Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 313 bits (802), Expect = 5e-90 Identities = 173/362 (47%), Positives = 223/362 (61%), Gaps = 10/362 (2%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 GG +L + L I GEFVV +GPSGCGKST+LR+IAGL+ I GG L I G VNDL R Sbjct: 14 GGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPR 73 Query: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 ER V MVFQ+YALYPHMSVYDNI+FGL+ K + RV + A +L L+ LL+RKP+ Sbjct: 74 ERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKE 133 Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 +SGGQ+QR A+ RA+ + P + LFDEPLSNLDA LR Q+R +I RLH RL +T +YVTHD Sbjct: 134 LSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHD 193 Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Q+EAMTLAD+++++ GR+ Q GSP ELY P + F AGF+G+P MNFLS +Q Sbjct: 194 QVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETS 253 Query: 255 FIETAHQRWALTGERF--SRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEIL 312 ++T W +T F S L + L +RP+HV + AA T V V VE L Sbjct: 254 LVDTL--VWGITSLPFDSSNLAAGTPLSLGIRPEHVSL-----KAADGTAGVVVTAVEYL 306 Query: 313 GADALLTTRCG-DQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENLSLPDAALT 371 G++ + G D+ L Q G + L LD LH+FD + P A T Sbjct: 307 GSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSRHPHAIET 366 Query: 372 AP 373 P Sbjct: 367 LP 368 Lambda K H 0.321 0.137 0.403 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: 422 Number of extensions: 21 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: 406 Length of database: 381 Length adjustment: 31 Effective length of query: 375 Effective length of database: 350 Effective search space: 131250 Effective search space used: 131250 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 Apr 09 2024. 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