Align Amino-acid permease RocE (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 286 bits (731), Expect = 1e-81 Identities = 159/445 (35%), Positives = 256/445 (57%), Gaps = 9/445 (2%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 L++++K RH+ MI+LGGVIG G F+G+G I AGP A+LSYL+GG ++ L M LGE+ Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGP-AAILSYLIGGVMVTLVMFMLGEM 64 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 A P SGSF TYA ++ GFA GWLYW +T +E + G ++ + P + V Sbjct: 65 ASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPA 124 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 L + NA + +AF E+E+W S K+ I++F++LG + +FGL + G AP Sbjct: 125 GALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGL---QPGIPAPG 181 Query: 191 LTHFYEDGLF-PNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249 L + + G F PNGI ++ ++ V F+ G+E+ VAAGESE+P K + R+IK + R Sbjct: 182 LLNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRV 241 Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309 +VF+V S+ ++ +PW ++SP+V++F G AA M V+ ++ +SV NS L+ Sbjct: 242 MVFYVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFLF 301 Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLL-TKFAQAETVYMVLLS 368 +++R+L++++ G A G+TN +GVPM +L++ + V C+S+L F ++++L Sbjct: 302 SNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCL-VVCVSILGIHFLSGGDLFLMLAK 360 Query: 369 LAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLA 428 +G + WI I ++ RR+ E + + F+ YPV + L VL S A Sbjct: 361 SSGAFVMIVWIFIIVAHFAMRRQTKHE--QRDPASFRAWFYPVSNWVALLALVAVLGSQA 418 Query: 429 FDPEQRIALYCGVPFMIICYIIYHV 453 F+PE R + V + Y+V Sbjct: 419 FNPESRFQFWFAVSTALAIVAWYYV 443 Lambda K H 0.329 0.142 0.438 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: 544 Number of extensions: 32 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: 467 Length of database: 459 Length adjustment: 33 Effective length of query: 434 Effective length of database: 426 Effective search space: 184884 Effective search space used: 184884 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