Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate 6938761 Sama_2864 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__SB2B:6938761 Length = 230 Score = 142 bits (358), Expect = 6e-39 Identities = 83/222 (37%), Positives = 135/222 (60%), Gaps = 8/222 (3%) Query: 1 MISIKNVNKWYG----DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 M+++KN+NK + + L D + EV +GE + V GPSGSGK+T + LE G Sbjct: 1 MLTMKNINKLFRTDLVETHALRDFNLEVAEGEFVAVTGPSGSGKTTFLNIAGLLENASGG 60 Query: 57 DVIVDGTSIADPKTNLP-KLRS-RVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEAS 114 + +DG ++A+ + ++R+ ++G +FQ F L P L++ +N+ + ++ G E Sbjct: 61 EYWLDGENVANLSDSAAARVRNQKIGFIFQGFNLIPDLNLAENVELP-LRYRGFGSSERK 119 Query: 115 KKALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174 ++ Q L +VGL+A K P QLSGGQQQRVAIARALA +P +L DEPT LD M + Sbjct: 120 RRVEQALSQVGLAARQKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQ 179 Query: 175 VLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIE 216 V++++ + +G T++ VTH+ AR+ A+R I + G++ + Sbjct: 180 VMELLEDINRQGTTIIMVTHDGELARR-AERNIQIVDGQVCD 220 Lambda K H 0.321 0.135 0.390 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: 124 Number of extensions: 7 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: 244 Length of database: 230 Length adjustment: 23 Effective length of query: 221 Effective length of database: 207 Effective search space: 45747 Effective search space used: 45747 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 (21.9 bits) S2: 46 (22.3 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