Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 87.8 bits (216), Expect = 3e-22 Identities = 65/199 (32%), Positives = 99/199 (49%), Gaps = 6/199 (3%) Query: 175 QTPGWLVVIL-AIALVLFVSWLAQRQRSPRDWRWLYGA-IAVVTVLMLLTQLSWPQQLQP 232 +T WL +I ++ LVL R RW I V+ LL Q+ + P Sbjct: 57 RTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFVYFALP 116 Query: 233 GQIRGGLRLSL-EFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLW 291 + G L+L +F A +L L GA+ E IR G+L+VP GQ EAA ALGL R + Sbjct: 117 VLVPG---LNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGLGRMHVFF 173 Query: 292 QIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILML 351 +V PQA ++ +P L S +V K+SSLA A+G +L + T +P+ + + Sbjct: 174 DVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSATFQPIATLSTVAI 233 Query: 352 TYLAINAVISAGMNGLQQR 370 TYL + +++ N ++ R Sbjct: 234 TYLLLTTLVTQISNAVEYR 252 Score = 37.7 bits (86), Expect = 4e-07 Identities = 24/79 (30%), Positives = 42/79 (53%) Query: 77 SYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLL 136 S A+A G +L + I + V+GT A +A + ++R + Y+ V+R TPLL+ Sbjct: 47 SNAQAFSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLV 106 Query: 137 QLIVWYFPILLSLPAAQQP 155 Q++ YF + + +P P Sbjct: 107 QILFVYFALPVLVPGLNLP 125 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: 252 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 260 Length adjustment: 27 Effective length of query: 350 Effective length of database: 233 Effective search space: 81550 Effective search space used: 81550 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: 48 (23.1 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