Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate HSERO_RS21620 HSERO_RS21620 amino acid ABC transporter permease
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__HerbieS:HSERO_RS21620 Length = 247 Score = 115 bits (289), Expect = 6e-31 Identities = 77/252 (30%), Positives = 124/252 (49%), Gaps = 22/252 (8%) Query: 3 IDWNWGIFLQQAPFGNTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTV------ 56 +D+ W I AP G +T+ +S+ + +I ++G G+LR Sbjct: 1 MDFRWSIIQGYAPL--------FAKGVLMTLQVSLISILIGTVIGLLVGMLRLAEVQHGP 52 Query: 57 ---PNRFLSGLGTLYVELFRNVPLIVQFFT-WYLVIPELLPEKIGMWFKAELDPNIQ--- 109 P + + L YV FR PL VQ + V+P L+ ++ G+ EL I+ Sbjct: 53 WKWPLKSMRWLAGFYVAFFRGTPLFVQIMLIHFAVMPVLVQQEHGLLITGELARTIKQDY 112 Query: 110 -FFLSSMLCLGLFTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVI 168 FLS + L L A + E RA IQS+ RGQ AA ++G+ RYV+LP A+R + Sbjct: 113 GAFLSGTVALSLNAGAYISEIFRAGIQSIERGQSYAAASLGMNYGLTMRYVVLPQAFRRM 172 Query: 169 VPPMTSEMMNLVKNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIML 228 +PP+ +E + L+K+S++ S IGL ++A A + A WE + I++ Y + + L Sbjct: 173 LPPLGNEAITLLKDSSLVSAIGLAELAYAARTVAGTYARYWEPYITISVLYFSMTICLAL 232 Query: 229 VMTLVERKVRLP 240 V+ +E K P Sbjct: 233 VVARLESKYSAP 244 Lambda K H 0.328 0.140 0.443 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: 170 Number of extensions: 14 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: 246 Length of database: 247 Length adjustment: 24 Effective length of query: 222 Effective length of database: 223 Effective search space: 49506 Effective search space used: 49506 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: 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