Align Solute-binding protein Bamb_6123 (characterized)
to candidate SM_b20295 SM_b20295 ABC transporter substrate-binding protein
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__Smeli:SM_b20295 Length = 323 Score = 142 bits (359), Expect = 9e-39 Identities = 93/300 (31%), Positives = 154/300 (51%), Gaps = 6/300 (2%) Query: 11 ALAVALMAGFAMSAQARVFRSADVHGDSFPTNMAVKFMGDELSKLTGGKDSIKVFGNSAL 70 ALA LMA AM+ +AR R P V + + +GG+ ++++F NS L Sbjct: 9 ALAGLLMASQAMAQEARTLRLGMQGTAGDPQFEGVTEAARIIKEKSGGRLTLEIFPNSQL 68 Query: 71 GSEKDTVDQVRIGAIDMARVNGASFNEIVPESLIPSFPFLFRDVDHFRKAMYGPAGQKIL 130 G+ + ++QV +G +D + VP +++ S ++ D DH +K + G+ I+ Sbjct: 69 GTFTEMMEQVTLGELDFTLNPFGGMDAWVPRAVLASTAYVVGDFDHLQKIIASDWGKGIV 128 Query: 131 DAFAA--KGMIALTFYESGARSIYAKRPVRTPADMKGLKVRVQPSDLMVDEIRAMGGTPT 188 D K + ++Y G R AK+P+ PAD G+K+RV S ++ +AMG +PT Sbjct: 129 DEMRTEHKWRMVDSWY-FGTRHTTAKKPIEKPADFAGMKLRVPNSAPLLTWAKAMGASPT 187 Query: 189 PMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPDYSETQHAMTPEVLVFSKKIWDTL 248 P+ FAEVY L+T VD EN LP + K EV S T H + +V++ S+ W+ L Sbjct: 188 PVAFAEVYLALQTNQVDGQENPLPIIDSMKFTEVQSHVSLTGHLVQDQVILMSEDTWNAL 247 Query: 249 SPQEQAAIRKAAADSVPYYQKLWTAREASAQQAVTKGGANILPAAQVDRAAFVKAMQPLW 308 P +Q + +A KL + +EA+ + G ++ + D+AAF +AM+P++ Sbjct: 248 EPADQKVVMEAFEAGGALNDKLVSDKEANLVSDFRERGITVV---EPDKAAFQEAMKPVY 304 Lambda K H 0.318 0.131 0.375 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: 247 Number of extensions: 13 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: 328 Length of database: 323 Length adjustment: 28 Effective length of query: 300 Effective length of database: 295 Effective search space: 88500 Effective search space used: 88500 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 (21.7 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