Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF770 HP15_749 iron(III) ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Marino:GFF770 Length = 357 Score = 221 bits (563), Expect = 2e-62 Identities = 134/346 (38%), Positives = 185/346 (53%), Gaps = 28/346 (8%) Query: 4 LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63 L++ N+ +G V+KD++ + G+ +GPSGCGKST+LR ++G + GEIS+ Sbjct: 13 LEVNNLSCGYGGDSVVKDVSFALSHGDIGCLLGPSGCGKSTILRALAGFLPLSGGEISLQ 72 Query: 64 GQTVT----TTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASR 119 Q ++ T PP KR I MVFQ YAL+PHL++ +N+ L+ K E +V E Sbjct: 73 SQAISLPGRTLPPEKRRIGMVFQDYALFPHLTIADNVGFGLRNLN--KAEKRQKVMELLN 130 Query: 120 MLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179 ++ L+D D P ELSGGQ+QRVA+ RA+ EP L L DEP SNLDA LR L++ + Sbjct: 131 VVHLQDLADNYPHELSGGQQQRVALARALAPEPTLILLDEPFSNLDADLRRRLSLDVREI 190 Query: 180 HRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAM 239 + L S I VTHDQ EA + D++ VLRDGRI+Q P LY+ PANRFVA F+G Sbjct: 191 LKTLGISAILVTHDQQEAFAMCDQVAVLRDGRIQQWDVPYNLYHEPANRFVASFVGQG-- 248 Query: 240 NFVPAQRLG------------GN------PGQFIG--IRPEYARISPVGPLAGEVIHVEK 279 FVP LG GN PG + IRP+ P L +V+ Sbjct: 249 GFVPGTALGPDTIESELGVIHGNRAYKWEPGTLVDVLIRPDDIVHDPDSDLQPKVVEKTF 308 Query: 280 LGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFD 325 G T ED F A D N+GE + + + ++F+ Sbjct: 309 AGTSTLYRFRCSEDTEFEALFRSHLDFNLGEHVPVRVEADHLIAFE 354 Lambda K H 0.320 0.137 0.391 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: 316 Number of extensions: 18 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: 331 Length of database: 357 Length adjustment: 29 Effective length of query: 302 Effective length of database: 328 Effective search space: 99056 Effective search space used: 99056 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