Align Solute-binding protein Bpro_3107 (characterized)
to candidate AZOBR_RS27160 AZOBR_RS27160 C4-dicarboxylate ABC transporter substrate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS27160 Length = 327 Score = 224 bits (570), Expect = 3e-63 Identities = 114/319 (35%), Positives = 184/319 (57%), Gaps = 1/319 (0%) Query: 13 SAALAALLAGLGMGAAQATEFRSADTHN-ADDYPTVAAVKYMGELLEKKSGGKHKIKVFN 71 +A LAA + GL + A + H A +P ++ +L+ ++S G+ IKVF Sbjct: 9 AALLAAAVLGLTLAGPAAAKTTLRLGHGLAKGHPVDVSLDEFAKLVRERSKGELDIKVFP 68 Query: 72 KQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGPVG 131 LG ++E I+Q++ GALD N P+ A P V MPFLF H K ++G VG Sbjct: 69 AGQLGQQRELIEQMQNGALDLVHANASPLAAFEPGFGVYDMPFLFRDNDHFFKVVEGAVG 128 Query: 132 DEILKSCESAGFIGLAFYDSGARSIYAKKPIRTVADAKGLKIRVQQSDLWVALVSAMGAN 191 DEIL S + F+GLA+YD+G RS YA KP+ D KGLK+RVQ + +++ +GA Sbjct: 129 DEILASSRAKAFVGLAYYDNGTRSFYANKPLAKPEDLKGLKVRVQPGPIATRMINLLGAT 188 Query: 192 ATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKIIYD 251 ATP+ +GEVYT L++G++D AENN+ + A+H E +KVY++ EH+ P++++++ D Sbjct: 189 ATPLAWGEVYTALQSGVVDGAENNVTALTLARHGEVMKVYTRDEHTRVPDVVLVATSTLD 248 Query: 252 KLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEVDKKSFQAVMGPVYD 311 +L +Q+++R AA++S +W + K+ G + V+ DK +++ ++ P+YD Sbjct: 249 RLKPEQQELLRQAARDSAKAHNARWTAELEKAEGEAAKMGVKFVDADKAAYRQMVQPMYD 308 Query: 312 KFMTTPDMKRLVKAVQDTK 330 TP + L +Q K Sbjct: 309 DLKATPALATLADRIQAVK 327 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: 225 Number of extensions: 6 Number of successful extensions: 1 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