Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 153 bits (387), Expect = 6e-42 Identities = 98/244 (40%), Positives = 134/244 (54%), Gaps = 14/244 (5%) Query: 15 EVETLKGI----DIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIGER----S 66 ++ KGI D + +GEFL ++G SG GK+TLL +IAGLA+P G I G+R S Sbjct: 10 QIRQTKGIRIEADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDS 69 Query: 67 VLGVH--PKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQIE 124 G+H P++R I V Q + L+P LS NI L+ +P E + + Sbjct: 70 DEGIHCSPQNRHIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLH 127 Query: 125 NLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQMLR 184 L DR PSQLSGGQ+QRVA+ RAL R P+V L DEP S +D + R + EL RL L Sbjct: 128 GLTDRLPSQLSGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELN 187 Query: 185 TTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILDA 244 V+ VTHD EA+ LA + ++ G + Q P +V+ RP VA +G NI +A Sbjct: 188 IPVIMVTHDLNEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMGL--RNIFNA 245 Query: 245 EMTA 248 + A Sbjct: 246 HVVA 249 Lambda K H 0.320 0.136 0.385 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: 264 Number of extensions: 11 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: 360 Length of database: 370 Length adjustment: 30 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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