Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 213 bits (543), Expect = 7e-60 Identities = 145/415 (34%), Positives = 223/415 (53%), Gaps = 58/415 (13%) Query: 17 WLRQNLFSSWLNSAITLLLVVIIVTVVGRL------GLWITTE-------------ARWT 57 W+R+NLFSS NS +TL + +I ++ G+W T A ++ Sbjct: 32 WIRENLFSSVPNSILTLAALALIYALLSSTLPWLLNGVWTTNSLAECREVLDGKLGACFS 91 Query: 58 VLVDNWTLFFVG-RYPAAEQWR----LWLWLGLLSPTLG-------LTWGCLATGSHRWQ 105 VL + W G +YP E WR L L L L+P L L + + W Sbjct: 92 VLTERWNQLLYGFKYPGTEYWRPNLALVLLLVALAPVLFFDLPRKLLAFTAIYPFLAFWL 151 Query: 106 RRSLWGWAGLAAAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRC-RGQAWLRFLPTLWG 164 +WG + L +A LG A A ++ Q+ +G L F + Sbjct: 152 ---IWGGSILVPIVA---------LLGFVA-------AGFVFQKFGKGSFALGFFGAIVA 192 Query: 165 --VLFLVGLWLLQGGLG----LRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQS 218 V++ +G +L+ G L V S D G +L + + + S+PLGI LALGRQS Sbjct: 193 AVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSVPLGIALALGRQS 252 Query: 219 SLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYL 278 ++P I+W+ V +IE RG+PL+T+LF VM+ + +D LR ++ +T+F +AY+ Sbjct: 253 NMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRVVIMITLFSAAYI 312 Query: 279 AETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLL 338 AE +RGGL A+P+GQ+EAA +LGL+ Q R I+LPQAL+ISIP IV + + L +DTTL+ Sbjct: 313 AEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVNVAVGLFKDTTLV 372 Query: 339 SIVGLLELLGISRS-ILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392 S++ + +L+G+ R ILA+ + G Y E+ F L+++ CYG++Q S+ LE+RL Sbjct: 373 SVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFFIVCYGISQYSQWLERRL 427 Lambda K H 0.329 0.142 0.471 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: 452 Number of extensions: 17 Number of successful extensions: 4 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: 396 Length of database: 432 Length adjustment: 31 Effective length of query: 365 Effective length of database: 401 Effective search space: 146365 Effective search space used: 146365 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