Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 306 bits (784), Expect = 5e-88 Identities = 172/366 (46%), Positives = 228/366 (62%), Gaps = 36/366 (9%) Query: 1 MTALQLTNVCKSFGP--VEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAG 58 M L+L NV K++G + LK+I L++++GEF++ VGPSGCGKSTL+ I+GLE T G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 EISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEAS 118 I IG Q V+ P R IAMVFQSYALYP +SVREN+ LK + P+ +I A VA + Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 119 RMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIAR 178 ++L +E L+R+P +LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LR+ R E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPA 238 +H++L + +YVTHDQIEAMTL DK+ V++DG I+Q GTP E+YNNPAN+FVA FIG+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 239 MNFVP--AQRLGG------NPGQ-------------------FIGIRPEYARIS-----P 266 MNFVP QR G + GQ +G+RPE ++ Sbjct: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 Query: 267 VGPLAGEVIHVEKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFD- 325 + EV E G DT + V + D RL VGETL FDP+ L FD Sbjct: 301 ASSIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 Query: 326 EAGQRI 331 G+R+ Sbjct: 360 NTGERL 365 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: 372 Number of extensions: 17 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: 386 Length adjustment: 29 Effective length of query: 302 Effective length of database: 357 Effective search space: 107814 Effective search space used: 107814 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