Align ABC transporter (characterized, see rationale)
to candidate SM_b20630 SM_b20630 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Smeli:SM_b20630 Length = 361 Score = 364 bits (934), Expect = e-105 Identities = 186/351 (52%), Positives = 240/351 (68%), Gaps = 7/351 (1%) Query: 6 LDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGR 65 L ++ K GG+ ++ + L I G+FVVFVGPSGCGKSTLLR+IAGL+ + G++ I GR Sbjct: 12 LSDIRKSYGGLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVSEGEIAIKGR 71 Query: 66 RVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDK 125 V DL+P ERG+ MVFQSYALYPHMSV +N+ FGLK+A+TD + RV + + IL++D Sbjct: 72 DVTDLDPSERGIAMVFQSYALYPHMSVSENLGFGLKMARTDPAEIARRVAQVSAILKIDH 131 Query: 126 LLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGS 185 LL R+P +LSGGQRQRVA+GRA+ R+PD+ LFDEPLSNLDA LRV MR EIARLH LG+ Sbjct: 132 LLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHRELGN 191 Query: 186 TMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSAR 245 TM+YVTHDQ EAMTLAD+IVVL GR+EQ GSPR++YE PA+ FVAGF+GSPRMNFL A Sbjct: 192 TMVYVTHDQTEAMTLADQIVVLRDGRIEQAGSPRDVYEDPANMFVAGFIGSPRMNFLDAE 251 Query: 246 LQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVV--VTAV 303 Q G + +T + D +L G L LGIRPEH+++ A G + V Sbjct: 252 WQGDGTIRVGETTL----EAAIDGGSLKHGERLLLGIRPEHIAV-AEPGPERIAAQVEFS 306 Query: 304 EYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADG 354 EYLG Y++ + + L+ WQAG+++ + D F DG Sbjct: 307 EYLGGTRYLYCQLEDGQSLVVEQREGPNWQAGEKLSFAVPDDRRRFFAEDG 357 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: 368 Number of extensions: 17 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: 381 Length of database: 361 Length adjustment: 30 Effective length of query: 351 Effective length of database: 331 Effective search space: 116181 Effective search space used: 116181 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: 49 (23.5 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