Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate 16032 b1918 predicted transporter subunit: membrane component of ABC superfamily (NCBI)
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__Keio:16032 Length = 222 Score = 139 bits (350), Expect = 4e-38 Identities = 80/214 (37%), Positives = 122/214 (57%), Gaps = 8/214 (3%) Query: 9 IVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPL 68 ++ SLP+LL G TL++++ + G+L G +LA+MRLS PV W A+ Y+++FR PL Sbjct: 8 VIDSLPFLLKGAGYTLQLSIGGMFFGLLLGFILALMRLSPIWPVRWLARFYISIFRGTPL 67 Query: 69 VMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQS 128 + L Y +P F + L P + SAM+ S+ AAY +E +RA I SI +GQ Sbjct: 68 IAQLFMIYYGLPQF---GIELDP-----IPSAMIGLSLNTAAYAAETLRAAISSIDKGQW 119 Query: 129 SAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG 188 AA ++GMT WQ+M+ ILPQA R +P L I L +DTSL + + + FR A I Sbjct: 120 EAAASIGMTPWQTMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLIT 179 Query: 189 ERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 R M L A +Y++++ S L ++ + + Sbjct: 180 SRTLEVFTMYLAASLIYWIMATVLSTLQNHFENQ 213 Lambda K H 0.330 0.140 0.412 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: 126 Number of extensions: 8 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: 224 Length of database: 222 Length adjustment: 22 Effective length of query: 202 Effective length of database: 200 Effective search space: 40400 Effective search space used: 40400 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 (21.9 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