Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 92.0 bits (227), Expect = 2e-23 Identities = 73/231 (31%), Positives = 111/231 (48%), Gaps = 26/231 (11%) Query: 24 WIWSGFQVTIALSICAWIIAFLVGSFFGILRTV--------------PNRFLSGLGTLYV 69 W SGF + AL+ +IA LVGSF ++R + P L LG V Sbjct: 188 WFESGFFASGALNWLV-VIAALVGSFL-VMRRIEANATKTQEKTGVRPKTKLIALGVWLV 245 Query: 70 ELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQ 129 L + L V +W + PE G FK + ++ L ++T A + E Sbjct: 246 PLA--LVLFVMGLSWEV------PELKGFNFKGGIKIGGPL-IALWFALSIYTGAFIAEN 296 Query: 130 VRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTI 189 VRA IQ++ +GQ AA A+GL + V+LP A RVI+PP+ S +N+ KNS++A + Sbjct: 297 VRAGIQAINKGQTEAAAALGLRPGRIMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAV 356 Query: 190 GLVDMAAQAGKL-LDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRL 239 G D+ A G + L+ + A E + L Y+ + I +VM + V+L Sbjct: 357 GYADITATLGGITLNQTGRAIECVLLLMLFYLTASLLISMVMNVYNASVKL 407 Score = 42.7 bits (99), Expect = 1e-08 Identities = 19/62 (30%), Positives = 37/62 (59%) Query: 32 TIALSICAWIIAFLVGSFFGILRTVPNRFLSGLGTLYVELFRNVPLIVQFFTWYLVIPEL 91 T+ +++ A I A + G G+LR N +S L +YVE+FRN+P+++ + ++ + Sbjct: 95 TLLVAVLACITATIFGVVAGVLRLSNNWLVSKLMAVYVEIFRNIPVLIWIIIIFTIMTAV 154 Query: 92 LP 93 +P Sbjct: 155 MP 156 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: 265 Number of extensions: 21 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: 246 Length of database: 410 Length adjustment: 27 Effective length of query: 219 Effective length of database: 383 Effective search space: 83877 Effective search space used: 83877 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