Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease
Query= reanno::Phaeo:GFF2752 (280 letters) >NCBI__GCF_003217355.1:WP_110804034.1 Length = 382 Score = 126 bits (316), Expect = 8e-34 Identities = 65/207 (31%), Positives = 121/207 (58%), Gaps = 1/207 (0%) Query: 75 FQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELM 134 F N+M VT+ + + +L A AA+ALA RF G LL + +++P+++ + +L+L Sbjct: 174 FLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRALLVATIVGLLVVPLQLALIPLLKLH 233 Query: 135 VDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLP 194 GL + + L +T GLPLA+++L +M + ++ + R+DG +E+ IF R+VLP Sbjct: 234 NQIGLNQSYLGIWLAHTGFGLPLAIYLLRNYMVGLPREIIESARVDGATEFQIFRRIVLP 293 Query: 195 LVRPAMATVAVFNMIPIWNDLWFPLI-LAPAEETKTLTLGSQVFIGQFVTDWNAVLSALS 253 L PA+A+ A+F + +WNDL + L A +T+ +T + +G DW + ++ Sbjct: 294 LSFPALASFAIFQFLWVWNDLLVATVFLGNATDTQVMTGALRALLGSRGGDWEILAASAF 353 Query: 254 MAILPVMVLYVIFSRQLIRGITSGAVK 280 ++I ++++ + L+RG+ +G+VK Sbjct: 354 VSIAVPLIVFFALQKYLVRGLLAGSVK 380 Lambda K H 0.330 0.143 0.414 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: 280 Number of extensions: 19 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: 280 Length of database: 382 Length adjustment: 28 Effective length of query: 252 Effective length of database: 354 Effective search space: 89208 Effective search space used: 89208 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 (21.8 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