Align Solute-binding protein Bpro_3107 (characterized)
to candidate CCNA_01513 CCNA_01513 C4-dicarboxylate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__Caulo:CCNA_01513 Length = 327 Score = 273 bits (699), Expect = 3e-78 Identities = 150/324 (46%), Positives = 208/324 (64%), Gaps = 4/324 (1%) Query: 6 PRISAIRSAALAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKH 65 P A+ + ALAA LA + R AD+H A YPTV AV + G L+ +++ G+ Sbjct: 3 PSRRALITTALAAPLAACVQEIGERP-LRGADSHPAG-YPTVEAVNHFGALISQRTNGRL 60 Query: 66 KIKVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKS 125 +++ + LG EK+T++ G LD RVN+ P+N I PLT VP++PFLF S HMR+S Sbjct: 61 RLQNYAGGQLGEEKDTLEITVFGGLDINRVNLAPLNPIEPLTLVPSLPFLFQSTDHMRRS 120 Query: 126 LDGPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVAL 184 LDG G IL S E G IGLAFYDSG RS Y + PIRT AD +GLK+RVQ S+L +A+ Sbjct: 121 LDGAPGRTILNSLERHGLIGLAFYDSGERSFYNTRGPIRTPADMRGLKLRVQTSNLPIAM 180 Query: 185 VSAMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILV 244 V A+GA+ PM YGEV+ L G+ID AENN PS+ ++H E + YS T H MAPE+LV Sbjct: 181 VQALGASPIPMSYGEVFQALVQGVIDGAENNWPSYQDSRHFEVARFYSVTRHVMAPEVLV 240 Query: 245 MSKIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVE-VDKKSFQ 303 S + KL +++++IR AA ESV F R+ W+ +E + + AG E+VE +D+ +FQ Sbjct: 241 ASARTWAKLSSSDREIIRDAATESVPFMRRLWEARETSARQAMIDAGVEVVEDLDRSAFQ 300 Query: 304 AVMGPVYDKFMTTPDMKRLVKAVQ 327 A M PV+D+F+T+P LV ++ Sbjct: 301 AAMAPVWDRFITSPAQTALVNQIR 324 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: 223 Number of extensions: 12 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: 327 Length adjustment: 28 Effective length of query: 302 Effective length of database: 299 Effective search space: 90298 Effective search space used: 90298 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