Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_084933742.1 HA51_RS07075 urea ABC transporter permease subunit UrtB
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_002095475.1:WP_084933742.1 Length = 521 Score = 121 bits (304), Expect = 3e-32 Identities = 86/288 (29%), Positives = 143/288 (49%), Gaps = 5/288 (1%) Query: 7 QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVP 66 Q GLSLG+I L A+G + YG++G+IN AHGE+ M+GA+ W+ Sbjct: 228 QAFTGLSLGSILLLAALGLAITYGLLGVINMAHGEMLMLGAYATWFVQNLFQQFAPQWLA 287 Query: 67 LALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGARS 126 L+ L + L TA G +ER R L P L L++ G+S+ L V++L GA++ Sbjct: 288 WYPLLALPVAFLVTAGIGMLLERTIIRHLYGRP-LETLLATWGISLMLIQLVRMLFGAQN 346 Query: 127 KPL--QPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDK 184 + L G ++ V + Y R+A I+ A++ L+ +T LG + RA Q++ Sbjct: 347 LEVANPSWLSGGWQVLPNLV-LPYNRIAVILFVFAVLGLTWLLLNKTRLGLSVRAVTQNR 405 Query: 185 KMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGI 244 MA GV R+ L F +G+ +A + G + L G + +G + +F VLGG+ Sbjct: 406 AMADCCGVPTGRIDMLAFGLGSGIAGLGG-VALSQLGNVGPELGQGYIIDSFLVVVLGGV 464 Query: 245 GSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292 G L G ++ +G++ +G+ + +++L + RP GL Sbjct: 465 GQLAGTVVAAFGLGILNKVLEPQIGAVLGKILILVLIILFIQKRPQGL 512 Lambda K H 0.329 0.144 0.425 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: 359 Number of extensions: 24 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: 301 Length of database: 521 Length adjustment: 31 Effective length of query: 270 Effective length of database: 490 Effective search space: 132300 Effective search space used: 132300 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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