Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::O30494 (367 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 191 bits (485), Expect = 2e-53 Identities = 115/330 (34%), Positives = 176/330 (53%), Gaps = 28/330 (8%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 M+ L I+ L + G +++G++L + E +GPSGCGK+TLLR IAGL+++S G+I Sbjct: 1 MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60 Query: 61 ELDGRDITE----VTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNE 116 ++G+ ++ V P KR + M+FQ YAL+PH++V N+ F + +DKQ ++ E Sbjct: 61 AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGV--RQLDKQSRSVRLEE 118 Query: 117 AARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLEL 176 +++L L +R P +LSGGQ+QRV+I RA+ P + L DEP SN+DA +R + LE+ Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178 Query: 177 ARLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGT 236 + K + ++VTH + EA AD + + +GRI Q G P LY P +VA FLG Sbjct: 179 RAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGA 238 Query: 237 PKMGFLKGKVTRVDGQGCEVQLDAGTLIS----LPLSGASLSVGSAVTLGIRPEHLEIAS 292 +V+L+AG LIS PL + +RPE L I Sbjct: 239 SNY--------------LDVRLEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLI-- 282 Query: 293 PGQTTLTVTADVGERLGSDTFCHVITSNGE 322 + ++ ER CH + GE Sbjct: 283 --EARADGAGEILERRFLGNGCHYLVRLGE 310 Lambda K H 0.319 0.137 0.387 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: 278 Number of extensions: 15 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: 367 Length of database: 341 Length adjustment: 29 Effective length of query: 338 Effective length of database: 312 Effective search space: 105456 Effective search space used: 105456 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