Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate SM_b20975 SM_b20975 amino acid uptake ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__Smeli:SM_b20975 Length = 549 Score = 90.1 bits (222), Expect = 8e-23 Identities = 66/228 (28%), Positives = 115/228 (50%), Gaps = 19/228 (8%) Query: 10 PSLLPAFWVTIKLT-------IYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNT 62 P LP W T L I A+ A+I G + + L S ++T+R Sbjct: 329 PGGLPLLWETAALNDRDRAAGITFAVLAIILGLLTFGGYLHRRHPLAIGSEFVVDTIRGI 388 Query: 63 PLTLVVLFCSFGLYQNLGLTLAG--RESSTFLVDN-NFRLAVLGFILYTSTFVAESLRSG 119 P+ ++VL+ +GL L+G ++++ ++D N ++ L S ++AE RSG Sbjct: 389 PMLVIVLY--------VGLPLSGALKDATQGVLDPPNLMRGIVAMALAYSAYLAEIFRSG 440 Query: 120 INTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE 179 IN + GQ EAARS+GL T R ++ PQA R I PLGN LIA+ K+T++ S++ + + Sbjct: 441 INAIPIGQIEAARSIGLNRWQTARLVVLPQAFRIIIPPLGNELIAILKDTSLLSILSIRD 500 Query: 180 ASLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVK 227 + M+ ++ + + F + A+ ++ LTL + + + +K Sbjct: 501 ITQRMR-EFQSASFLPFAPYNSAAIFYIFLTLAAASLINMIERKYDIK 547 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: 356 Number of extensions: 33 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: 549 Length adjustment: 29 Effective length of query: 199 Effective length of database: 520 Effective search space: 103480 Effective search space used: 103480 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: 49 (23.5 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