Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Pf1N1B4_916 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_916 Length = 375 Score = 260 bits (664), Expect = 5e-74 Identities = 153/370 (41%), Positives = 221/370 (59%), Gaps = 21/370 (5%) Query: 20 WVWQLL-VLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSY 78 W++Q++ V+ VVG+G +L DN NL RG++ FD+L++SAGF I + I Y +DSY Sbjct: 4 WLFQIITVVAVVGMGW-YLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYTESDSY 62 Query: 79 ARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQL 138 AR V+GL+N+L V IG+IL T++G + GVA S+NW++ +L+ YV V RN P LLQ+ Sbjct: 63 ARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIPPLLQI 122 Query: 139 IVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP--------WPQTPGWLVVILAIALVL 190 + WYF + L++P + ++ + ++S +G+ +P WP +V+ +A+VL Sbjct: 123 LFWYFAVFLTMPGPRNSHNFGDTFFVSSRGLNMPAALAADGFWPFVAS--IVVAIVAIVL 180 Query: 191 FVSWLAQRQRS---PRDWRW----LYGAIAVVTVLMLLTQLSWPQ-QLQPGQIRGGLRLS 242 W +R + P W L+ I + L+ L W +L+ GG L Sbjct: 181 MSRWATKRFEATGVPFHKFWAGLALFLVIPALCALIFGAPLHWEMPELKGFNFVGGWVLI 240 Query: 243 LEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVI 302 E AL L L YT AFI EI+R GI SV GQ EAA +LGL TL ++++PQALRVI Sbjct: 241 PELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAAHSLGLRNGPTLRKVIIPQALRVI 300 Query: 303 VPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAINAVIS 361 +P L SQY+ AKNSSLA +GYP++ + A T LNQTG+ +EV I M YLAI+ IS Sbjct: 301 IPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISIS 360 Query: 362 AGMNGLQQRL 371 MN +R+ Sbjct: 361 LLMNWYNKRI 370 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: 376 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: 375 Length adjustment: 30 Effective length of query: 347 Effective length of database: 345 Effective search space: 119715 Effective search space used: 119715 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