Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Putida:PP_1298 Length = 392 Score = 259 bits (661), Expect = 1e-73 Identities = 158/374 (42%), Positives = 221/374 (59%), Gaps = 17/374 (4%) Query: 14 DERLWRWVWQLL-VLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAY 72 D R+ W++Q+L ++ VVGLG +L N NL RG++ FD+LD+SAGF I + I Y Sbjct: 15 DPRVRAWLFQILTIVFVVGLGW-YLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLIPY 73 Query: 73 RTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNT 132 +DSYAR V+GL+N+L V IG+IL T++G + GVA S NW++ +L+ YV RN Sbjct: 74 VESDSYARVFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFRNI 133 Query: 133 PLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP--------WPQTPGWLVVIL 184 P LLQ++ WYF + L+LP + + ++S +G+ +P WP + I Sbjct: 134 PPLLQILFWYFAVFLTLPGPRGSINIEDMFFISNRGLNMPGASIADGFWPFVVALALAIA 193 Query: 185 AIAL-VLFVSWLAQRQRSPRDWRW----LYGAIAVVTVLMLLTQLSWPQ-QLQPGQIRGG 238 AIAL V + + P W L+ AI ++VL+ + ++W QL+ GG Sbjct: 194 AIALMVRYANKRFNETGVPFHKFWAGLLLFIAIPSLSVLLFGSPVTWDMPQLKGFNFVGG 253 Query: 239 LRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQA 298 L E AL L L YT AFI EI+R GI SV GQ EAA +LGL TL ++++PQA Sbjct: 254 WVLIPELLALTLALTIYTAAFIAEIVRSGIRSVSHGQTEAARSLGLREGPTLRKVIIPQA 313 Query: 299 LRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAIN 357 LRVI+P L SQY+ AKNSSLA +GYP++ + A T LNQTG+ +EV I M YLAI+ Sbjct: 314 LRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAIS 373 Query: 358 AVISAGMNGLQQRL 371 IS MN +R+ Sbjct: 374 ISISLLMNWYNKRI 387 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: 387 Number of extensions: 12 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: 392 Length adjustment: 30 Effective length of query: 347 Effective length of database: 362 Effective search space: 125614 Effective search space used: 125614 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