Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 280 bits (716), Expect = 5e-80 Identities = 176/418 (42%), Positives = 229/418 (54%), Gaps = 65/418 (15%) Query: 17 APVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRAI 76 AP + +KWMRENLFSG NT LT L LV + P L +AN + + Sbjct: 9 APKKALRPVKWMRENLFSGWFNTVLT---LGVAYLLVTSVGPLLNWFFLDANFVGSDPSA 65 Query: 77 IAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRKL 136 GACW I R N F++GFYP + WR+ V F L ++ P + P Sbjct: 66 CT------GAGACWLFISQRLNFFIYGFYPDELQWRVDVMFLLLAVSFVPQFIERFP--- 116 Query: 137 IWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVVAALF 196 G W L F I GL P+ G L+ F Sbjct: 117 -----------------GRKW-----LGLFGIFGL-----------PI-VGYFLIPGGSF 142 Query: 197 WLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSDM 256 L EV S ++GG +L L++ I+ SLP+GILLALGR+SDM Sbjct: 143 ------------------GLEEVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDM 184 Query: 257 LIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFAAAYIAE 316 I++ + V IE R VPLIT+LF AS++L FLP G NF+ + R +I +TL+ +AY+AE Sbjct: 185 PIIRGICVVFIEVWRAVPLITVLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAE 244 Query: 317 VIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAF 376 VIRGGL A+PRGQYEAADALGL YW+ L+I+PQALK+ IPGIV++FI LFKDTTLV Sbjct: 245 VIRGGLQAIPRGQYEAADALGLGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLI 304 Query: 377 VGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434 +GLFD L + + V +D AW+ E Y+FVA F++F F +SRYS LERKL H+ Sbjct: 305 IGLFDILGTVQSTV-TDPAWQNVAIEGYVFVAFCFWVFCFGISRYSQNLERKLDTGHK 361 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: 587 Number of extensions: 28 Number of successful extensions: 5 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: 434 Length of database: 362 Length adjustment: 31 Effective length of query: 403 Effective length of database: 331 Effective search space: 133393 Effective search space used: 133393 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