Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate PP_0282 PP_0282 L-arginine ABC transporter - periplasmic binding subunit
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Putida:PP_0282 Length = 250 Score = 413 bits (1062), Expect = e-120 Identities = 204/250 (81%), Positives = 226/250 (90%), Gaps = 1/250 (0%) Query: 1 MQTYKKFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA 60 M TYKKFLLAAA +LV SANAMAA+KL+MGIEAAYPPFNNKDASG VVGFDKDIGDALCA Sbjct: 1 MHTYKKFLLAAAATLVMSANAMAAEKLRMGIEAAYPPFNNKDASGNVVGFDKDIGDALCA 60 Query: 61 KMKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKS 120 KMKVEC VVTSDWDGIIPALNAKKFDFL+SSLSIT+ERKQAVDFT+PYYSNKLQFIAPK+ Sbjct: 61 KMKVECSVVTSDWDGIIPALNAKKFDFLVSSLSITDERKQAVDFTNPYYSNKLQFIAPKN 120 Query: 121 AEFKTDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILA 180 +FKTDK+SLKGKVIG QRATLAGT+LED D+ KLYDTQENAYLDL SGR+D ILA Sbjct: 121 VDFKTDKESLKGKVIGTQRATLAGTYLEDNY-PDVEIKLYDTQENAYLDLVSGRIDGILA 179 Query: 181 DKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKK 240 DKYV Y+WLK++ G +EFKG+PV++SDKIGIAVRKGD +LR+ LN AL EI ADGTYKK Sbjct: 180 DKYVQYEWLKSKDGSNFEFKGEPVMDSDKIGIAVRKGDTKLRDDLNKALAEIKADGTYKK 239 Query: 241 INDKYFPFNI 250 INDKYFPF+I Sbjct: 240 INDKYFPFSI 249 Lambda K H 0.316 0.133 0.381 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: 315 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: 251 Length of database: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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