Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::psRCH2:GFF851 (296 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 102 bits (253), Expect = 1e-26 Identities = 70/222 (31%), Positives = 111/222 (50%), Gaps = 14/222 (6%) Query: 78 PFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIF----QMFPP 133 P VL NS+ I F S+ L + L T +AYAF+R K P+ +L F +M PP Sbjct: 105 PSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRF----KVPLADDLLFFILSTRMMPP 160 Query: 134 VLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAI 193 + + IY ++ LG S++G+ +++ + ++L +W +KG+ + I EEAA+ Sbjct: 161 IAVAIPIYLMYRALGLSDSYVGM-----IVLYTAVNVSLAVWLLKGFMDEIPREYEEAAL 215 Query: 194 VDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYL 253 VDG T QAF ++LP ++ +A I I + EY AS LL D T+ + Sbjct: 216 VDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFAS-LLTSGDAQTMPPFIPFII 274 Query: 254 YPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 W AAA L +PI + +K ++ G+T G V+ Sbjct: 275 GEGGQDWPAVAAATTLFVVPILIFTVVLRKHLLRGITFGAVR 316 Lambda K H 0.327 0.139 0.433 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: 247 Number of extensions: 13 Number of successful extensions: 3 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: 317 Length adjustment: 27 Effective length of query: 269 Effective length of database: 290 Effective search space: 78010 Effective search space used: 78010 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: 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