Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate GFF356 PS417_01815 peptide ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__WCS417:GFF356 Length = 244 Score = 280 bits (717), Expect = 1e-80 Identities = 143/228 (62%), Positives = 174/228 (76%), Gaps = 2/228 (0%) Query: 15 QVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVVDGTSIADPKTDLPK 74 + + + +T+V KGEV+VV GPSGSGKST ++C+N LE F G V +DG +ADPKTD+ Sbjct: 19 RAVDNVTTQVAKGEVLVVIGPSGSGKSTFLRCLNGLEEFDSGSVSIDGLQLADPKTDVNA 78 Query: 75 LRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQLLERVGLSAHAHKHP 134 R VGMVFQHF LFPH+T+ ENL +AQ V RSK+E+ K L LLE+VG++ A++ P Sbjct: 79 YRREVGMVFQHFNLFPHMTVLENLCLAQKVVRKRSKKESEAKALALLEKVGIAQKANEFP 138 Query: 135 GQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQLANEGMTMMCVTH 194 +LSGGQQQRVAIARALAMDP VMLFDEPTSALDPEMV EVLDVM LA EGMTM+CVTH Sbjct: 139 SRLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPEMVGEVLDVMKTLALEGMTMVCVTH 198 Query: 195 EMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQHFLDKIL 242 EMGFAR+VADRV+F D GK++ED EFF + RAQ FL ++L Sbjct: 199 EMGFAREVADRVLFFDHGKLLEDAAPAEFFD--APKDPRAQAFLRQVL 244 Lambda K H 0.321 0.136 0.394 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: 235 Number of extensions: 8 Number of successful extensions: 1 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: 244 Length of database: 244 Length adjustment: 24 Effective length of query: 220 Effective length of database: 220 Effective search space: 48400 Effective search space used: 48400 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: 46 (22.3 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