Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 118 bits (295), Expect = 2e-31 Identities = 75/222 (33%), Positives = 125/222 (56%), Gaps = 28/222 (12%) Query: 144 VFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRG 203 +F L AV QW TL ++ + +G +G+V+AL R S++ A+R+ +I+ ++G Sbjct: 10 LFLLSAV---QW-----TLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQG 61 Query: 204 VPLITVLFM----SSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKG 259 PL+ LF+ ++VM G++ + A +G+ L SA++ E+ RG +QA+P+G Sbjct: 62 TPLLMQLFLVFFGATVM-------GLDLNPWAAAALGLTLNASAFLGEIWRGCIQAVPRG 114 Query: 260 QYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNS--- 316 Q+EAA+A+GL Y M VILPQA+K+ +P V + L K TSL IIG +L + Sbjct: 115 QWEAASALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQI 174 Query: 317 VKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERK 358 V A P + + A+++++ C+ +S S LER+ Sbjct: 175 VNNATFQPFLV------FGIVAVLYFLMCWPLSLLSARLERR 210 Lambda K H 0.330 0.144 0.469 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: 263 Number of extensions: 17 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: 365 Length of database: 216 Length adjustment: 26 Effective length of query: 339 Effective length of database: 190 Effective search space: 64410 Effective search space used: 64410 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 (21.9 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