Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 221 bits (564), Expect = 2e-62 Identities = 125/304 (41%), Positives = 176/304 (57%), Gaps = 16/304 (5%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M+ ++L NV K FG V + +NL + GE +GPSGCGK+T LR+++G ED GEI Sbjct: 1 MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI 60 Query: 61 SIGGQTVTTT------PPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARV 114 +G + ++ PP KR MVFQ++A++PHLSV EN+A L+ R EI R Sbjct: 61 HVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRT 120 Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174 EA SL D + P +LSGG +QRVA+ RA+ P + L DEPLS+LD LR R Sbjct: 121 REALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRF 180 Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFI 234 EI L R S++YVTHDQ EAM L+D+I+V+R+G ++QVGTP+++Y NPAN FV FI Sbjct: 181 EIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFI 240 Query: 235 GAPAMNFVPAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHVEKLGGDTNILVDMGEDL 294 G NF+ P + + AR++P P + ++ + L ++ Sbjct: 241 G--LSNFLDVNL---TPEGLVRVNGGDARVTPATPPSARLVSAGRAA-----LASRPSEI 290 Query: 295 TFTA 298 FTA Sbjct: 291 DFTA 294 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: 319 Number of extensions: 9 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: 331 Length of database: 354 Length adjustment: 29 Effective length of query: 302 Effective length of database: 325 Effective search space: 98150 Effective search space used: 98150 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 Apr 09 2024. 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