Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 1936759 b2423 sulfate/thiosulfate transporter subunit (NCBI)
Query= reanno::Koxy:BWI76_RS01820 (296 letters) >FitnessBrowser__Keio:1936759 Length = 291 Score = 58.9 bits (141), Expect = 1e-13 Identities = 64/207 (30%), Positives = 98/207 (47%), Gaps = 16/207 (7%) Query: 85 LWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLI-FQMFPAVLSLVALYAL 143 +W ++ +A I + A+ R FPG+ LL + I F + P V LV Y L Sbjct: 66 IWLTVMIALIAVPVNLVFGILLAWLVTRFNFPGRQLLLTLLDIPFAVSPVVAGLV--YLL 123 Query: 144 FDRLGQYVPFVG-LNTHG-GVIFAYMGGIALHVWTIKGYF--ETI-----DGSLE-EAAA 193 F G P G L+ H ++F++ G + + ++ + E + GS E EAA Sbjct: 124 F--YGSNGPLGGWLDEHNLQIMFSWPGMVLVTIFVTCPFVVRELVPVMLSQGSQEDEAAI 181 Query: 194 LDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYL 253 L GA+ WQ FR V LP L +L+ AI E S++ + TL++ +Q L Sbjct: 182 LLGASGWQMFRRVTLPNIRWALLYGVVLTNARAIGEFGAVSVVSGSIRGETLSLPLQIEL 241 Query: 254 NPQNY-LWGDFAAAAVLSAIPITVVFL 279 Q+Y G F AAA+L+ + I +FL Sbjct: 242 LEQDYNTVGSFTAAALLTLMAIITLFL 268 Lambda K H 0.328 0.141 0.438 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: 234 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 296 Length of database: 291 Length adjustment: 26 Effective length of query: 270 Effective length of database: 265 Effective search space: 71550 Effective search space used: 71550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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