Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_1641 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1641 Length = 248 Score = 415 bits (1067), Expect = e-121 Identities = 211/251 (84%), Positives = 227/251 (90%), Gaps = 3/251 (1%) Query: 1 MQTYKKFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA 60 MQ YKK LAAAV+L FSA A AA+ LKMGIEAAYPPFNNKDASG VVGFDKDIGDALCA Sbjct: 1 MQNYKKIFLAAAVTLAFSAGA-AAETLKMGIEAAYPPFNNKDASGNVVGFDKDIGDALCA 59 Query: 61 KMKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKS 120 KMKVEC VVTSDWDGIIPALNAKKFDFLISS+SIT+ERKQAVDFT PYYSNKLQFIAPK+ Sbjct: 60 KMKVECTVVTSDWDGIIPALNAKKFDFLISSMSITDERKQAVDFTAPYYSNKLQFIAPKN 119 Query: 121 AEFKTDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILA 180 +FKTDK SL+GKVIGAQRATLAGTWLED + + KLYDTQENAYLDLTSGR+D ILA Sbjct: 120 VDFKTDKASLQGKVIGAQRATLAGTWLEDNM-EGVEIKLYDTQENAYLDLTSGRLDGILA 178 Query: 181 DKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKK 240 DKYVNY+WLK++AGRAYEFKGDPV ESDKIGIAVRK D +R KL+AALKEIVADGTYKK Sbjct: 179 DKYVNYEWLKSDAGRAYEFKGDPVEESDKIGIAVRKND-PIREKLDAALKEIVADGTYKK 237 Query: 241 INDKYFPFNIY 251 INDKYFPF+IY Sbjct: 238 INDKYFPFSIY 248 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: 311 Number of extensions: 14 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: 251 Length of database: 248 Length adjustment: 24 Effective length of query: 227 Effective length of database: 224 Effective search space: 50848 Effective search space used: 50848 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