Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_043917488.1 jaqu_RS03105 urea ABC transporter permease subunit UrtB
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000877395.1:WP_043917488.1 Length = 652 Score = 134 bits (336), Expect = 7e-36 Identities = 91/294 (30%), Positives = 155/294 (52%), Gaps = 22/294 (7%) Query: 9 INGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVPLA 68 ++ LSL +IY L AIG + +G++G+IN AHGE MIGA+ + L + L+ Sbjct: 363 LDALSLASIYFLAAIGLAVTFGVMGVINMAHGEFIMIGAYTGYVVQLFVPD-----YTLS 417 Query: 69 LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGARSKP 128 L++ L + + G +ER+ R L P L L++ G+S+ LQ + + G +++P Sbjct: 418 LVIALPLAFCTAGLAGVALERLVIRHLMHRP-LETLLATFGISVALQQIAKNVFGTQARP 476 Query: 129 L-QPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDKKMA 187 L P + +SVS++R+A V+ + + ++ RT LG RA Q+ MA Sbjct: 477 LTSPDWLAGSWQISEVISVSWIRVAIFVLALIFLAAIVYVLRRTRLGLEVRAVTQNPGMA 536 Query: 188 GLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGIGSL 247 +G++ R+ LTF +G+ +A VAG+ + L Y + +G V++F V+GG+GS+ Sbjct: 537 ASMGIDPGRIGMLTFGLGSGIAGVAGVAIGL-YAQVTSEMGAGYIVQSFMTVVVGGVGSV 595 Query: 248 PGAMLGGVVIGLIEAFWSGYMGSEW----KDVATFTILVLVLI----FRPTGLL 293 G + G +IG ++ G EW +A T ++L +I FRP G++ Sbjct: 596 FGTLAGAGLIGGLQ------KGIEWLNPSNTLAAQTFMILFIIAFIQFRPRGIV 643 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: 423 Number of extensions: 26 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: 301 Length of database: 652 Length adjustment: 32 Effective length of query: 269 Effective length of database: 620 Effective search space: 166780 Effective search space used: 166780 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: 51 (24.3 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