Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate HSERO_RS05830 HSERO_RS05830 amino acid ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__HerbieS:HSERO_RS05830 Length = 218 Score = 104 bits (259), Expect = 2e-27 Identities = 67/221 (30%), Positives = 117/221 (52%), Gaps = 21/221 (9%) Query: 7 DLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTL 66 D P LL VT+++TIYS + + + G +L M+VS +K + +N +R P+ + Sbjct: 8 DFLPILLKGALVTVEVTIYSFLLSSVIGLLLALMKVSRLKPVALAGATIVNIIRGLPI-I 66 Query: 67 VVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFG 126 V LF + + ++G+ L+ F+ V+G + S + AE+ R+GI V G Sbjct: 67 VQLFYIYFVLPDIGIQLSA-----------FQAGVVGLGIAYSAYQAENFRAGIEAVDMG 115 Query: 127 QAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE----ASL 182 Q EAA+S+G+ R ++ PQA R A+ P GNTL+ + K++++ S I V E + Sbjct: 116 QIEAAQSIGMRGPLIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLVSTITVLEMTRAGQM 175 Query: 183 LMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSER 223 + +T +N V+ AV +++L+LP+ + +L R Sbjct: 176 IASSTFQN-----MTVYTTVAVLYLLLSLPLVFLIRRLEIR 211 Lambda K H 0.327 0.139 0.397 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: 140 Number of extensions: 4 Number of successful extensions: 2 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: 228 Length of database: 218 Length adjustment: 22 Effective length of query: 206 Effective length of database: 196 Effective search space: 40376 Effective search space used: 40376 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 (21.7 bits) S2: 46 (22.3 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