Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_003545407.1 RL_RS03360 carbohydrate ABC transporter permease
Query= TCDB::O30493 (276 letters) >NCBI__GCF_000009265.1:WP_003545407.1 Length = 278 Score = 162 bits (410), Expect = 7e-45 Identities = 84/270 (31%), Positives = 144/270 (53%), Gaps = 7/270 (2%) Query: 14 LGTLAWA-IAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINERSNYFSYA 72 L + W I++ FPI+W+ + S K D F+TP + + +NY + Y Sbjct: 8 LPVVLWTLISLATLFPIYWLFVISVKQPFDLFSTPDVILRSFFWKNYQDVLTNPTLRGYM 67 Query: 73 WNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAK 132 NS++IS L + A Y++ ++ +S W ++ +M PP L+P++LL Sbjct: 68 LNSMIISSGNALLVTTLGFLACYALTRFDLAGKESIFFWTITNRMAPPAVFLLPLFLLLT 127 Query: 133 S------FGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMV 186 F L D+++ +I++Y NLP +W + + IPK++ EAA +DGA+ W + Sbjct: 128 QVYKIGDFSLADSKLGMILVYCSFNLPFAIWTLRPTVEGIPKELDEAAYMDGASPWTVLY 187 Query: 187 RVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKLSA 246 ++ P+A+ GLA T++L+ + WNE + LT+ +A LT ++ Y + G W ++A Sbjct: 188 DIIFPLARPGLAVTLILTWVFAWNEYLLAATLTNFHARTLTTGLSEYVTTTGTAWGIMAA 247 Query: 247 VSTLACAPILIFGWISQKQLVRGLSFGAVK 276 +S L P LI + Q+ +V GL+FGAVK Sbjct: 248 ISMLTLVPALIVFSVVQRHIVAGLTFGAVK 277 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: 268 Number of extensions: 13 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: 276 Length of database: 278 Length adjustment: 25 Effective length of query: 251 Effective length of database: 253 Effective search space: 63503 Effective search space used: 63503 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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