Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_106712951.1 CU102_RS20480 carbohydrate ABC transporter permease
Query= reanno::Koxy:BWI76_RS01820 (296 letters) >NCBI__GCF_003010955.1:WP_106712951.1 Length = 282 Score = 129 bits (323), Expect = 1e-34 Identities = 87/278 (31%), Positives = 143/278 (51%), Gaps = 23/278 (8%) Query: 23 FIAAIMFPLLMVIAISLREGN--FATG-SLIPESISWEHWRLALGFSVEHADGRVTPPPF 79 ++ +FPL + IS+ + ++ G ++ P + +WE++ L R T P Sbjct: 24 YVIFALFPLFWTLKISVTPQSLLYSEGITMWPSTSTWENYATVL---------RATDFP- 73 Query: 80 PVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVA 139 + NS+ V+ ITAI + ++ YA +R F GK T+ +L+ Q FP V+ + Sbjct: 74 ---RYFLNSVIVSVITAILVTMIAAAAGYAMSRFSFRGKTTVAVTLLLTQTFPLVMVIPP 130 Query: 140 LYALFDRLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAALDGAT 198 +Y + +LG N+ G+I Y IA + ++ +F+ I LEEAA +DG + Sbjct: 131 MYRIMGQLGL------TNSLTGLIIIYTAFNIAFATFLMQSFFDGIPKDLEEAAMIDGCS 184 Query: 199 PWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNY 258 QA R +++PL++P + F AA +E+ A +L+ + T AVG+ ++ Sbjct: 185 RSQALRKIIIPLTLPGMGATLGFVFTAAWSELLFALMLISSDSQKTFAVGLLTFIGKFAV 244 Query: 259 LWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 WG AA+VL+ IP + F QR+LV GLTAG VKG Sbjct: 245 DWGQMMAASVLALIPACLFFAFLQRYLVTGLTAGAVKG 282 Lambda K H 0.328 0.141 0.438 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: 238 Number of extensions: 14 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: 296 Length of database: 282 Length adjustment: 26 Effective length of query: 270 Effective length of database: 256 Effective search space: 69120 Effective search space used: 69120 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