Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 186 bits (473), Expect = 1e-51 Identities = 134/437 (30%), Positives = 216/437 (49%), Gaps = 20/437 (4%) Query: 10 MMFVGALVFLGCGYPVAFSLGGVAILFAIIG-AALGSFDPIFLSAMPQRIFGIMANGTLL 68 ++ + + +G G PVA+SLG ++L ++ AA+ S ++ + QR+ + + +LL Sbjct: 8 ILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPS-----MTTIAQRMGAGLNSFSLL 62 Query: 69 AIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVA 128 AIPFFI G ++ + GIA +L+ + G L GGL ++ + A G A A Sbjct: 63 AIPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASA 122 Query: 129 MGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLA-DQLGVSVGDLFIGSLL 187 +G I M GY KEL V V S T G +IPPS VLIV + GVS+ LF+ + Sbjct: 123 LGGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYI 182 Query: 188 PGLMMAGSFALYVLIIAWL--KPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVL 245 PGL M L +L A+ K L P + +G ++ P L L+++V+ Sbjct: 183 PGLFMG---LLLMLTAAYFIKKKKLPAGEPTSFKELG------KVFFSAAPSLTLLVIVI 233 Query: 246 GSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAF 305 G I G+ + TEA A+ + + L+ F L + L + + T++V +++ S A Sbjct: 234 GGIVMGVFTATEASAIAVLYCLGLSFFYGELKPRDLPAILLKSSATTAVVAMLIATSMAM 293 Query: 306 SLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAE 365 S V + + + +L +L + L I + + +G F+D I P+F PV Sbjct: 294 SWVMSSEDIPQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVT 353 Query: 366 ALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLV 425 L +D + +G+I+ NL TPP G LF GVA S++ + + +PF ++ Sbjct: 354 ELGIDPVHFGIIMVLNLCIGLCTPPVGSVLFIGVGVAKTSIS--NVVKPLLPFFIAMIIG 411 Query: 426 LLLIIIFPALINWLPSL 442 L +I I+P L WLPSL Sbjct: 412 LAVITIWPQLTLWLPSL 428 Lambda K H 0.331 0.148 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: 493 Number of extensions: 28 Number of successful extensions: 5 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: 445 Length of database: 431 Length adjustment: 32 Effective length of query: 413 Effective length of database: 399 Effective search space: 164787 Effective search space used: 164787 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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