Align Solute-binding protein Bpro_3107 (characterized)
to candidate AZOBR_RS30130 AZOBR_RS30130 C4-dicarboxylate ABC transporter
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS30130 Length = 319 Score = 350 bits (898), Expect = e-101 Identities = 176/319 (55%), Positives = 238/319 (74%), Gaps = 3/319 (0%) Query: 14 AALAALLAGLGMGA-AQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKVFNK 72 A LAA AG + A A +FRSAD H D YPTV AVKYMG+LL ++S GK +KV+ Sbjct: 2 ALLAACAAGALLAAPVSARDFRSADIHPGD-YPTVEAVKYMGKLLSERSNGKLGVKVYPN 60 Query: 73 QALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGPVGD 132 ALG+E++TI+Q+KIG LD R+NV P+N + P + V +PF+F HM LDGP+GD Sbjct: 61 GALGNERDTIEQIKIGGLDMMRINVAPLNNVVPESMVVALPFIFRDTDHMHAVLDGPIGD 120 Query: 133 EILKSCESAGFIGLAFYDSGARSIYAKKPIRTVADAKGLKIRVQQSDLWVALVSAMGANA 192 EIL + ES G IGLAFYDSG+RS+Y+KKP+ ++AD KG+KIRVQQSDL+V+++ A+GAN Sbjct: 121 EILAAMESQGLIGLAFYDSGSRSLYSKKPVSSLADLKGMKIRVQQSDLFVSMIEALGANP 180 Query: 193 TPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKIIYDK 252 TPMP GEVYTGLKTG+IDAAENN PS+++++H EA K +++TEH+MAPE+LV SK+ +D+ Sbjct: 181 TPMPMGEVYTGLKTGIIDAAENNYPSYESSRHFEAAKYFTRTEHAMAPEVLVFSKVTWDR 240 Query: 253 LPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEV-DKKSFQAVMGPVYD 311 L K +Q IR AAK+SV + R+ W E+E S A V+ AG++I +V +K+ F M PV+ Sbjct: 241 LSKDDQAAIRKAAKDSVPYMRKLWTEREEASRAIVEKAGSQISDVKNKQEFIDAMKPVFA 300 Query: 312 KFMTTPDMKRLVKAVQDTK 330 KF TP ++ LV+ +QDTK Sbjct: 301 KFANTPKLQGLVQRIQDTK 319 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: 299 Number of extensions: 7 Number of successful extensions: 3 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: 319 Length adjustment: 28 Effective length of query: 302 Effective length of database: 291 Effective search space: 87882 Effective search space used: 87882 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