Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 106 bits (264), Expect = 5e-28 Identities = 72/220 (32%), Positives = 119/220 (54%), Gaps = 12/220 (5%) Query: 16 LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWF 75 L G+ IT+ +T+ A ++ G +LAV LS A+ Y V R +P++++LL+ Sbjct: 40 LSKGIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYV 99 Query: 76 -YLIVPGFLQ--NVLGLSPKNDIR----LISAMVAFSMFEAAYYSEIIRAGIQSISRGQS 128 + +VP + N LGL P+ +R L A++A + AA+ +E+ RAG+ S+ RGQ Sbjct: 100 AFALVPAVVAGWNALGL-PEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQI 158 Query: 129 SAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG 188 AA ALG+ W +LII PQAFR ++P L + + +D+SLV VL +AD + Sbjct: 159 EAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTA 218 Query: 189 ERDGTQVEMILFAGFVYFVISLSASL----LVSYLKRRTA 224 + E +Y ++++ SL L ++L++R A Sbjct: 219 AGNFRYFETYNVVALIYLAMTVTLSLALRKLEAHLRKRGA 258 Lambda K H 0.330 0.140 0.412 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: 160 Number of extensions: 13 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: 224 Length of database: 262 Length adjustment: 23 Effective length of query: 201 Effective length of database: 239 Effective search space: 48039 Effective search space used: 48039 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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