Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 77.4 bits (189), Expect = 4e-19 Identities = 52/157 (33%), Positives = 89/157 (56%), Gaps = 11/157 (7%) Query: 66 IPLVMVLLWFYLIVPGFLQNVLGLSPKNDIR----LISAMVAFSMFEAAYYSEIIRAGIQ 121 +PL +VL F + + + + G + K I+ LI+ A S++ A+ +E +RAGIQ Sbjct: 245 VPLALVL--FVMGLSWEVPELKGFNFKGGIKIGGPLIALWFALSIYTGAFIAENVRAGIQ 302 Query: 122 SISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFF 181 +I++GQ+ AA ALG+ + M L++LPQA R ++P L++ + + +++SL + AD Sbjct: 303 AINKGQTEAAAALGLRPGRIMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAVGYADIT 362 Query: 182 RTASTIG-ERDGTQVEMILFAGFVYFVISLSASLLVS 217 T I + G +E +L Y L+ASLL+S Sbjct: 363 ATLGGITLNQTGRAIECVLLLMLFY----LTASLLIS 395 Score = 39.7 bits (91), Expect = 9e-08 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 3/60 (5%) Query: 19 GLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWFYLI 78 G++ TL + V A + ++G + V+RLS+ V+ YV +FR+IP VL+W +I Sbjct: 91 GVLNTLLVAVLACITATIFGVVAGVLRLSNNWLVSKLMAVYVEIFRNIP---VLIWIIII 147 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: 222 Number of extensions: 15 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: 224 Length of database: 410 Length adjustment: 27 Effective length of query: 197 Effective length of database: 383 Effective search space: 75451 Effective search space used: 75451 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: 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