Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 203 bits (517), Expect = 5e-57 Identities = 114/293 (38%), Positives = 172/293 (58%), Gaps = 14/293 (4%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NL I DG+ L+GPSG GK+T LR++AGLE +G I KDVT + RDR + VFQ Sbjct: 22 NLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDVTDLHVRDRRVGFVFQ 81 Query: 85 NYALYPHMTVGENMGFALKIAGKSQ----DEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 +YAL+ HMTV EN+ F L + + + EI KRV + + L +R P LSGGQ Sbjct: 82 HYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLEMVQLEHLADRYPAQLSGGQ 141 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 +QR+A+ RA+ P++ L+DEP LDAK+R R + +L +L T+V+VTHDQ EAL Sbjct: 142 KQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSLHDELHFTSVFVTHDQEEAL 201 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 + D++ V+ +G ++QV P ELY RP + FV F+G +N+ + ++DG G A I Sbjct: 202 ELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQ--VNVLSGKIRDGVMRQGDAWI 259 Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSD 313 +L PE +N + RP + + + S D +P +++ + +G++ Sbjct: 260 RL-PEGC------ENDDAQLYLRPHEVR-LTQSASDDAHLPFRIEAINLIGAE 304 Lambda K H 0.316 0.135 0.380 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: 360 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: 376 Length of database: 362 Length adjustment: 30 Effective length of query: 346 Effective length of database: 332 Effective search space: 114872 Effective search space used: 114872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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