Align Solute-binding protein Bpro_3107 (characterized)
to candidate SM_b21353 SM_b21353 periplasmic C4-dicarboxylate transport protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__Smeli:SM_b21353 Length = 325 Score = 307 bits (787), Expect = 2e-88 Identities = 154/316 (48%), Positives = 220/316 (69%), Gaps = 2/316 (0%) Query: 13 SAALAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKVFNK 72 +A L + +G A T RS+DTH D YPTV VKY GEL+++++ G++ ++V++ Sbjct: 8 AAGLLVAASFMGNAANAQTVLRSSDTH-PDGYPTVEGVKYFGELVKERTAGRYSVEVYHS 66 Query: 73 QALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGPVGD 132 LG EK+TI+QV+ G ++ RV++ P N + VP +P+LF S HM K +DG +GD Sbjct: 67 AQLGEEKDTIEQVRSGVIELNRVSMAPFNGTVKESIVPALPYLFRSEEHMHKVMDGAIGD 126 Query: 133 EILKSCESAGFIGLAFYDSGARSIYAK-KPIRTVADAKGLKIRVQQSDLWVALVSAMGAN 191 +I K+ E AG + LAFYD+GARS Y K KPI TV D KGLK RV QSD++V +V+A+GAN Sbjct: 127 QIKKAFEGAGVVVLAFYDAGARSFYNKQKPINTVEDMKGLKFRVIQSDIFVDMVAALGAN 186 Query: 192 ATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKIIYD 251 ATPMPYGEVY+G++TG+ID AENN PS+DTAKH E K YS EH++ PE+ VM+K +D Sbjct: 187 ATPMPYGEVYSGIETGVIDGAENNFPSYDTAKHFEVAKNYSLDEHTILPEVFVMNKAAFD 246 Query: 252 KLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEVDKKSFQAVMGPVYD 311 KL +Q++ + AAK+SVA +R+ W + +S A V+AAGA+I +K+ F M PVY+ Sbjct: 247 KLTPEDQEIFKQAAKDSVAKQRELWAAKVKESRAKVEAAGAKITTPEKQGFIDAMKPVYE 306 Query: 312 KFMTTPDMKRLVKAVQ 327 K +T +K++V+ V+ Sbjct: 307 KHVTDEVLKKMVEDVR 322 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: 298 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 330 Length of database: 325 Length adjustment: 28 Effective length of query: 302 Effective length of database: 297 Effective search space: 89694 Effective search space used: 89694 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: 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