Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate HSERO_RS01340 HSERO_RS01340 sugar ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2943 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS01340 Length = 311 Score = 127 bits (318), Expect = 4e-34 Identities = 81/264 (30%), Positives = 142/264 (53%), Gaps = 8/264 (3%) Query: 40 LTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDPSFGTAVVNTI 99 L PA ++++ P++ TIY S ++ M + F GL N+ P+F TA+ N + Sbjct: 42 LAPACVMTLVYVLYPILYTIYLSFFSWDGMTEPR--FVGLANYVELFHAPTFYTALKNNV 99 Query: 100 LLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFFVMPTVNALMWKNMMMNPIYG 159 L L + L+ +G+AIAL +N+ G +V+ L +PF + V LM+ + +P +G Sbjct: 100 LWL-LMFLLAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMY-SWFYDPSFG 157 Query: 160 VLAQVWIFFGAAPVDWLTDHPLFSVIVMVSWQWLPFATLIFMTALQSMNHEQLEASRMDG 219 +L+ +F PV + F +I W + ++F+T L ++NH+Q+EA+RM+G Sbjct: 158 LLSL--LFGQGVPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTALNHDQVEAARMEG 215 Query: 220 ANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPGDASTNVTFLIFKQA 279 A LRY+ +P L + + ++ +I L F I T+GGP ++ST + + + QA Sbjct: 216 AKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYESSTVLAYYAYDQA 275 Query: 280 LLNFDAGVASAGA--LFAVVLANI 301 + + G ++A A LFA++L I Sbjct: 276 IKYYRQGYSAAVAVTLFAIMLVYI 299 Lambda K H 0.331 0.142 0.436 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: 271 Number of extensions: 15 Number of successful extensions: 3 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: 316 Length of database: 311 Length adjustment: 27 Effective length of query: 289 Effective length of database: 284 Effective search space: 82076 Effective search space used: 82076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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