GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Williamsia sterculiae CPCC 203464

Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_076478911.1 BW971_RS08980 sugar ABC transporter permease

Query= TCDB::O30832
         (290 letters)



>NCBI__GCF_900156495.1:WP_076478911.1
          Length = 318

 Score =  220 bits (560), Expect = 4e-62
 Identities = 108/272 (39%), Positives = 171/272 (62%), Gaps = 1/272 (0%)

Query: 16  PAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSAALTNTILL 75
           PA+I + +   +P  +TLY+S   +NL+ PG   F   +NY     D  F +   NT+LL
Sbjct: 40  PALIFMIIVTQIPFLVTLYYSTQSWNLVRPGSRKFNWLNNYVEVFKDSQFWSVTGNTVLL 99

Query: 76  VVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPVNGMF 135
           +VG ++I+V+ G++ ALLLD+ F G+ +VR L+I PF V P  SAL+WK   ++P NG+ 
Sbjct: 100 IVGTVVISVILGLIFALLLDRKFVGRSVVRTLLITPFLVTPVASALLWKTSLLSPTNGLV 159

Query: 136 AHIARGLGLPPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQSLDREQMEAAEMDGAS 195
               R LGL   D+LS+ PLAS++  + WQW PF  L++L  LQS+ R+  EAA +DGA+
Sbjct: 160 NWALRPLGLD-VDWLSEFPLASVMAELVWQWTPFMMLLILAGLQSMPRDIQEAARVDGAT 218

Query: 196 ALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTASTNITYLVYAQSLL 255
           +   F  +T+PHL R I +  ++  I+L+  F  + + T+GGPG AS+N+ + +Y ++ L
Sbjct: 219 SFRLFRELTLPHLRRFIELGTVLGAIYLVNTFDAVYMMTSGGPGVASSNLPFYIYQRAFL 278

Query: 256 NYDVGGGSAGGIVAVVLANIVAIFLMRMIGKN 287
            +D+G  +A G+V V+   +VA   +R+I K+
Sbjct: 279 GFDIGQAAAMGVVTVIGTIVVATLALRLIFKS 310


Lambda     K      H
   0.329    0.142    0.429 

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: 247
Number of extensions: 9
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: 290
Length of database: 318
Length adjustment: 27
Effective length of query: 263
Effective length of database: 291
Effective search space:    76533
Effective search space used:    76533
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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