Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 167 bits (423), Expect = 3e-46 Identities = 88/242 (36%), Positives = 150/242 (61%), Gaps = 8/242 (3%) Query: 21 IAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKII 80 + IQ+SQ++K +G F ++D++LTV G + + GPSGSGKST++R I LE+ SG+I Sbjct: 1 VGIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIF 60 Query: 81 VDGIELTSDLKNIDKVRS-EVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAM 139 + G + T+ + VR ++G VFQH+ LF HLT+ +N+ + +RK K + Sbjct: 61 LTGRDATN-----ESVRDRQIGFVFQHYALFKHLTVRKNIAFG-LELRKHTKEKVRARVE 114 Query: 140 YYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDT 199 LE V++ +YP QLSGGQ+QRVA+AR+L ++P+++L DEP ALD ++ K++ Sbjct: 115 ELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSW 174 Query: 200 MIQLAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLS 258 + +L +E +T + VTH+ A VA++++ M G++ + +P + + NP + F+ Sbjct: 175 LRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG 234 Query: 259 QI 260 + Sbjct: 235 PV 236 Lambda K H 0.320 0.134 0.391 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: 243 Number of extensions: 13 Number of successful extensions: 4 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: 263 Length of database: 338 Length adjustment: 26 Effective length of query: 237 Effective length of database: 312 Effective search space: 73944 Effective search space used: 73944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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