Align SmoG, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease
Query= TCDB::O30833 (276 letters) >NCBI__GCF_000319285.1:WP_007675527.1 Length = 280 Score = 115 bits (287), Expect = 1e-30 Identities = 80/266 (30%), Positives = 139/266 (52%), Gaps = 7/266 (2%) Query: 15 LAAWTIAFLI-FFPILWTVLMSFKSEGDAIKAPFAMLFSDWTLQSYADVQERS--NYARH 71 LA + IA L+ FF +L T SFKS +AI + WTL Y D+ + + Sbjct: 17 LALFLIATLLPFFVMLMT---SFKSPKEAISLHPTLFPQHWTLAHYLDIFNPIIFPFVTY 73 Query: 72 FMNSVVISLGSTLVALAIAIPAAWAMAFVPGRRTKDVLMWMLSTKMMPAVGVLIPLYLIF 131 F NS+V+S+ ++ VA+ I I A+A++ + + + + M + +++PL+ I Sbjct: 74 FRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTINASFYAVYMFSGILLVVPLFKII 133 Query: 132 RDTGLLDTRIGLVIVLTLINLPIVVWMLYTYFKEIPGEILEAARMDGATLGSEILYILTP 191 G+ DT++ +++ + LP V+ML +YF IP EI EAA MDG I I P Sbjct: 134 TALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFRITVP 193 Query: 192 MAVPGIASTLLLNVILAWNE-AFWTLQLTTSRAAPLTQFIASYSSPEGLFYAKLSAASTM 250 +AV G+ S + ++AWN+ F ++ L+++ L + + S + ++ AAS + Sbjct: 194 LAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNTLFSTPDYIWGRMMAASLV 253 Query: 251 AIAPILILGWFSQKQLVRGLTFGAVK 276 P++++ S++ + GLT G VK Sbjct: 254 TALPVVVMYALSERFIKSGLTDGGVK 279 Lambda K H 0.327 0.137 0.416 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: 173 Number of extensions: 9 Number of successful extensions: 4 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: 276 Length of database: 280 Length adjustment: 25 Effective length of query: 251 Effective length of database: 255 Effective search space: 64005 Effective search space used: 64005 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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