Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_011840164.1 RSPH17029_RS00495 ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >NCBI__GCF_000015985.1:WP_011840164.1 Length = 367 Score = 344 bits (882), Expect = 2e-99 Identities = 187/362 (51%), Positives = 241/362 (66%), Gaps = 8/362 (2%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA L+I++L K FE + ++K IDL + EFVVFVGPSGCGKSTLLR+I GLE + GTI Sbjct: 1 MAFLEIRSLCKSFESYPVLKDIDLSIEKGEFVVFVGPSGCGKSTLLRMITGLETPTSGTI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120 ++ I +V PA+R AMVFQ+YALYPHM+V +N+SF L ++ K L+ +V +AA I Sbjct: 61 AIEDEVINDVDPARRGTAMVFQSYALYPHMTVFQNISFGLRMSRKPKALIRERVEKAAAI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L L LL+RKP QLSGGQ+QRVAIGRAIVR P++FLFDEPLSNLDA LRVQMR EL LH Sbjct: 121 LRLDKLLDRKPAQLSGGQKQRVAIGRAIVREPRVFLFDEPLSNLDAELRVQMRAELLELH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + L TMIYVTHDQVEAMTLADK+VV++ GRI+Q G PL+LY P N FVAGF+G+PKM Sbjct: 181 ERLGTTMIYVTHDQVEAMTLADKMVVMSGGRIQQYGRPLDLYDDPDNRFVAGFVGSPKMN 240 Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTV 300 FL VT G L AG +LPL SL+ G+ + +GIRPE L + GQ Sbjct: 241 FLSATVTSAGADGLRADLAAGGAAALPLI-ESLAPGARIDIGIRPEQLSVVPAGQAPSAD 299 Query: 301 TADVG------ERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDT 354 V E LG++++ H+ ++ + +R A+ GE + + + +FD Sbjct: 300 AVSVAGRVALIEDLGAESYLHLHLADDSRIGVR-TARHAAHLGEEVRVAAPASGVLVFDE 358 Query: 355 DG 356 G Sbjct: 359 AG 360 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: 432 Number of extensions: 22 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: 367 Length of database: 367 Length adjustment: 30 Effective length of query: 337 Effective length of database: 337 Effective search space: 113569 Effective search space used: 113569 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 Apr 10 2024. 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