Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 126 bits (317), Expect = 7e-34 Identities = 75/224 (33%), Positives = 125/224 (55%), Gaps = 9/224 (4%) Query: 35 GGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTN----LSTQSRNIAQVFQFP 90 G ALLGPSGCGKTTLL I+GL S G I +GK V+ ++ + R+I +FQ Sbjct: 29 GEITALLGPSGCGKTTLLRTIAGLQDISAGSIAINGKTVSADGCFVAPEKRSIGMIFQDY 88 Query: 91 VIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQKQKISL 150 ++ +TV DN+ F +R V R+ ++L ++ L +R L+ Q+Q++S+ Sbjct: 89 ALFPHLTVADNILFGVRQLDKQSRSV--RLEEMLSLVKLEGLGKRYPHELSGGQQQRVSI 146 Query: 151 GRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEK 210 R L + + +L DEP + ID ++ L +++ + K + V+VTH + EA FA+ Sbjct: 147 ARALAY-EPDLLLLDEPFSNIDAQVRRALMLEIRAILKARNVSAVFVTHSKDEAFAFADT 205 Query: 211 VVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIE 254 + + G+IVQ G P L++ P+ +V F+G+ N++ R+E Sbjct: 206 LALFEAGRIVQHGIPETLYQSPNTPYVADFLGA--SNYLDVRLE 247 Lambda K H 0.321 0.137 0.405 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: 234 Number of extensions: 11 Number of successful extensions: 3 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: 356 Length of database: 341 Length adjustment: 29 Effective length of query: 327 Effective length of database: 312 Effective search space: 102024 Effective search space used: 102024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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