Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate WP_090439690.1 BLS63_RS03220 C4-dicarboxylate ABC transporter
Query= uniprot:Q930R1 (334 letters) >NCBI__GCF_900100495.1:WP_090439690.1 Length = 324 Score = 149 bits (376), Expect = 9e-41 Identities = 99/295 (33%), Positives = 150/295 (50%), Gaps = 16/295 (5%) Query: 2 RKLLLATTAIAFGLSAAAPAFAEFNDRNIRVSNGINEDHPVGNG-IKAMQAC---LDQKS 57 RKLL+A +AF L+ A A I E HP G + AM+ LD + Sbjct: 5 RKLLIAALPLAFCLAGLAQAATTLK---------IAEIHPAGYPTVVAMENLGKKLDAAT 55 Query: 58 GGKLKLTAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGVFDLPFLFANAQE 117 G++ F GG LG + + + + G + S + ++P + VF++PF+F + Sbjct: 56 NGEITYRLFAGGVLGSEKEVIEQTQIGAVQLTRVSLGAVGPVVPDVNVFNMPFVFRDHAH 115 Query: 118 AYTVLDGDFGDMMNEKLEAA--GLVNLAYWENGFRNLSNSVRPVTKWEDFEGMKVRVMQN 175 V+DG G + +K+ A+ +V LA+ + G RNL +PV ED +GMK+RVM N Sbjct: 116 MRKVIDGAIGQEILDKITASEFNMVGLAWMDGGTRNLYTK-KPVRSLEDLKGMKIRVMGN 174 Query: 176 NIFLDTFQNLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQKYVTETNHAY 235 +F+DT +GAN M GE+FSAL+T ID EN T+ + Y + T H Sbjct: 175 PLFIDTLNAMGANGIAMDTGEIFSALQTGVIDGAENNPPTMLEHNHYRNANYYSLTGHLI 234 Query: 236 TPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEERKVIQDLNKKSLEKIKEAGLE 290 P + SK +D TPE+QA +++ A + EER + + S K+KEAG+E Sbjct: 235 IPEPLMMSKTTWDQLTPEQQALVKKFAREAQMEERVLWDAKSASSETKLKEAGVE 289 Lambda K H 0.317 0.133 0.374 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: 262 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: 334 Length of database: 324 Length adjustment: 28 Effective length of query: 306 Effective length of database: 296 Effective search space: 90576 Effective search space used: 90576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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