Align ABC transporter (characterized, see rationale)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 653 bits (1684), Expect = 0.0 Identities = 332/381 (87%), Positives = 354/381 (92%), Gaps = 2/381 (0%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 +IKLKLDNVNKQLGG RILRDVSLEI+AGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL Sbjct: 1 VIKLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKT+KTSLRERVLKTAQI Sbjct: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQLDKLLQRKP+ELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH Sbjct: 121 LQLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLGSTMIYVTHDQVEAMTLADKIVVLNGGR+EQVGSPRELYERPASRFVAGFLGSPRMN Sbjct: 181 GRLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVVV 300 FL+A L TPGETS V++LV G+TSLPFDSS LAA T LSLGIRPEH++LKAA GTAG+ V Sbjct: 241 FLAAFLHTPGETSQVESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIALKAAQGTAGIAV 300 Query: 301 TAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSRH 360 + VEYLGSETYVHL+TGQD+P++CRCEV+AGW+ GDRVEL LD+DNLH+FD G AL R Sbjct: 301 SGVEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFDTHGTALQR- 359 Query: 361 PHAIETLPAGVPLRSARASAL 381 HAI+ LP V LR A A AL Sbjct: 360 -HAIDRLPDDVALRPAHAGAL 379 Lambda K H 0.320 0.137 0.394 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: 536 Number of extensions: 10 Number of successful extensions: 1 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: 381 Length of database: 379 Length adjustment: 30 Effective length of query: 351 Effective length of database: 349 Effective search space: 122499 Effective search space used: 122499 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 (21.8 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