Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS08920 Length = 655 Score = 244 bits (622), Expect = 4e-69 Identities = 124/250 (49%), Positives = 170/250 (68%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +LKV I +FGGL+AL+ V + +++G V+GLIGPNG+GK+T NV+TG+Y P G E Sbjct: 392 LLKVNQILMQFGGLKALNRVDLDVRKGTVHGLIGPNGSGKSTMMNVLTGIYRPTDGVVEY 451 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 G+P +A G+ARTFQN++LF EMTA ENV+VG H S + + T + Sbjct: 452 DGRPISGNVPSAIALGGVARTFQNVQLFGEMTATENVLVGLHHTFNSNVVDVMANTPRYV 511 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 EE A +RA +L++VG+ A+ +AR L YG QR LEI RAL +P L+ LDEPAAG+ Sbjct: 512 REEQAARERAAAILEFVGLANLANEEARNLPYGKQRLLEIGRALGLNPSLLLLDEPAAGL 571 Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 A + +L +I +IR TI+LIEH + +VM +CD VTVLD+G++IAEG PA+VQ + Sbjct: 572 TAPDIKELVAIIRKIREAGITIILIEHHMDVVMSICDTVTVLDFGQKIAEGKPAQVQADP 631 Query: 249 KVIEAYLGTG 258 KVIEAYLG+G Sbjct: 632 KVIEAYLGSG 641 Lambda K H 0.319 0.137 0.384 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: 441 Number of extensions: 20 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: 1 Length of query: 260 Length of database: 655 Length adjustment: 31 Effective length of query: 229 Effective length of database: 624 Effective search space: 142896 Effective search space used: 142896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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