Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 411 bits (1057), Expect = e-119 Identities = 225/441 (51%), Positives = 288/441 (65%), Gaps = 18/441 (4%) Query: 1 MSDT-----SFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQA 55 MSDT +FVR + P P P + G KW+RENLFS N+ LT+ L L+ + Sbjct: 1 MSDTHAQTVAFVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSS 60 Query: 56 AAPWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGF-YPVDQYWRLF 114 PWLL+GVW NSL ECR ++ + GAC++V+ RWNQ L+GF YP +YWR Sbjct: 61 TLPWLLNGVWTTNSLAECREVLDGK-----LGACFSVLTERWNQLLYGFKYPGTEYWRPN 115 Query: 115 VTFAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFT 174 + L +ALAPVLF LPRKL+ T +YP AFWL+WGG I P+ L GF G +F Sbjct: 116 LALVLLLVALAPVLFFDLPRKLLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQ 175 Query: 175 ALAPKLGVPVSAGIGLVVAALF-WLYAAAPI-EAALQSALPLALPEVDSDQFGGFLLALV 232 G G +VAA+ W I E A +A+ A+P D GGF+L ++ Sbjct: 176 KFGK--GSFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRD---LGGFMLNMM 230 Query: 233 IGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP 292 +GVT + +S+PLGI LALGRQS+M ++K + V IEFVRGVPLITLLF AS++L YF PP Sbjct: 231 LGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPP 290 Query: 293 GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQA 352 DL LRVVI++TLF+AAYIAEVIRGGLAALP+GQYEAAD+LGLDY QA RLII+PQA Sbjct: 291 DATVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQA 350 Query: 353 LKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFF 412 LKISIPGIV+ +GLFKDTTLV+ + +FD + I + + W G YWE F A +FF Sbjct: 351 LKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFF 410 Query: 413 LFNFSMSRYSMYLERKLKRDH 433 + + +S+YS +LER+L DH Sbjct: 411 IVCYGISQYSQWLERRLATDH 431 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: 688 Number of extensions: 34 Number of successful extensions: 4 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: 432 Length adjustment: 32 Effective length of query: 402 Effective length of database: 400 Effective search space: 160800 Effective search space used: 160800 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: 51 (24.3 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