Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate 8500827 DvMF_1568 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__Miya:8500827 Length = 224 Score = 126 bits (316), Expect = 4e-34 Identities = 74/233 (31%), Positives = 135/233 (57%), Gaps = 12/233 (5%) Query: 2 IFDYNVIWEAL-PLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTY 60 +FD + + + + P GL ++KL+ S +FGLL + +G++RV +P + A YT Sbjct: 1 MFDVDFLVDRVFPSLNAGLWMSVKLIVPSAVFGLLFGVIIGIVRVFGKPWMQRIANAYTA 60 Query: 61 VIRGTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120 + RG P+LVQLF++Y+GL +L P+ +S L F + ++AY +E + G+L Sbjct: 61 LFRGVPLLVQLFILYFGLPNIGI----YLEPYAASV-----LGFILCSAAYNSEYVRGAL 111 Query: 121 RATPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180 + G++ AA+A+G S + I++P A+RRALP NE++ +++ +SLA ++T I++ Sbjct: 112 LSIRQGQLRAAQALGFSTMQTLVSIVVPQAVRRALPGCGNEIVYLIKYSSLAYVITCIEL 171 Query: 181 TGAARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRW--LGYLAPRK 231 TG A+ + ++ + E ++ G +YL + + L E R+ G+ PR+ Sbjct: 172 TGEAKVLASRTFRFTEVFLVVGAYYLFLVTVASWLLHKLEERFHIPGFGRPRQ 224 Lambda K H 0.329 0.139 0.427 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: 137 Number of extensions: 4 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: 232 Length of database: 224 Length adjustment: 23 Effective length of query: 209 Effective length of database: 201 Effective search space: 42009 Effective search space used: 42009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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