Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 182 bits (463), Expect = 1e-50 Identities = 109/262 (41%), Positives = 158/262 (60%), Gaps = 14/262 (5%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 + +L++ + M+F GL A+ND +RG I LIGPNG+GK+T+ N +TG Y PT G + Sbjct: 389 EDILQLRGILMQFSGLKALNDVDLTVQRGTIHGLIGPNGSGKSTMMNVLTGIYVPTAGTL 448 Query: 72 TFNQKS--GKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129 + S GK L + +ARTFQN++LF +T LEN+LV H+ + Sbjct: 449 EYRGASLAGKTSAQIAL--------SGIARTFQNVQLFGEMTALENVLVGLHHTFN--AN 498 Query: 130 YTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189 +GL+ Y+RE A E A L L + A + A +LPYG QR LEIARA+ Sbjct: 499 LADVGLMS-SRYRREERAARERAFGMLRFVGLDNVAAEEARNLPYGKQRLLEIARALALD 557 Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249 P+LL LDEPAAGL + L A+++ +R + G +++LIEH M VVM + D V VL++GQ Sbjct: 558 PQLLLLDEPAAGLTAPDIKELVAIIRKVR-DHGITVVLIEHHMDVVMSVCDRVSVLDFGQ 616 Query: 250 KISDGTPDHVKNDPRVIAAYLG 271 KI++G P ++++ +VI AYLG Sbjct: 617 KIAEGKPADIQSNEKVIEAYLG 638 Lambda K H 0.318 0.136 0.386 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: 394 Number of extensions: 22 Number of successful extensions: 4 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: 292 Length of database: 646 Length adjustment: 32 Effective length of query: 260 Effective length of database: 614 Effective search space: 159640 Effective search space used: 159640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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