Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 369 bits (948), Expect = e-107 Identities = 199/362 (54%), Positives = 252/362 (69%), Gaps = 7/362 (1%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63 LK+ N+ K G I++ + LE++ EFVVFVGPSGCGKSTLLRLIAGL+ + G + +D Sbjct: 4 LKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLID 63 Query: 64 GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILEL 123 GR + ++ P +R + MVFQ+YALYPHMSV N+SF L LA KA + ++V + A+IL+L Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQL 123 Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKEL 183 +L+RKP++LSGGQRQRVA+GRA+ R P I LFDEPLSNLDA+LRVQMR E+ RLH L Sbjct: 124 DKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRL 183 Query: 184 QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLK 243 +TMIYVTHDQVEAMT+ADK+VVLNGG+IEQVGSP +LY PA+ FVAGFLG+PKM FL Sbjct: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFLP 243 Query: 244 GKITRVDSQGCEVQLDAGT--RVSLPLGGRHLSVGSAVTLGIRPEHLEL-AKPGDCALQV 300 R+ S G Q+D+ LP HL+VGS +TLGIRPEH+ L A G + V Sbjct: 244 ---ARLHSPGETSQIDSPLLGMTPLPFDSAHLAVGSPLTLGIRPEHMSLKAAQGSAGVGV 300 Query: 301 TADVS-ERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVAL 359 V E LGS+T+ H+ + E L R + R G+ + L L HLFDADG AL Sbjct: 301 VGVVGVEYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDADGTAL 360 Query: 360 TR 361 R Sbjct: 361 RR 362 Lambda K H 0.320 0.137 0.389 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: 429 Number of extensions: 14 Number of successful extensions: 3 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: 367 Length of database: 384 Length adjustment: 30 Effective length of query: 337 Effective length of database: 354 Effective search space: 119298 Effective search space used: 119298 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