Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__azobra:AZOBR_RS08665 Length = 367 Score = 378 bits (970), Expect = e-109 Identities = 186/361 (51%), Positives = 250/361 (69%), Gaps = 7/361 (1%) Query: 8 PDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRA 67 PD PP +++G VAW+R N+F++W N LLT+ +L++ +PPL+ W I AN GT Sbjct: 11 PDERPPANTVGPVAWLRNNLFNTWYNALLTILIAWLLFKAIPPLLDWLIFSANSFGTPPQ 70 Query: 68 DCTKEG-ACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRF--PRKAIY 124 C +EG ACW F+ ++ M+G +P D +WR +T+ + + V RF P A+ Sbjct: 71 VCRQEGGACWTFVSEKLRFVMFGTFPYDEQWRPLITIVIIIALVLASCDRRFWKPWLALV 130 Query: 125 GLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRR 184 ++ L + W GGV GL V + WGGL LTL+++ VG+ A P ++LALGRR Sbjct: 131 WIAGLTAVGVLMW----GGVLGLTYVENTLWGGLPLTLMLSVVGLSVAFPASVLLALGRR 186 Query: 185 SNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAY 244 S +PAIRV+ VT+IE RGVPLI++LFM+SVM PLFLP G+NFDKLLRA I I+F +AY Sbjct: 187 SQLPAIRVISVTYIELIRGVPLISLLFMASVMFPLFLPTGVNFDKLLRAQIAFIMFAAAY 246 Query: 245 IAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSL 304 +AE +RGGLQAIPKGQYEAA A+GL YW++MG +ILPQAL + IP +VNTFI+ FKDTSL Sbjct: 247 MAEAIRGGLQAIPKGQYEAADALGLNYWQAMGKIILPQALAISIPPLVNTFISFFKDTSL 306 Query: 305 VIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHK 364 VIIIGL+DLL + K A +DP W G E Y+F +++W+FC+ MS+YS LER L GH+ Sbjct: 307 VIIIGLYDLLGTAKAALSDPAWRGFYREAYLFIGVIYWVFCYSMSKYSQKLERDLRRGHR 366 Query: 365 R 365 R Sbjct: 367 R 367 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: 618 Number of extensions: 42 Number of successful extensions: 4 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: 367 Length adjustment: 30 Effective length of query: 335 Effective length of database: 337 Effective search space: 112895 Effective search space used: 112895 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: 49 (23.5 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