Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF770 HP15_749 iron(III) ABC transporter, ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Marino:GFF770 Length = 357 Score = 209 bits (532), Expect = 9e-59 Identities = 128/354 (36%), Positives = 190/354 (53%), Gaps = 16/354 (4%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63 L++ NL G+ G S++K + ++ + +GPSGCGKST+LR +AG +SGG I L Sbjct: 13 LEVNNLSCGYGGDSVVKDVSFALSHGDIGCLLGPSGCGKSTILRALAGFLPLSGGEISLQ 72 Query: 64 GRDIT----EVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119 + I+ + P KR + MVFQ YAL+PH+++ N+ F L + KAE +KV E Sbjct: 73 SQAISLPGRTLPPEKRRIGMVFQDYALFPHLTIADNVGFGL--RNLNKAEKRQKVMELLN 130 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 ++ L + + P +LSGGQ+QRVA+ RA+ P + L DEP SNLDA LR ++ L++ + Sbjct: 131 VVHLQDLADNYPHELSGGQQQRVALARALAPEPTLILLDEPFSNLDADLRRRLSLDVREI 190 Query: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 K L + I VTHDQ EA M D+V VL G+I+Q P +LYH+PAN FVA F+G + Sbjct: 191 LKTLGISAILVTHDQQEAFAMCDQVAVLRDGRIQQWDVPYNLYHEPANRFVASFVG--QG 248 Query: 240 GFLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQ 299 GF+ G D+ E+ + G R G+ V + IRP+ ++ D LQ Sbjct: 249 GFVPGTALGPDTIESELGVIHGNR------AYKWEPGTLVDVLIRPD--DIVHDPDSDLQ 300 Query: 300 VTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFD 353 G+ T R + R L GE + + ++A H F+ Sbjct: 301 PKVVEKTFAGTSTLYRFRCSEDTEFEALFRSHLDFNLGEHVPVRVEADHLIAFE 354 Lambda K H 0.320 0.137 0.389 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: 324 Number of extensions: 16 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: 367 Length of database: 357 Length adjustment: 29 Effective length of query: 338 Effective length of database: 328 Effective search space: 110864 Effective search space used: 110864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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