Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate 18061 b4033 maltose transporter subunit (NCBI)
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Keio:18061 Length = 514 Score = 87.4 bits (215), Expect = 7e-22 Identities = 75/256 (29%), Positives = 114/256 (44%), Gaps = 25/256 (9%) Query: 54 GQLTFVGLGNFKVLFGDPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRF 113 G G NF +F D F VF LI + + +G+ LA ++ LR Sbjct: 254 GYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRG 313 Query: 114 GAFYRTAIFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFG---PWLGKPDTA 170 A YR + LP + I I+K + + +G +L +LFG W P TA Sbjct: 314 KAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLS-----ALFGVKPAWFSDPTTA 368 Query: 171 LIAVSLISVWQYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGI 230 + +++ W M+L L IPD++ EA+ +DG + F+KI LPL++ + Sbjct: 369 RTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTP 428 Query: 231 VSILTFVGNFNAFDLIYTVQGALAGPDK--------STDILGTLLYRTFF---GFQLQLG 279 + I +F NFN F LI + GPD+ TD+L YR F G Q Sbjct: 429 LMIASFAFNFNNFVLIQLLTN--GGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQ---- 482 Query: 280 DRSMGATIAAIMFLII 295 D + A IA ++FL++ Sbjct: 483 DFGLAAAIATLIFLLV 498 Lambda K H 0.331 0.146 0.461 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: 445 Number of extensions: 26 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: 315 Length of database: 514 Length adjustment: 31 Effective length of query: 284 Effective length of database: 483 Effective search space: 137172 Effective search space used: 137172 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: 50 (23.9 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