Align Rhizopine-binding protein (characterized, see rationale)
to candidate WP_008507131.1 BIBO1_RS11580 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A0N9WNI6 (308 letters) >NCBI__GCF_000182725.1:WP_008507131.1 Length = 329 Score = 161 bits (407), Expect = 2e-44 Identities = 105/325 (32%), Positives = 172/325 (52%), Gaps = 26/325 (8%) Query: 4 KIRFASLALSLMLASGAALAD--LRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQF 61 K+ A A S ++A+ + D L+IG + + ++ E++ K V+L Sbjct: 3 KLLIALAAASALIATPSLAQDKKLKIGAAPYGLNAEFMQVWSEALKKHPAVKNGEVELTI 62 Query: 62 EDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK 121 D R D + Q Q + I+QK DAI+ P+D A +AA AGIP+V N R + Sbjct: 63 FDGRYDALVQQEQFNTMITQKFDAIIFVPIDIEAGATAVQAASDAGIPVVGSNTRVNSDL 122 Query: 122 LPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLAKYP 181 L V S+D +G M+ + + +K+ KG++VIL G + ++ +R +G K+ LA+ P Sbjct: 123 L---AAYVGSDDTVSGYMEAKDVLDKIGCKGNVVILEGPIGQSAQISRLEGNKKALAECP 179 Query: 182 GIKIDQEQTGTWSRDKGMTLVNDWLT-QGRKFDAIVSNNDEMAIGAAMALKQAGVEKGSV 240 +K+ ++QT WSR + TL+ +WLT + + ++ NDEMA+GA A+K A ++ G Sbjct: 180 NVKVLEDQTANWSRAEAQTLMENWLTAHPGQINGVIGQNDEMALGAIEAIKAANLKPGDF 239 Query: 241 LIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAK---------------- 284 IAG+DG D L AVK+G + S+ QDAN QA ++D A+ A+ Sbjct: 240 AIAGIDGITDALHAVKEGTM-TSILQDANAQAQGALDLAIFHARKGDYKPQSDIWAQYPD 298 Query: 285 ---NEPVEQAVWVPYRLITPENVDQ 306 N+ ++ VP+ +T +NVD+ Sbjct: 299 MPFNDGKDKNYNVPWTPVTAQNVDK 323 Lambda K H 0.315 0.130 0.360 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: 238 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 329 Length adjustment: 27 Effective length of query: 281 Effective length of database: 302 Effective search space: 84862 Effective search space used: 84862 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 (21.5 bits) S2: 48 (23.1 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