Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate 3607126 Dshi_0548 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2943 (316 letters) >FitnessBrowser__Dino:3607126 Length = 288 Score = 131 bits (330), Expect = 2e-35 Identities = 86/279 (30%), Positives = 149/279 (53%), Gaps = 12/279 (4%) Query: 42 PAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDPSFGTAVVNTILL 101 PA+ L L I PL+ ++ SL YNL + + F GLEN+ +TD F A+ T L Sbjct: 16 PAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTFFL 75 Query: 102 LGSVILITVVLGVAIALLINEPFPGRGIVRVL----LISPFFVMPTVNALMWKNMMMNPI 157 LG+ + + + LG+ IAL++++P G +V+ L L+ P V L+ + +M N Sbjct: 76 LGTALPLQIALGLGIALVLHQP--GLTLVKTLARLSLVLPMATTYAVVGLLGQ-VMFNQK 132 Query: 158 YGVLAQVWIFFGAAPVDWLTD-HPLFSVIVMVS-WQWLPFATLIFMTALQSMNHEQLEAS 215 +GV+ Q+ G A ++W+ D F++I+ WQW PF L+ + L + E EA+ Sbjct: 133 FGVVNQL---LGGADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEAA 189 Query: 216 RMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPGDASTNVTFLI 275 R++ + LRY+ +P L + V+++ L +F ++T T GGPG ++ ++ +I Sbjct: 190 RLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLMI 249 Query: 276 FKQALLNFDAGVASAGALFAVVLANIAAVFLIRMVGKNL 314 + FD G+ASA A+ +++ + A IR+ K + Sbjct: 250 QRVGFRGFDQGLASAQAIILLIITIVLAQIYIRVFYKEV 288 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: 252 Number of extensions: 12 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: 316 Length of database: 288 Length adjustment: 27 Effective length of query: 289 Effective length of database: 261 Effective search space: 75429 Effective search space used: 75429 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