Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Ac3H11_227 Hemin ABC transporter, permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_227 Length = 360 Score = 184 bits (467), Expect = 3e-51 Identities = 115/287 (40%), Positives = 165/287 (57%), Gaps = 12/287 (4%) Query: 44 YYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLL- 102 Y V + RLPRLL+ + GA L +AG L+QG+ RNPLA P ++GV+ A+LA+ ++L Sbjct: 71 YLVFINIRLPRLLMGVAAGAGLGLAGALMQGLFRNPLADPGLVGVSSGAALAAAVTIVLG 130 Query: 103 ---MPSLPVMV----LPLLAFAGGMAGLILLKMLAKTHQPMKLAL---TGVALSACWASL 152 +P +P + L +AF GG+ L+ LA+ ++ L GVA++A + Sbjct: 131 MHWLPDMPRTLGSWALVSMAFGGGLLVTALIYALAQGDGGTRMGLMLLAGVAVNALALAG 190 Query: 153 TDYL-MLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGD 211 YL +S + + N +WL GSL G WS V + ++ + L L R L+ +ALG+ Sbjct: 191 LGYLNFISTDEQLRNLQMWLLGSLGGARWSAVALVGAIVAVACGLGLVLARPLNAIALGE 250 Query: 212 ARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPV 271 A+A LGV V T+ A+L+ AA G I FIGLV PH +R + G HR +LP Sbjct: 251 AQAALLGVPVERTKRLAVLVTALAVGAVTAATGIIGFIGLVAPHWVRLVAGPDHRVVLPG 310 Query: 272 SALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 SAL GA L++ AD +AR I P ELP+GVLTA IG P F+ +L + R Sbjct: 311 SALLGAALVLAADGVARTIVQPAELPLGVLTAFIGVPLFLAMLRQFR 357 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: 309 Number of extensions: 5 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: 318 Length of database: 360 Length adjustment: 28 Effective length of query: 290 Effective length of database: 332 Effective search space: 96280 Effective search space used: 96280 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