Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 206 bits (524), Expect = 8e-58 Identities = 116/289 (40%), Positives = 166/289 (57%), Gaps = 4/289 (1%) Query: 7 KNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELDGRD 66 + L + F + + + L+V F +GPSGCGK+TLLRL+AG ++ G I + G Sbjct: 8 EGLVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGER 67 Query: 67 ITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILELGPM 126 + +V P +R + MVFQ AL+P M+V N+++ L + E K++ + L + Sbjct: 68 MNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDL 127 Query: 127 LERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQAT 186 R P++LSGGQRQRVA+ R +V P + L DEPL LD LR QM++EL L K+ T Sbjct: 128 EHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTT 187 Query: 187 MIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKV 246 +Y+THDQ EAM ++D+V V+ GR +QV P ELY +PA FVAGF+G L G++ Sbjct: 188 FVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNR--LSGEL 245 Query: 247 TRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGD 295 V E+ LD G + ++ NL G L IRPE +L L GD Sbjct: 246 VSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPE--SLVLSGD 292 Lambda K H 0.321 0.137 0.390 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: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 367 Length of database: 362 Length adjustment: 29 Effective length of query: 338 Effective length of database: 333 Effective search space: 112554 Effective search space used: 112554 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