Align ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 639 bits (1648), Expect = 0.0 Identities = 326/384 (84%), Positives = 350/384 (91%), Gaps = 3/384 (0%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 +IKLKLDNVNKQLGG RILRDVSLEI+AGEFVVFVGPSGCGKSTLLRLIAGLDSIC GDL Sbjct: 1 VIKLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKT+K SLRERVLKTAQI Sbjct: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQLDKLLQRKP+ELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH Sbjct: 121 LQLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 RLGSTMIYVTHDQVEAMTLADKIVVLNGGR+EQVGSPRELYE PASRFVAGFLGSP+MN Sbjct: 181 GRLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAG--- 297 FL ARL +PGETS +D+ + G+T LPFDS++LA G+PL+LGIRPEH+SLKAA G+AG Sbjct: 241 FLPARLHSPGETSQIDSPLLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKAAQGSAGVGV 300 Query: 298 VVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357 V V VEYLGSETYVHLE+G+DEPLICRCEV+AGW+ GDRVEL L ++HLFDADG AL Sbjct: 301 VGVVGVEYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTAL 360 Query: 358 SRHPHAIETLPAGVPLRSARASAL 381 RHP IE LP VP RS +A AL Sbjct: 361 RRHPAVIEVLPEDVPQRSPKAGAL 384 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: 550 Number of extensions: 9 Number of successful extensions: 2 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: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 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