Align Amino-acid permease RocE (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 373 bits (958), Expect = e-108 Identities = 194/466 (41%), Positives = 285/466 (61%), Gaps = 18/466 (3%) Query: 9 NQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLG 68 + LQR +K+RHL MI++GG +GTG F+ +G +I+QAGP GA+L Y + G +++ M LG Sbjct: 16 DDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLG 75 Query: 69 ELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDV 128 ELAV PV+GSF TY+ ++ FGFA GW YW AVT A+E +A +MQ WFPH+ Sbjct: 76 ELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSG 135 Query: 129 WIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQA 188 +W F LMF LNA + + F E+E+WF+ IK+ IL+F+ G +FG+ ++GG Q+ Sbjct: 136 VVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGI--MQGGPQS 193 Query: 189 PFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWR 248 + D F GI AM + F+FQGTE +GVAAGE+ DP +TIPR+I+QT WR Sbjct: 194 GWHNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQTFWR 253 Query: 249 TLVFFVLSIIVIAGMIPWKQAGVVE--------SPFVAVFEQIGIPYAADIMNFVILIAL 300 L+F+VL+I++I +IP+ ++ SPF VF G+ +AA +MN V+L AL Sbjct: 254 ILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVLTAL 313 Query: 301 LSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAE 360 LS S +YASTRILY +A G+A +AL + + GVP +L T AV L L+ + Sbjct: 314 LSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLFGDK 373 Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420 VY+ LL+ +GM+ + W+ I++S FRR + +G K DL +++PLYP PL + L Sbjct: 374 AVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAIVLC 433 Query: 421 TVVLISLAF----DPEQR----IALYCGVPFMIICYIIYHVVIKKR 458 V+++ + D R + Y GVP ++ ++ Y +V K R Sbjct: 434 VVIVLGQNYQAFSDVRGRWLEIVGTYIGVPLFLVLWLGYRLVKKTR 479 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: 678 Number of extensions: 29 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: 509 Length adjustment: 34 Effective length of query: 433 Effective length of database: 475 Effective search space: 205675 Effective search space used: 205675 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: 52 (24.6 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