Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate BPHYT_RS13290 BPHYT_RS13290 cysteine ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__BFirm:BPHYT_RS13290 Length = 225 Score = 91.3 bits (225), Expect = 3e-23 Identities = 68/216 (31%), Positives = 112/216 (51%), Gaps = 23/216 (10%) Query: 224 FGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFV----RGVPLITLL 279 + G + + + + + + L L L+AL R L +V I+ F RG PL+ L Sbjct: 17 YAGLVFTVPLTLISFAIGLALAFLVALVR----LFGPKWAVAIVRFYVWLFRGSPLLVQL 72 Query: 280 FTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGL 338 F ++ Y LP G D + +I +L AY +EVIRG + ++P+GQ+EAA ++G+ Sbjct: 73 F----VIFYGLPNVGIVLDPLTAAIIGFSLNVGAYNSEVIRGVIESIPKGQWEAAYSMGM 128 Query: 339 DYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKG 398 QA R I+PQA ++++P + +SFI L KDT+L A + + V ++ Sbjct: 129 TREQALRRAILPQAARVALPPLSNSFIALVKDTSLAAVL-------TVPEVFQAAQRIAS 181 Query: 399 TYWEP---YIFVALIFFLFNFSMSRYSMYLERKLKR 431 +EP Y AL++ +F+ +S + LERK R Sbjct: 182 VTYEPLILYTEAALVYLVFSSVLSSAQVRLERKFGR 217 Lambda K H 0.329 0.143 0.457 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: 314 Number of extensions: 26 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: 434 Length of database: 225 Length adjustment: 27 Effective length of query: 407 Effective length of database: 198 Effective search space: 80586 Effective search space used: 80586 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