Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 297 bits (760), Expect = 3e-85 Identities = 146/265 (55%), Positives = 201/265 (75%) Query: 1 MADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMG 60 M+ IEI+++Y +FG++ +KAL M+++G K++IL +GCTV + D +L I G+IFVIMG Sbjct: 1 MSKIEIKDLYLVFGNEKQKALKMLKEGKTKSEILKATGCTVAVKDANLSINEGEIFVIMG 60 Query: 61 LSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHR 120 LSGSGKSTL+R INRLI PTSGEV+ +G +I + K L R + ++MVFQ+F L+PHR Sbjct: 61 LSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQIRRKELAMVFQNFGLLPHR 120 Query: 121 TVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAA 180 +VL N+ +G ++GV K + + M+ + VGL GY+ + +LSGGM+QRVGLARALA Sbjct: 121 SVLHNIAFGLELQGVKKGEREQKAMESMQLVGLKGYENQMVSELSGGMQQRVGLARALAN 180 Query: 181 DTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDG 240 + +V+LMDEAFSALDPLIR MQD+LL LQ + KTIVFITHDL EA+++G IAI++DG Sbjct: 181 NPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDG 240 Query: 241 QVVQVGTPNDILDNPANDYVARFVQ 265 ++VQ+GT +IL PAN YV RFV+ Sbjct: 241 EIVQIGTSEEILTEPANAYVERFVE 265 Lambda K H 0.323 0.139 0.397 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: 287 Number of extensions: 5 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: 275 Length of database: 408 Length adjustment: 28 Effective length of query: 247 Effective length of database: 380 Effective search space: 93860 Effective search space used: 93860 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 (21.9 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