Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate HSERO_RS23035 HSERO_RS23035 ABC transporter permease
Query= TCDB::P48245 (273 letters) >FitnessBrowser__HerbieS:HSERO_RS23035 Length = 277 Score = 94.7 bits (234), Expect = 2e-24 Identities = 74/247 (29%), Positives = 125/247 (50%), Gaps = 18/247 (7%) Query: 5 NGQLDANKWTPFINSQTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRW 64 N LD + P+ W + L G W TLK +VI+ + +G + + S R L Sbjct: 2 NFSLDFSPLAPY-----WPVF-LHGAWLTLKMTTLAVIVGVAIGIFVAFAKNSPHRWLAR 55 Query: 65 FCAVIIETFRAIPVLILMIFAYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSG 124 C+ IE R P L+ + Y A I FAA V + + + AEI+R+G Sbjct: 56 GCSAYIEVVRNTPFLVQIFLLYFGLASLGI---RMPTFAAAVLAMIINIAAYAAEIIRAG 112 Query: 125 IASLPKGQKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIE 184 + S+P+GQ EAA LG+S + W ++L A+ + PAL SQ ++ ++ SA+ QI E Sbjct: 113 LDSVPRGQIEAAQCLGLSVWRIRWHVMLQPAIERVYPALTSQFLLMMQASAMASQISAEE 172 Query: 185 V--VRSGIQSASVN--RNYL--AALFVVALIMI-VLNFSLTALASRIERQLR--AGRARK 235 + + + +QS + YL AAL++V I++ ++ +++ + R LR A + R+ Sbjct: 173 LTAIANTVQSDTFRSLETYLVVAALYLVLAILVKLVAYAIGETIFKRRRTLRRAAAQGRR 232 Query: 236 NIVAKVP 242 V+++P Sbjct: 233 TPVSRLP 239 Lambda K H 0.323 0.136 0.395 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: 158 Number of extensions: 11 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: 273 Length of database: 277 Length adjustment: 25 Effective length of query: 248 Effective length of database: 252 Effective search space: 62496 Effective search space used: 62496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 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