Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00160 BPHYT_RS00160 ABC transporter substrate-binding protein
Query= reanno::BFirm:BPHYT_RS07735 (264 letters) >FitnessBrowser__BFirm:BPHYT_RS00160 Length = 262 Score = 306 bits (785), Expect = 2e-88 Identities = 152/256 (59%), Positives = 186/256 (72%), Gaps = 3/256 (1%) Query: 1 MKMNWRNIAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVG 60 MK+ +A FA+ +A++G +AA ++ FG+EA Y PFESK P+GELQG DIDVG Sbjct: 1 MKLLKPLLALACAFASLAASSGASAADTLR---FGLEAQYPPFESKGPNGELQGLDIDVG 57 Query: 61 NAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQM 120 NAVC C WVE SFDGLIPALQ RKF+AINS M TD RRQA+DFT +Y +P Q+ Sbjct: 58 NAVCVAAHMTCKWVETSFDGLIPALQGRKFDAINSAMNATDARRQAIDFTTVVYRVPTQL 117 Query: 121 IAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGR 180 IAK+ SGLLPTPASLKGK VGVLQ +IQETYAKA W AGV VVPYQ Q+Q+Y DL +GR Sbjct: 118 IAKRDSGLLPTPASLKGKRVGVLQASIQETYAKAHWESAGVTVVPYQDQNQVYTDLVAGR 177 Query: 181 LDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQAL 240 LDA A A GFL KP G G+ F G V D+K+LG+G+ +G+RKGD AL+D LN A+ Sbjct: 178 LDATLVLAPAGQTGFLSKPSGEGYAFVGEPVRDDKILGSGIAYGIRKGDTALRDRLNAAI 237 Query: 241 KELKADGTIDRFAAKY 256 +++ADGT+ AAKY Sbjct: 238 AKVQADGTVKTLAAKY 253 Lambda K H 0.317 0.133 0.383 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: 230 Number of extensions: 5 Number of successful extensions: 1 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: 264 Length of database: 262 Length adjustment: 25 Effective length of query: 239 Effective length of database: 237 Effective search space: 56643 Effective search space used: 56643 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 (21.7 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