Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate YP_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_000185905.1:YP_004141766.1 Length = 387 Score = 195 bits (495), Expect = 2e-54 Identities = 125/371 (33%), Positives = 205/371 (55%), Gaps = 29/371 (7%) Query: 24 LLVLLVVGLGAIWLVDNLVY---NLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYAR 80 LL +L VG A ++ +V NL+ +G++ FD+L +S G+++ S + D Y Sbjct: 14 LLQVLYVGSIAAMVLAGIVIARRNLADQGITSGFDFLFKSTGWDVNFSLLPATANDPYWW 73 Query: 81 ALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIV 140 ++G++N+L + ++GLIL T++GT+ G+A S N L R L R YV + RN PL+LQ+ Sbjct: 74 YFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYVDIFRNIPLILQVFF 133 Query: 141 WYFPILLSLP---AAQQPWHWLGSLYLSKQGIYLPWPQTPGWL---VVILAIALVLFVSW 194 WY I+ LP +A + W +L L+ +G+Y+P+P + IA ++ +W Sbjct: 134 WY-AIITHLPTPRSAHEAWGFL----LTSRGLYIPFPNVGSAAFAAATVAVIAAIVLPAW 188 Query: 195 LAQR--------QRSPRDWRWLYGAIAVVTVLMLLTQL------SWPQQLQPGQIRGGLR 240 L + QR + A+A T+++ L +L +P LQ +RGGLR Sbjct: 189 LGRTSLLAQPIGQRRTIQFAAAAAALACATIILALGRLPDTPLLDFPA-LQGLNLRGGLR 247 Query: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300 + EF L + + Y G++I EI+RGG SV GQ EAA +LGL+ + + +P ALR Sbjct: 248 IPPEFATLAIAIAIYGGSYIAEIVRGGFKSVGTGQVEAALSLGLSPWRVFTLVRLPLALR 307 Query: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360 ++P L +QYV K +++ IAVG+ D + T+N +G+ +E ILM +LAIN + Sbjct: 308 AMLPILANQYVWLMKATTMGIAVGFTDFFMIVALTINHSGQTLEAIGILMAGFLAINLSL 367 Query: 361 SAGMNGLQQRL 371 +A N + + + Sbjct: 368 AAVFNRINKAI 378 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: 381 Number of extensions: 16 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: 377 Length of database: 387 Length adjustment: 30 Effective length of query: 347 Effective length of database: 357 Effective search space: 123879 Effective search space used: 123879 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