Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate AZOBR_RS19150 AZOBR_RS19150 ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__azobra:AZOBR_RS19150 Length = 339 Score = 174 bits (440), Expect = 4e-48 Identities = 121/325 (37%), Positives = 175/325 (53%), Gaps = 14/325 (4%) Query: 4 ALVIFIT-LALAGCALLSLHMGVIPVPWRALLTDWQAGHEHY--YVLMEYRLPRLLLALF 60 ALV +T LALA CA+ S +G +P L+DW AG VL E RLPR L+ L Sbjct: 15 ALVAGLTGLALALCAV-SAAVGYVPFDLGVALSDWLAGRPTLGALVLAELRLPRALIGLL 73 Query: 61 VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGM 120 VG +L + G +QG +RNPLA P ++GV+ AA+L GA+++ S L L GGM Sbjct: 74 VGFSLGLTGAAMQGWLRNPLAEPGLVGVSSAAAL---GAVIVFYSGLSAALSLALPLGGM 130 Query: 121 AG-----LILLKMLAKTHQPMKLALTGVALSACWASLTDYLM--LSRPQDVNNALLWLTG 173 AG ++L M A+ L + G+A+++ SLT + P + WL G Sbjct: 131 AGAATAAVLLNLMAARGAGTTALVIGGIAINSLAGSLTALALNLAPNPYAALEIVFWLMG 190 Query: 174 SLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAV 233 SL R + + +P M+ L LS R LD L LG+ A +LG + R + A Sbjct: 191 SLADRGTDQLWLVLPPMLAGWALCLSGARALDALTLGEDAARSLGFDLTGLRVRLIAGAA 250 Query: 234 AMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPP 293 + V+ G + F+GLV PH+MR + G R RLL ++ L GA L + AD+ R++ Sbjct: 251 LAVGSAVSVTGAVGFVGLVAPHLMRPLAGARPGRLLLLAGLAGACLTLAADIAVRLLPTR 310 Query: 294 LELPVGVLTAIIGAPWFVWLLVRMR 318 EL +GV+TA+IGAP+ + L+ R+R Sbjct: 311 PELKLGVVTALIGAPFLIVLIARLR 335 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: 315 Number of extensions: 16 Number of successful extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 290 Effective length of database: 311 Effective search space: 90190 Effective search space used: 90190 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