GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglE' in Sinorhizobium meliloti 1021

Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate SMc03061 SMc03061 alpha-glucoside ABC transporter periplasmic-binding protein

Query= uniprot:A8LLL6
         (452 letters)



>FitnessBrowser__Smeli:SMc03061
          Length = 458

 Score =  563 bits (1450), Expect = e-165
 Identities = 275/459 (59%), Positives = 329/459 (71%), Gaps = 8/459 (1%)

Query: 1   MRHTLHASAAALALSAGMAGAGG-----HLAFTPGE-GEFNWDSYQAFAEATDLSGQDLS 54
           M+ +L    AA AL AG AG  G      L F PGE   FNW S + F +  DL GQ L+
Sbjct: 1   MKRSLLIGVAAFALLAGTAGLAGTAGAADLKFKPGEDSRFNWASLEEFKKGHDLKGQTLT 60

Query: 55  IFGPWLAGEADAFSNLVAFFNEATGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGL 114
           IFGPW   +   F ++ A+F EATG    Y  S++ EQQIVID +AGS PD+ + PQPGL
Sbjct: 61  IFGPWRGEDEALFKSVYAYFVEATGVELKYSSSENYEQQIVIDTQAGSPPDVAILPQPGL 120

Query: 115 ATTMAARGFLTPLPDGTDDWLRENYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVW 174
              +AA+G LTPL D T  WL +NYAAGQSW+DL TY    G   LY F + ++VKSLVW
Sbjct: 121 IADLAAKGLLTPLGDETKQWLLDNYAAGQSWVDLSTYNGKDGTSALYAFPYKIDVKSLVW 180

Query: 175 YIPENFEDFDYEVPETMEEFKALMDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRT 234
           Y+PENFED  YEVP+TMEE KAL +++ EDG+ P C+GLGSGGATGWPATDWVEDLMLRT
Sbjct: 181 YVPENFEDAGYEVPKTMEELKALTEKIAEDGEKPWCIGLGSGGATGWPATDWVEDLMLRT 240

Query: 235 QPPEVYDAWVSNEMPFDDPRVVAAIEEYGSFTRNDDYVVGNANDTASVDFRESPLGLFAS 294
           QP E YD WV NE+PF D  V  A+EE+G F RND +V G A   AS DFR+SP GLF+S
Sbjct: 241 QPAETYDKWVKNEIPFTDAAVTGALEEFGWFARNDAFVDGGAAAVASTDFRDSPKGLFSS 300

Query: 295 PPACMMHRQASFIPAYFPEGTELGEDADFFYFPAFE-EKDLGRPVLGAGTLFAITNENPA 353
           PP C +H QASFIP++FPEG  +GEDADFFY P +E +K+LG PVLGAGTL  IT + PA
Sbjct: 301 PPKCYLHHQASFIPSFFPEGKVVGEDADFFYMPPYESKKELGNPVLGAGTLAMITKDTPA 360

Query: 354 ASAFIEFLKTPFAHEIMMAQDGFLTPFKGANPAAYASDTLRGQGEILTNATTFRFDGSDL 413
           A AFIEFLKTP AHE+ MAQ  FLTP+K  N   Y +  L+ QGEIL NATTFRFDGSDL
Sbjct: 361 ARAFIEFLKTPIAHEVWMAQTSFLTPYKSVNVDVYGNPPLKKQGEILLNATTFRFDGSDL 420

Query: 414 MPGGVGAGTFWTGMVDYSSGAKSAADVASEIQASWESLK 452
           MPG +GAG FWTGMVD+  G KS+ADVA+ +Q +W+S+K
Sbjct: 421 MPGKIGAGAFWTGMVDF-VGGKSSADVAAGVQKAWDSIK 458


Lambda     K      H
   0.317    0.134    0.413 

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: 808
Number of extensions: 45
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: 452
Length of database: 458
Length adjustment: 33
Effective length of query: 419
Effective length of database: 425
Effective search space:   178075
Effective search space used:   178075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

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

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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