Align Solute-binding protein Bpro_3107 (characterized)
to candidate AZOBR_RS31400 AZOBR_RS31400 C4-dicarboxylate ABC transporter
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS31400 Length = 329 Score = 355 bits (912), Expect = e-103 Identities = 185/323 (57%), Positives = 242/323 (74%), Gaps = 4/323 (1%) Query: 11 IRSAALAALLAGLGMGA-AQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKV 69 IR+A LAA A + A +FRSAD H AD YPTV AVKY+ +LL++++GGK +KV Sbjct: 8 IRAALLAACAACTLLATPVVARDFRSADIHPAD-YPTVEAVKYVDKLLKERTGGKLGVKV 66 Query: 70 FNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGP 129 + ALG+EK+TI+Q+KIG LD R+NV P+N + P T V +PF+F S HMR LDGP Sbjct: 67 YPNGALGTEKDTIEQLKIGGLDMMRINVAPLNNVVPETMVTALPFIFRSTEHMRAVLDGP 126 Query: 130 VGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVSAM 188 +GDEIL + ES G IGLAFYDSG+RS+Y A KP +T+AD KG KIRVQQSDL+VA++ A+ Sbjct: 127 IGDEILAAMESQGMIGLAFYDSGSRSMYSAAKPYKTLADMKGAKIRVQQSDLFVAMIQAL 186 Query: 189 GANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKI 248 GANATPMP+GEVYT LKTG++DAAENN PS+++++H EA K ++ TEH+MAPE+LV SK+ Sbjct: 187 GANATPMPFGEVYTALKTGIVDAAENNYPSYESSRHFEAAKYFTLTEHAMAPEVLVFSKV 246 Query: 249 IYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEV-DKKSFQAVMG 307 +D+L K +Q IR AAK+SV + R+ WDE+E KS V AGA+IVEV +K+ F M Sbjct: 247 SWDRLSKDDQAAIRKAAKDSVPYMRKLWDEREQKSKDVVVKAGAQIVEVTNKQEFIDAMA 306 Query: 308 PVYDKFMTTPDMKRLVKAVQDTK 330 PVY +F +TP + LVK +QDTK Sbjct: 307 PVYKQFASTPKLDGLVKRIQDTK 329 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: 294 Number of extensions: 8 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: 330 Length of database: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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