Aligments for a candidate for aglE' in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc03061 SMc03061 alpha-glucoside ABC
           transporter periplasmic-binding protein
          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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources