Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__psRCH2:GFF3102 Length = 365 Score = 285 bits (730), Expect = 1e-81 Identities = 177/424 (41%), Positives = 235/424 (55%), Gaps = 75/424 (17%) Query: 16 PAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRA 75 P P +GA+ W+R NLFS +NT LT+ GL +WL+ P L ++ A+ E RA Sbjct: 11 PPPTISIGALGWLRANLFSSWINTLLTLVGLYL-LWLI--VPPVLEWAIFKADWTGETRA 67 Query: 76 IIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRK 135 + GACW I+ R+ QF++GFYP + WR+ Sbjct: 68 DCSRE------GACWVFIQTRFGQFMYGFYPTELRWRVD--------------------- 100 Query: 136 LIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGL--LFTALAPKLGVPVSAGIGLVVA 193 AA WL AI+G LF P + GIG ++ Sbjct: 101 ----------AAAWL----------------AIIGAAPLFLRQMPH---KLRYGIGYLLV 131 Query: 194 ---ALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLAL 250 +WL L L V + Q+GG +L +VI I +LPLGILLAL Sbjct: 132 YPLLAYWLLHGGF----------LGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLAL 181 Query: 251 GRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFA 310 GR+SDM ++ L V IEF RGVPLIT+LF +S++L FLP G N D +LR +++V F Sbjct: 182 GRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNLDKLLRAMLMVVFFE 241 Query: 311 AAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKD 370 AAYIAEV+RGGL A+P+GQYEAA A+GL YW++ L+I+PQALK+ IPGIV++FI LFKD Sbjct: 242 AAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKD 301 Query: 371 TTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLK 430 T+LV +GLFD L I +D AW G E Y+F AL++++F F MSRYSM LERKL Sbjct: 302 TSLVIIIGLFDFLNSIKRAT-ADPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERKLD 360 Query: 431 RDHR 434 H+ Sbjct: 361 TGHK 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: 594 Number of extensions: 33 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