Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P48243 (242 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 162 bits (411), Expect = 7e-45 Identities = 90/240 (37%), Positives = 141/240 (58%), Gaps = 6/240 (2%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 ++K+ V K F D A+ D+ L I +G++ +LG SGSGKSTL R + E EG I + Sbjct: 20 LLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYL 79 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120 DG+ + + L + M+FQS+ LFPH+T++ N+ +K KM K++ + + Sbjct: 80 DGQDITD----LPPYERPINMMFQSYALFPHMTVEQNIAFG-LKQDKMSKADISQRVQEM 134 Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEV-LDVM 179 L+ V + A + P QLSGGQ+QRVA+AR+LA PK++L DEP ALD ++ ++ L+V+ Sbjct: 135 LKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVV 194 Query: 180 ASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLGKI 239 L + G+T V VTH+ A A R+ M+DG I + P + +P S +F+G + Sbjct: 195 EILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGTV 254 Lambda K H 0.319 0.135 0.379 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: 193 Number of extensions: 8 Number of successful extensions: 4 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: 242 Length of database: 378 Length adjustment: 27 Effective length of query: 215 Effective length of database: 351 Effective search space: 75465 Effective search space used: 75465 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: 48 (23.1 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