Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 18061 b4033 maltose transporter subunit (NCBI)
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Keio:18061 Length = 514 Score = 114 bits (285), Expect = 5e-30 Identities = 72/228 (31%), Positives = 119/228 (52%), Gaps = 14/228 (6%) Query: 64 FQRALVTTTWFAVISVAAEMVLG-VLAALLLNQQFRGRTALRALMILPWALPTVVNATLW 122 F V T F++I+V + +G VLA L+ + RG+ R L+ILP+A+P+ ++ ++ Sbjct: 277 FLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIF 336 Query: 123 RLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQA 182 + ++N +G +N L+ L +W +P TA LI+ + W +P + ++ + L+A Sbjct: 337 KGLFNQSFGEINMMLS--ALFGVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKA 394 Query: 183 VPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGG--- 239 +P D+ AS +DGAGPF F + +P L PL ++ F F +I ++T GG Sbjct: 395 IPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDR 454 Query: 240 -----PANSTRTLSILVYQEAF---SFQRAGSGASLALIVTLLVTILA 279 PA T L Y+ AF Q G A++A ++ LLV LA Sbjct: 455 LGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLIFLLVGALA 502 Lambda K H 0.326 0.138 0.417 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: 352 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 293 Length of database: 514 Length adjustment: 30 Effective length of query: 263 Effective length of database: 484 Effective search space: 127292 Effective search space used: 127292 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: 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