Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate YP_004143815.1 Mesci_4656 polar amino acid ABC transporter inner membrane subunit
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_000185905.1:YP_004143815.1 Length = 395 Score = 253 bits (645), Expect = 8e-72 Identities = 147/380 (38%), Positives = 220/380 (57%), Gaps = 18/380 (4%) Query: 8 QGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGE 67 +G F D ++ +Q+LV++++ G W+ N++ NL++ ++ F +L AGF+I E Sbjct: 13 RGSFINDPKIRGIFFQVLVVVLLVAGVWWIAHNVIDNLTRLRIASGFGFLKGRAGFDISE 72 Query: 68 SAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVA 127 SAIAY + +Y RA++VGL+N++ V +G+I T+IG + G+ S+NWL+R++ YV Sbjct: 73 SAIAYSSDSTYGRAILVGLLNTVIVAIVGIITATIIGFVIGIGRLSKNWLIRKICTVYVE 132 Query: 128 VVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP---WPQTPGWLVVIL 184 V RN P LL + WY +L LPA + + +L+++G Y P W WL+ + Sbjct: 133 VFRNIPPLLVIFFWYSGVLAVLPAPRDSINLPFGSFLNQRGFYFPRAVWGDG-SWLIFV- 190 Query: 185 AIALVLFVSWLAQRQRSPRDWR--------WLYGAIAVVTVLMLLTQLSWPQQLQ-PGQ- 234 A+ + + ++W R+ R W A+ V L+ +P P Q Sbjct: 191 ALLVGIAMAWFVARKARQRQMATGQQFPVFWTSAALIVGLPLLAYALSGFPLSFDYPKQS 250 Query: 235 ---IRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLW 291 + GG ++ EF +L L L YT AFI EI+R GI V AGQ EAA ALGL L Sbjct: 251 TFNLTGGFQVRPEFLSLYLALSCYTAAFIAEIVRAGIRGVSAGQTEAAGALGLRSGSILR 310 Query: 292 QIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILML 351 +VVPQA+R+++P L SQY+ KNSSLAIA+GYPDL ATA T LNQTG+ VE +I+M+ Sbjct: 311 LVVVPQAMRIVIPPLTSQYLNLTKNSSLAIAIGYPDLTATAGTVLNQTGQAVEGVVIMMV 370 Query: 352 TYLAINAVISAGMNGLQQRL 371 YLAI+ + S MN ++ Sbjct: 371 IYLAISLLTSLVMNWFNAKM 390 Lambda K H 0.326 0.140 0.445 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: 443 Number of extensions: 22 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: 377 Length of database: 395 Length adjustment: 30 Effective length of query: 347 Effective length of database: 365 Effective search space: 126655 Effective search space used: 126655 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 (21.7 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