Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 273 bits (699), Expect = 5e-78 Identities = 152/377 (40%), Positives = 227/377 (60%), Gaps = 15/377 (3%) Query: 10 PFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESA 69 PFWRD ++Q+L++ V ++++ N NL+ RG++ F +LD++AGF IG+S Sbjct: 15 PFWRDRAKRALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQSL 74 Query: 70 IAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVV 129 I Y + +Y R VVGL+N+L V A+G+I T+IG + G+A S NWL+ +L+ GY+ + Sbjct: 75 IEYSSQSTYGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIEIF 134 Query: 130 RNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGWL------VVI 183 RN PLLLQ+ WYF +L ++PAA+ + ++L+ +G+YLP P V+ Sbjct: 135 RNIPLLLQIFFWYFAVLRAMPAARDSYSLGEVIFLNVRGLYLPEPLFESGFGLIPLTFVV 194 Query: 184 LAIALVLFVSWLAQR-----QRSPRDWRWLYGAIAVVTVLMLLT--QLSWP-QQLQPGQI 235 +A + V W +R +R P W L + + ++++ T ++W +L+ Sbjct: 195 AIVASIALVIWNKRRHEATGKRLPAGWISLALILGLPMLVLVATGVPVTWDVPELRGFNF 254 Query: 236 RGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVV 295 RGG+ + EF AL L L YT +FI EI+R GI ++P GQ EAA AL L + L +VV Sbjct: 255 RGGITIIPEFLALWLALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVV 314 Query: 296 PQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYL 354 PQALRVI+P L SQY+ KNSSLA A+GYPDL + A TTLNQTG+ +EV + M YL Sbjct: 315 PQALRVIIPPLTSQYLNLIKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVISMTMAVYL 374 Query: 355 AINAVISAGMNGLQQRL 371 I+ ++S MN R+ Sbjct: 375 IISLLVSMFMNWFNARV 391 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: 398 Number of extensions: 14 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: 396 Length adjustment: 30 Effective length of query: 347 Effective length of database: 366 Effective search space: 127002 Effective search space used: 127002 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