Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 338 bits (866), Expect = 2e-97 Identities = 187/358 (52%), Positives = 239/358 (66%), Gaps = 11/358 (3%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M + ++ ++K +G+ +I G+D+DI +GEF V VGPSGCGKSTLLRM+AGLEEITGG++ Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I G VN+V P R IAMVFQ+YALYPHMTV DNMAF + +A++ K +D RV+ AAD+ Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L L LDR P+ LSGGQRQRVA+GRAI R+P+VFLFDEPLSNLDA LRV R EI +L Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 +R+ TT IYVTHDQ+EAMT+AD+IVV+ G +EQ G PL+LY+ PANLFVA FIGSPAM Sbjct: 181 QRLK-TTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAM 239 Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNAS---ENGKTASFGVRPEDLRVTEADDFL 297 N IPAT+ V A G V P A+ +G+ ++GVRPE L + A + Sbjct: 240 NFIPATLRRNATGAEVEFADGTRV--PAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGI 297 Query: 298 FEGTVSIVEALGEVTLLYIE-GLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354 V +VE G T ++ G I + G GD + D ++ HLFD Sbjct: 298 -ATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDF---GAGDVIHLVPDHSRTHLFD 351 Lambda K H 0.320 0.137 0.387 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: 386 Number of extensions: 21 Number of successful extensions: 4 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: 362 Length of database: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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