GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Brucella inopinata BO1

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_008507649.1 BIBO1_RS12560 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>NCBI__GCF_000182725.1:WP_008507649.1
          Length = 756

 Score =  262 bits (670), Expect = 5e-74
 Identities = 194/607 (31%), Positives = 295/607 (48%), Gaps = 22/607 (3%)

Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVA 295
           E  E     LA+++A G G     + +  P +E        + G   + G   G+VV   
Sbjct: 147 EALETTAMVLAEIIATGDG-----LRLARPGIELDLGRPMNVTGHGFNDGIGLGHVVLHE 201

Query: 296 ERTLEMPEFAADQQLERESLERALMHATQALQRL---RDNAAGEAQADIFKAHQELLEDP 352
            R +    F  D Q E   L+ AL     ++  +   RD A      ++ +A++    D 
Sbjct: 202 PRIVVTNLFNEDSQAELNRLDEALGSLRISIDDMLSRRDVAVEGEHREVLEAYRMFAHDR 261

Query: 353 SLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILG- 411
             + + +  +  G +A  A       T      L    + ER  D  D+  R+L+ ++G 
Sbjct: 262 GWVRRLEEAVHNGLTAEAAVEKVQSDTRARMVHLTDPYMRERLSDFDDLANRLLRQLMGR 321

Query: 412 -VPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVC 470
            V      L   AI++A  +  ++       ++ G     G ATSHV I+ARA+G+P V 
Sbjct: 322 DVKTIAESLAKDAIIVARSMGAAELLDYPRERLRGVVLEDGAATSHVVIVARAMGIPVV- 380

Query: 471 GLPLQVLSLASGT-RVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQ-HELENAARAA 528
           G    V+S+A     +++D D+G +HL P   V E  +A++ + R R Q H  E   + A
Sbjct: 381 GQAKGVVSMAENNDAIIVDGDEGIVHLRPQADV-ESAYAEKVRFRARRQAHYRELRDKPA 439

Query: 529 VTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA 588
           +T+DG    +  N   L +  Q  + GA GIGL R+E  +   S  P  ++Q   Y ++ 
Sbjct: 440 ITKDGVDIALLMNAGLLVDLPQLSASGAAGIGLFRTELQFMVASTFPRSEQQERLYRSVI 499

Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDS-EANPFLGMRGIRLCLERPQLLREQFRAILS 647
            A G  + +  RTLD+GGDK L Y    + E NP LG R IRL L+RP LLR Q RA+L 
Sbjct: 500 DAAG-DKPVTFRTLDIGGDKVLPYFRATAQEENPALGWRAIRLTLDRPGLLRTQLRALLK 558

Query: 648 SAGLARLHIMLPMVSQLSELRLARLMLEEEALALG--LRELP---KLGIMIEVPAAALMA 702
           +AG   L +MLPMV+++SE++ AR ++E E   L      LP   KLG M+EVPA     
Sbjct: 559 AAGGRELKLMLPMVTEVSEVKAAREIIEREVRHLSRFAHSLPLCLKLGAMVEVPALLWQL 618

Query: 703 DLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWV 762
           D     VDF S+G+NDL Q+ +A DR +  ++ + D   PS LR +   VKA   H K V
Sbjct: 619 DELMTAVDFVSVGSNDLFQFLMAADRGNSLISDRFDQLSPSFLRALRHIVKAGARHDKPV 678

Query: 763 GVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGL-ESA 821
            +CG +A   L    L+GLG   +S+S   I  +KA +  ++     A+  + L    +A
Sbjct: 679 TLCGEMAGRPLTAMTLIGLGFRSISMSAAAIGPVKAMLGALDAGKLNALLLEELNKPNNA 738

Query: 822 EQVREAL 828
             +RE L
Sbjct: 739 HSLRELL 745


Lambda     K      H
   0.318    0.132    0.370 

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: 1224
Number of extensions: 47
Number of successful extensions: 6
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: 844
Length of database: 756
Length adjustment: 41
Effective length of query: 803
Effective length of database: 715
Effective search space:   574145
Effective search space used:   574145
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 (21.7 bits)
S2: 55 (25.8 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