Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate RR42_RS16445 RR42_RS16445 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__Cup4G11:RR42_RS16445 Length = 252 Score = 238 bits (606), Expect = 1e-67 Identities = 126/254 (49%), Positives = 176/254 (69%), Gaps = 13/254 (5%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60 MI ++++ K + + L + EV++GEV+ + GPSGSGKSTL++ +N LE +GD+ + Sbjct: 1 MIDVRDLYKHFDAVKALNGVNLEVQRGEVVCLIGPSGSGKSTLLRSINYLERPTRGDISI 60 Query: 61 DGTSI---------ADPKT--DLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRS 109 DG ++ A P + +L ++RS VGMVFQ F L+PHL++ EN+T+ ++V G Sbjct: 61 DGQTVGHVNQAGKKARPMSGRELARVRSEVGMVFQMFYLWPHLSVLENVTLGMVEVRGVR 120 Query: 110 KEEATKKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP 169 +A ++G QLL +VGLS +P QLSGGQ+QRVAIARALAMDP ++LFDEPTSALDP Sbjct: 121 LADAAQRGRQLLAKVGLSGKYDAYPEQLSGGQRQRVAIARALAMDPKIILFDEPTSALDP 180 Query: 170 EMVNEVLDVMVQLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINA 229 E V EVL M +A EGMTM+ THEMGFAR+VADRV+FMD+G+++E + F Sbjct: 181 ERVGEVLQTMETVAAEGMTMIVATHEMGFARRVADRVVFMDEGRVVEAGSPGDIFD--RP 238 Query: 230 RSDRAQHFLDKILQ 243 +S R + FLDK+LQ Sbjct: 239 QSARLKQFLDKVLQ 252 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: 207 Number of extensions: 10 Number of successful extensions: 3 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: 252 Length adjustment: 24 Effective length of query: 220 Effective length of database: 228 Effective search space: 50160 Effective search space used: 50160 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