Align Solute-binding protein Bpro_3107 (characterized)
to candidate 208331 DVU2822 TRAP dicarboxylate family transporter
Query= SwissProt::Q128M1 (330 letters) >MicrobesOnline__882:208331 Length = 336 Score = 132 bits (332), Expect = 1e-35 Identities = 95/324 (29%), Positives = 164/324 (50%), Gaps = 9/324 (2%) Query: 14 AALAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKVFNKQ 73 A +A L AG AA+ R A + T+ K+ E++E KS GK +I++F Sbjct: 14 ACIAMLAAGSYAEAAKRITIRLAHPMAPGNNVTLGYEKFK-EIVEAKSNGKVRIQLFGNC 72 Query: 74 ALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMR--KSLD-GPV 130 LGS++ T++ + G L+ + M V +P++ S + K+LD G + Sbjct: 73 MLGSDRVTMEATQRGTLEMASSSSPNMTNFSKEMMVFDLPYITSPEHQEKLYKALDEGAL 132 Query: 131 GDEILKSCESAGFIGLAFYDSGARSIYA-KKPIRTVADAKGLKIRVQQSDLWVALVSAMG 189 G+ + G + + + G R+ KKPI+T D K LK+R S + VA+ SA+G Sbjct: 133 GERLDAIAAGIGLKPIMYSEYGYRNFATTKKPIKTADDLKNLKVRTTDSPIEVAVASALG 192 Query: 190 ANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKII 249 N TP+ +GE YT L+ G +D N + AKH E ++ + H+ + +L+++K Sbjct: 193 MNPTPVSWGETYTALQQGTVDGEGNTFGLLNDAKHTEVLRHAMDSAHNYSMHLLMINKAY 252 Query: 250 YDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEV---DKKSFQAVM 306 +DKLP Q ++ + KE++A++R ++ E K+ G I ++ ++ + + Sbjct: 253 FDKLPADVQQILVDSGKEALAYQRAISNDLEKKAEQAFVERGIVITKLAPEERAKMRELT 312 Query: 307 GPVYDKFMTTPDMKRLVKAVQDTK 330 PV+DKF + LVK VQ+T+ Sbjct: 313 RPVWDKF-SNDIPADLVKLVQETQ 335 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: 203 Number of extensions: 9 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: 336 Length adjustment: 28 Effective length of query: 302 Effective length of database: 308 Effective search space: 93016 Effective search space used: 93016 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