Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 202 bits (515), Expect = 9e-57 Identities = 119/294 (40%), Positives = 175/294 (59%), Gaps = 15/294 (5%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NL+I +GE + L+GPSG GK+T LR++AGLE G I G++DVT V RDR + VFQ Sbjct: 22 NLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQVHVRDRRVGFVFQ 81 Query: 85 NYALYPHMTVGENMGFALKIAGKSQD----EINKRVDEAAATLGLTEFLERKPKALSGGQ 140 NYAL+ HMTV +N+ F L++ K Q EI KRV + L +R P+ LSGGQ Sbjct: 82 NYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQLGHLAQRYPEQLSGGQ 141 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 +QR+A+ RA+ P+V L+DEP LDAK+R + R + +L +L T+V+VTHDQ EAL Sbjct: 142 KQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVFVTHDQDEAL 201 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 + DR+ V+ +G ++QV P ELY +P + FV F+G+ +N S + T+G A + Sbjct: 202 ELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN--VNRFEASWQQNRWTNGDAFL 259 Query: 261 KLSPETLAAMTP-EDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSD 313 + PE TP + NG + + AL P ++ IP + + +G++ Sbjct: 260 -VPPE----QTPLQQNGALYVRSHELALADKPNSQA---HIPFTIVAITPVGAE 305 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: 337 Number of extensions: 11 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: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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: 50 (23.9 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