Align Solute-binding protein Bpro_3107 (characterized)
to candidate 17640 b3579 predicted transporter (NCBI)
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__Keio:17640 Length = 328 Score = 171 bits (434), Expect = 2e-47 Identities = 109/327 (33%), Positives = 178/327 (54%), Gaps = 8/327 (2%) Query: 11 IRSAALAALLAGLGM---GAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKI 67 +RS A +AGL + A R + D +AA K+ +LL++++ G+ K+ Sbjct: 3 LRSVTYALFIAGLAAFSTSSLAAQSLRFGYETSQTDSQHIAAKKF-NDLLQERTKGELKL 61 Query: 68 KVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLD 127 K+F LG+ + I V+ G +D + P+ + +PFLF AH K+LD Sbjct: 62 KLFPDSTLGNAQAMISGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLD 121 Query: 128 GPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVS 186 G VGD++ S E G LA++++G R + ++ P++T AD KGLKIR S + +A Sbjct: 122 GKVGDDLKASLEGKGLKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFK 181 Query: 187 AMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMS 246 GAN PMP+ EVYTGL+T IDA E+ I +AK E K S T H+ +P ++V++ Sbjct: 182 VFGANPIPMPFAEVYTGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVIN 241 Query: 247 KIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIV-EVDKKSFQAV 305 K +D L Q + ++A+E+ ++R+ E + K + +K AG E++ ++D+K+F Sbjct: 242 KAKFDGLSPEFQQALVSSAQEAGNYQRKLVAEDQQKIIDGMKEAGVEVITDLDRKAFSDA 301 Query: 306 MG-PVYDKFM-TTPDMKRLVKAVQDTK 330 +G V D F+ P L+KAV + + Sbjct: 302 LGNQVRDMFVKDVPQGADLLKAVDEVQ 328 Lambda K H 0.316 0.130 0.362 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: 221 Number of extensions: 10 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: 330 Length of database: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 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