Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 5210162 Shew_2606 ABC transporter-related protein (RefSeq)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__PV4:5210162 Length = 272 Score = 179 bits (453), Expect = 7e-50 Identities = 104/239 (43%), Positives = 149/239 (62%), Gaps = 8/239 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP-----S 58 LL + ++ Y + +L+G++ + GE+VT++GPNGAGKST K I GLL S Sbjct: 13 LLAINNIEVVYDDVIQVLRGVSIEVPQGEIVTLLGPNGAGKSTTLKAISGLLKTENGEVS 72 Query: 59 QGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQ-GPTQTLKD 117 +G+I F GE I +D +VR G+ V + + +TV ENL +GA+ + G + Sbjct: 73 RGDIHFMGERIDVKNADDVVRSGLFQVMEGRRIVEDMTVIENLKLGAYTRRDGQVNQDIE 132 Query: 118 RIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFA 177 ++ FP+L +R AG LSGGE+QMLA+GRALM P ++ LDEPS LSP+LVK+VF Sbjct: 133 MVFNYFPRLKERTGL-AGYLSGGEQQMLAIGRALMARPKMICLDEPSMGLSPLLVKEVFG 191 Query: 178 QIKAIN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 I+ IN G ++LVEQNA AL A+ GY++E+G+ L+G+ LLN+ V E YLG Sbjct: 192 IIEKINREQGITMLLVEQNANYALKAANYGYIMESGKIVLDGTKAQLLNNEDVKEFYLG 250 Lambda K H 0.320 0.139 0.393 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: 196 Number of extensions: 7 Number of successful extensions: 4 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: 240 Length of database: 272 Length adjustment: 24 Effective length of query: 216 Effective length of database: 248 Effective search space: 53568 Effective search space used: 53568 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: 47 (22.7 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