Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate AZOBR_RS27070 AZOBR_RS27070 ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__azobra:AZOBR_RS27070 Length = 220 Score = 144 bits (364), Expect = 1e-39 Identities = 68/205 (33%), Positives = 123/205 (60%), Gaps = 1/205 (0%) Query: 44 FINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFL 103 F+NG + T+ ++ +++ + G +GG+ SRF ++R + Y+ELF+ PL++Q+ + Sbjct: 16 FLNGTLVTIGLTAAVVVLGLLLGLVGGLAQLSRFAVLRWISWAYIELFRCTPLLVQLLWF 75 Query: 104 FYALPVL-GIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQM 162 +YALP+L GI++D T VL + Y G++ +EV+R G++++ GQ EA + G T + M Sbjct: 76 YYALPMLTGIQIDAVTASVLTLSLYGGSFYAEVIRGGVVSIEAGQTEAGLALGMTPAKVM 135 Query: 163 RYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAA 222 R I++PQ ++ ++PP+ NQ + KNTS++ +V +L++ A D Y A Sbjct: 136 RRIVLPQAVKRMIPPLMNQSIIQFKNTSLVSVVAVPDLLYQGQVAATDTFRPLEVYTIVA 195 Query: 223 VLYFIICYPLAYFAKAYENKLKKAH 247 ++YF++ PL K E +L+ H Sbjct: 196 LIYFVVLVPLTAIVKRGEKQLQTGH 220 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: 162 Number of extensions: 10 Number of successful extensions: 2 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: 250 Length of database: 220 Length adjustment: 23 Effective length of query: 227 Effective length of database: 197 Effective search space: 44719 Effective search space used: 44719 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: 46 (22.3 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