Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 220 bits (561), Expect = 5e-62 Identities = 154/423 (36%), Positives = 225/423 (53%), Gaps = 63/423 (14%) Query: 25 IKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRAIIAERWGPE 84 I W+R+NLFS LN+A+T+ ++ V +V W+ Sbjct: 15 IAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWI------------------------ 50 Query: 85 ATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRKLIWGTLLYP 144 T A W V+ W F G YP + WRL++ + GL L+P L L WG L Sbjct: 51 TTEARWTVLVDNWTLFFVGRYPAAEQWRLWL-WLGL---LSPTL------GLTWGCL--- 97 Query: 145 LAAFWLLWGG-PIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVVAALFWLYAAAP 203 A W +WG + A AI G+ KLG+ A I V A WL Sbjct: 98 -ATGSHRWQRRSLWGWAGLAA--AIAGIPLPWFPHKLGL---AAIAATVPAASWLAQRCR 151 Query: 204 IEAALQSALP-----------------LALPEVDSDQFGGFLLALVIGVTAIVVSLPLGI 246 +A L+ LP L L V S+ + G LL L + ++V SLPLGI Sbjct: 152 GQAWLRF-LPTLWGVLFLVGLWLLQGGLGLRPVSSNDWSGLLLTLATALISMVCSLPLGI 210 Query: 247 LLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILV 306 LLALGRQS + ++ LSV IE RG+PL+T+LF +++ L D ILR ++ + Sbjct: 211 LLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGL 270 Query: 307 TLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIG 366 T+F +AY+AE +RGGL A+P+GQ+EAA ALGL+ +Q R I++PQAL+ISIP IV F+ Sbjct: 271 TIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLN 330 Query: 367 LFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLE 426 L +DTTL++ VGL + L GIS + ++ A+ G Y E Y+F+ ++++L + +++ S LE Sbjct: 331 LLQDTTLLSIVGLLE-LLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLE 389 Query: 427 RKL 429 ++L Sbjct: 390 QRL 392 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: 717 Number of extensions: 58 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: 434 Length of database: 396 Length adjustment: 31 Effective length of query: 403 Effective length of database: 365 Effective search space: 147095 Effective search space used: 147095 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: 50 (23.9 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