Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 6938088 Sama_2209 C4-dicarboxylate-binding periplasmic protein (RefSeq)
Query= uniprot:A0A165IVH1 (339 letters) >FitnessBrowser__SB2B:6938088 Length = 339 Score = 137 bits (344), Expect = 5e-37 Identities = 80/252 (31%), Positives = 136/252 (53%), Gaps = 4/252 (1%) Query: 10 AALSVAAITCSFQAAAQDFKPRIIRFGYGLNEVSNQGRATKLFAEEVEKASGGKMKVRAI 69 A+L + SF A A+ P I+F + + E + +G+ F E VE G+ KV Sbjct: 18 ASLLATVLGFSFGAVAE---PVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVF 74 Query: 70 GAAALGSDVQMQQALIGGAQEMMVGSTATLVGITKEMAIWDTPFLFNNAKEADVVLDGPV 129 + L D AL+ +++ S + TK++ ++D PFLF + D Sbjct: 75 PNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEA 134 Query: 130 GQKVMDKLQEKGLVGLVYWENGFRNLTNSKRPVNKLEDMDGIKLRVMQNNVFLDSFKTLG 189 GQ++++ + KGLVGL Y NG + + + ++ D G K R+M ++V F+ +G Sbjct: 135 GQQLLNSMSRKGLVGLGYLHNGMKQFS-ANNALSLPGDAAGKKFRIMPSDVIAAQFEAVG 193 Query: 190 ANAVPLPFSELFTALETKTVDGQENPYNTILSSKFYEVQKYLTVTNHVYSPWIVLVSKKY 249 A V PFSE+FT L+T+ +DGQEN ++ I S KFYEVQ ++T +NH ++++ S+ + Sbjct: 194 AIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETF 253 Query: 250 WDGLSKAEQKVL 261 W L K +++++ Sbjct: 254 WKSLPKDKREII 265 Lambda K H 0.316 0.130 0.364 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: 254 Number of extensions: 17 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: 339 Length of database: 339 Length adjustment: 28 Effective length of query: 311 Effective length of database: 311 Effective search space: 96721 Effective search space used: 96721 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 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