Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 73.6 bits (179), Expect = 6e-18 Identities = 32/80 (40%), Positives = 55/80 (68%) Query: 122 LGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQ 181 L + Y ++++E+VRSGI A+P GQ EA+ + +R ++VPQ +R+I+PP+T+Q Sbjct: 269 LALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVVPQALRVIIPPLTSQ 328 Query: 182 MVNLIKNTSVLLIVGGAELM 201 +NLIKN+S+ +G +L+ Sbjct: 329 YLNLIKNSSLATAIGYPDLV 348 Score = 56.6 bits (135), Expect = 7e-13 Identities = 42/139 (30%), Positives = 70/139 (50%), Gaps = 8/139 (5%) Query: 12 RQILTSWGLYDENSISPFAVWKFLDALDNKDA----FINGFIYTLEVSILALLIATIFGT 67 R I T +G D + F + + L ++ F+ G + TL VS L ++ ATI G Sbjct: 53 RGITTGFGFLDRTA--GFGIGQSLIEYSSQSTYGRTFVVGLLNTLLVSALGVIAATIIGF 110 Query: 68 IGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYA-LPVLGIRLDIFTIGVLGVGA 126 I G+ S +I Y+E+F+N+PL++QIFF ++A L + D +++G + Sbjct: 111 IVGIARLSPNWLIARLASGYIEIFRNIPLLLQIFFWYFAVLRAMPAARDSYSLGEVIFLN 170 Query: 127 YHGAYVSE-VVRSGILAVP 144 G Y+ E + SG +P Sbjct: 171 VRGLYLPEPLFESGFGLIP 189 Lambda K H 0.328 0.143 0.422 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: 255 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 250 Length of database: 396 Length adjustment: 27 Effective length of query: 223 Effective length of database: 369 Effective search space: 82287 Effective search space used: 82287 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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