Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate HSERO_RS23035 HSERO_RS23035 ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS23035 Length = 277 Score = 80.9 bits (198), Expect = 4e-20 Identities = 57/183 (31%), Positives = 95/183 (51%), Gaps = 9/183 (4%) Query: 180 LVVILAIALVLFVSWLAQRQRSPRDW--RWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRG 237 L VI+ +A+ +FV++ + SP W R I VV L Q+ L G Sbjct: 30 LAVIVGVAIGIFVAFA---KNSPHRWLARGCSAYIEVVRNTPFLVQIFL---LYFGLASL 83 Query: 238 GLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQ 297 G+R+ F A +L ++ A+ EIIR G+ SVP GQ EAA LGL+ + W +++ Sbjct: 84 GIRMPT-FAAAVLAMIINIAAYAAEIIRAGLDSVPRGQIEAAQCLGLSVWRIRWHVMLQP 142 Query: 298 ALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAIN 357 A+ + P+L SQ++ + S++A + +L A A T + T R +E +L++ YL + Sbjct: 143 AIERVYPALTSQFLLMMQASAMASQISAEELTAIANTVQSDTFRSLETYLVVAALYLVLA 202 Query: 358 AVI 360 ++ Sbjct: 203 ILV 205 Score = 38.9 bits (89), Expect = 2e-07 Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 4/49 (8%) Query: 99 LTTVIGTLAGV-AAFSENWLLRQLSRG---YVAVVRNTPLLLQLIVWYF 143 L ++G G+ AF++N R L+RG Y+ VVRNTP L+Q+ + YF Sbjct: 30 LAVIVGVAIGIFVAFAKNSPHRWLARGCSAYIEVVRNTPFLVQIFLLYF 78 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: 249 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 277 Length adjustment: 28 Effective length of query: 349 Effective length of database: 249 Effective search space: 86901 Effective search space used: 86901 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