Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF968 PS417_04910 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__WCS417:GFF968 Length = 365 Score = 279 bits (713), Expect = 1e-79 Identities = 168/422 (39%), Positives = 231/422 (54%), Gaps = 71/422 (16%) Query: 16 PAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRA 75 P P G + WMR NLFS LNT LT LLA + P L + +AN + RA Sbjct: 11 PPPNKVFGPMAWMRANLFSSWLNTLLT---LLAFYLIYLVVPPILSWAIIDANWVGTTRA 67 Query: 76 IIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRK 135 + GACW I+ R+ QF++G+YP D WR+ +T + +AP+ RK Sbjct: 68 DCTKE------GACWVFIQQRFGQFMYGYYPGDLRWRVDLTVWLAIVGVAPLFISRFQRK 121 Query: 136 LIWGT---LLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVV 192 ++G +LYP ++A F + G +F Sbjct: 122 AVYGLGFLVLYP-----------------IIAFFLLHGGIF------------------- 145 Query: 193 AALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGR 252 L V + Q+GG +L LVI I +LPLGI+LALGR Sbjct: 146 ----------------------GLTNVATSQWGGLMLTLVIATVGIAGALPLGIMLALGR 183 Query: 253 QSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFAAA 312 +S+M ++ + V IEF RGVPLIT+LF +S++L FLP G D +LR +I V LF +A Sbjct: 184 RSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMGIDKLLRALIGVILFQSA 243 Query: 313 YIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTT 372 Y+AEV+RGGL A+P+GQYEAA A+GL YW++ L+I+PQALK+ IPGIV++FI LFKDT+ Sbjct: 244 YVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKMVIPGIVNTFIALFKDTS 303 Query: 373 LVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRD 432 LV +GLFD L + +D W G E Y+F AL+F++F F MSRYS++LE KL Sbjct: 304 LVIIIGLFDLLNSVKQAA-ADPKWLGMATEGYVFAALVFWIFCFGMSRYSIHLEHKLDTG 362 Query: 433 HR 434 H+ Sbjct: 363 HK 364 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: 590 Number of extensions: 35 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: 365 Length adjustment: 31 Effective length of query: 403 Effective length of database: 334 Effective search space: 134602 Effective search space used: 134602 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