Query: 123 FIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCM-GLTRITLLLAEDHAYGI 181 +A GG + L+ G T ++LAG+A++A + GL + + ++ + Sbjct: 148 SMAFGGGLLVTALIYALAQGDGGTR-MGLMLLAGVAVNALALAGLGYLNFISTDEQLRNL 206 Query: 182 FYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLV 241 WL G + ARW V + +V A + L+LA LN + L ++ A LGV + R + + Sbjct: 207 QMWLLGSLGGARWSAVALVGAIVAVACGLGLVLARPLNAIALGEAQAALLGVPVERTKRL 266 Query: 242 INMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLA 301 ++ L VGA + G + FIGL+ PH R AG D R VLP S LLGA L+L AD +A Sbjct: 267 AVLVTALAVGAVTAATGIIGFIGLVAPHWVRLVAGPDHRVVLPGSALLGAALVLAADGVA 326 Query: 302 RALAFPGDLPAGAVLALIGSPCFVWLVRR 330 R + P +LP G + A IG P F+ ++R+ Sbjct: 327 RTIVQPAELPLGVLTAFIGVPLFLAMLRQ 355 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: 369 Number of extensions: 11 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: 332 Length of database: 360 Length adjustment: 29 Effective length of query: 303 Effective length of database: 331 Effective search space: 100293 Effective search space used: 100293 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