Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__Marino:GFF2245 Length = 395 Score = 85.5 bits (210), Expect = 1e-21 Identities = 52/126 (41%), Positives = 78/126 (61%), Gaps = 3/126 (2%) Query: 116 LCLGLFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSE 175 + L L+TA+ + E VR+ I S+ +GQ A+ A+GL R V++P A RVI+PP+TS+ Sbjct: 268 IALSLYTASFIAEIVRSGILSVSKGQTEASKALGLPNGLTLRLVVIPQAMRVIIPPLTSQ 327 Query: 176 MMNLVKNSAIASTIGLVDMAAQ-AGKLLDYSAHAWESFTAITLA-YVLINAFIMLVMTLV 233 +NLVKNS++A+ IG D+ A G L+ + A E AIT+A Y+ I+ I L M + Sbjct: 328 YLNLVKNSSLATAIGYPDLVAVFMGTTLNQTGQAVE-VVAITMAVYLTISLLISLFMNIY 386 Query: 234 ERKVRL 239 R V + Sbjct: 387 NRAVAI 392 Score = 55.5 bits (132), Expect = 2e-12 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 1/88 (1%) Query: 7 WGIFLQQAPFGNTTYLG-WIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRFLSGLG 65 +GI + P+ T G W G T+ +S + A ++G G+ R N ++ + Sbjct: 67 FGIIMNLVPYDATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMA 126 Query: 66 TLYVELFRNVPLIVQFFTWYLVIPELLP 93 +Y+E+ RN+PL++Q F WY + LP Sbjct: 127 LVYIEVIRNIPLLLQIFFWYFAVLSNLP 154 Lambda K H 0.328 0.140 0.443 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: 279 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 246 Length of database: 395 Length adjustment: 27 Effective length of query: 219 Effective length of database: 368 Effective search space: 80592 Effective search space used: 80592 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 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