Align Probable c4-dicarboxylate-binding protein (characterized, see rationale)
to candidate GFF772 Psest_0786 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:Q9HVH5 (332 letters) >FitnessBrowser__psRCH2:GFF772 Length = 341 Score = 405 bits (1041), Expect = e-118 Identities = 205/331 (61%), Positives = 252/331 (76%) Query: 1 MFKPFVGVALAALFAVSAVAHAEDAGPVVIKFSHVVSDDTPKGKGALLFKKLAEERLPGK 60 +FK V AAL + A+ A P+VIKF+HVV DDTPKGKGALLF+ L ERL GK Sbjct: 11 VFKSLVVAPFAALVLTLSPLIAQAAEPIVIKFAHVVGDDTPKGKGALLFQTLVRERLAGK 70 Query: 61 VKVEVYPNSTLFGDADEIEALRANKVQMLATSLSKFEPYTKQLQVFDLPFLFDDLEALKR 120 V VEVYPNSTL GDADE++AL NKVQMLA SLSKF Y+ +L+VFDLPFLFDD A+ R Sbjct: 71 VDVEVYPNSTLVGDADEMQALLDNKVQMLAPSLSKFIEYSPKLEVFDLPFLFDDDAAVAR 130 Query: 121 FQKRDKSRELLRSMAKHGIYGLAYWNNGMKQLSATRELHRPDDAKGLVFRIQPSSVLEAQ 180 FQKR+ SR+LLRSMA GIYGLAYWNNG+KQLSA + L P DA GL FRIQPS VLEAQ Sbjct: 131 FQKREASRDLLRSMAGRGIYGLAYWNNGLKQLSANQPLQTPADAAGLAFRIQPSPVLEAQ 190 Query: 181 FAMLGATAKQLSYAETLKAMQAGSVQGTENTWSNLAGQKIDSVQPYITETNHGALSYMLI 240 FA + A A +L ++E KAMQ+G+VQGTE WSN+ GQ Q Y+TETNHG L+YML+ Sbjct: 191 FAAVDAKAVRLPFSEVSKAMQSGTVQGTEGPWSNIRGQNAGLKQSYVTETNHGVLNYMLV 250 Query: 241 TSSAFWTGIPYQTRTELESIVDEVTLVVNKEAEALNQKEREHLLAAGKSRLVSLSAEEHE 300 T+S FWT IP+ R+ELE+IV EVT VN EA A+NQ+ERE +LA+G + LV+L+ + + Sbjct: 251 TNSEFWTSIPFAVRSELENIVLEVTQTVNAEAAAINQREREQILASGNTTLVTLTPAQRQ 310 Query: 301 AWRNAMKPLWKNYEAQIGSDVLRAAQVVNRK 331 AWR M+P+WK++EA IG+D++RAA VNR+ Sbjct: 311 AWRVKMQPVWKSFEAHIGADIMRAALAVNRR 341 Lambda K H 0.316 0.130 0.367 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: 298 Number of extensions: 10 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: 332 Length of database: 341 Length adjustment: 28 Effective length of query: 304 Effective length of database: 313 Effective search space: 95152 Effective search space used: 95152 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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