Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate PfGW456L13_1699 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1699 Length = 393 Score = 262 bits (669), Expect = 1e-74 Identities = 152/375 (40%), Positives = 220/375 (58%), Gaps = 19/375 (5%) Query: 14 DERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYR 73 D R+ WV+Q++ ++ V +L DN NL RG++ FD+L++SAGF I + I Y Sbjct: 16 DPRVRAWVFQIITIIAVVSLGWYLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYT 75 Query: 74 TADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP 133 AD+YAR V+GL+N+L V IG+IL T++G + GVA S+NW++ +L+ YV V RN P Sbjct: 76 EADTYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIP 135 Query: 134 LLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP--------WPQTPGWLVVILA 185 LLQ++ WYF + L++P + ++ + ++S +G+ +P WP VV+ Sbjct: 136 PLLQILFWYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMPAALMADGFWPFMTS--VVVAI 193 Query: 186 IALVLFVSWLAQRQRS---PRDWRW----LYGAIAVVTVLMLLTQLSWPQ-QLQPGQIRG 237 +A+VL W +R + P W ++ I + L+ + W +LQ G Sbjct: 194 VAIVLMSRWATKRFEATGVPFHKFWVGLAMFLVIPALCALIFGAPVHWEMPKLQGFNFVG 253 Query: 238 GLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQ 297 G L E AL L L YT AFI EI+R GI SV GQ EAA +LGL TL ++++PQ Sbjct: 254 GWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAAHSLGLRNGPTLRKVIIPQ 313 Query: 298 ALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAI 356 ALRVI+P L SQY+ AKNSSLA +GYP++ + A T LNQTG+ +EV I M YLAI Sbjct: 314 ALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAI 373 Query: 357 NAVISAGMNGLQQRL 371 + IS MN +R+ Sbjct: 374 SISISLLMNWYNKRI 388 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: 393 Number of extensions: 11 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: 393 Length adjustment: 30 Effective length of query: 347 Effective length of database: 363 Effective search space: 125961 Effective search space used: 125961 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 17 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