Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate BPHYT_RS27970 BPHYT_RS27970 sugar ABC transporter permease
Query= TCDB::O30493 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS27970 Length = 317 Score = 174 bits (440), Expect = 3e-48 Identities = 96/288 (33%), Positives = 161/288 (55%), Gaps = 33/288 (11%) Query: 22 AILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHI----NERSNYF------SY 71 A+L P+ W+ LTSFKT+ DA A PP +F P++E Y+++ + ++ F + Sbjct: 29 ALLATLPMVWIFLTSFKTQEDAIAYPPVVLFQPSMEGYVNLFTIRSRQTPEFIASLPPAR 88 Query: 72 AW-----------------------NSVLISFSATALCLLISVPAAYSMAFYETKRTKST 108 W NS++I F +T L + + AAY+ + ++ Sbjct: 89 TWYERDVRKRNMVIAGPSKVLPRFANSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDL 148 Query: 109 LLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPK 168 L ++LST+M+PP+ V +PIYL+ ++ GL D+ + +I++YT +N+ + VW++ + +IP+ Sbjct: 149 LFFILSTRMMPPIAVAIPIYLMYRALGLSDSCVGMIVLYTAVNVSLAVWLLKGFMDEIPR 208 Query: 169 DILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTA 228 + EAA +DG T Q V+V+LP A G+A+T + LI WNE ++ LTS +A + Sbjct: 209 EYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLTSGDAQTMPP 268 Query: 229 LIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 I G W ++A +TL PILIF + +K L+RG++FGAV+ Sbjct: 269 FIPFIIGEGGQDWPAVAAATTLFVLPILIFTVVLRKHLLRGITFGAVR 316 Lambda K H 0.327 0.137 0.426 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: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 276 Length of database: 317 Length adjustment: 26 Effective length of query: 250 Effective length of database: 291 Effective search space: 72750 Effective search space used: 72750 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: 48 (23.1 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