GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Sinorhizobium meliloti 1021

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__Smeli:SM_b20402
          Length = 462

 Score =  228 bits (580), Expect = 4e-64
 Identities = 149/399 (37%), Positives = 210/399 (52%), Gaps = 52/399 (13%)

Query: 27  LVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDDF 86
           LV +G  LA  G+C+ACH+V G   FAGGL + TP GTIYSTNITPD+ TGIG +S   F
Sbjct: 45  LVAKGAQLAALGNCIACHTVPGRPAFAGGLALPTPFGTIYSTNITPDRETGIGGWSEAAF 104

Query: 87  QKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPLS 146
           ++A+R GV + G  LYPA PY  +  VS +D +ALYA+ M  VA  A+A  ++D+P+PL 
Sbjct: 105 ERAMREGVDREGSHLYPAFPYEHFTRVSADDNRALYAFLMTRVAVKAEA-LENDLPFPLK 163

Query: 147 MRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALSN 206
            R  LA W+ +F  D    +P   +     RGRYL EGLGHCGACHTPR+          
Sbjct: 164 FRPLLAGWKLLFL-DSGEREPDPGQSDAWNRGRYLAEGLGHCGACHTPRN------PFGA 216

Query: 207 DGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDHTAAFGGMTDVV 266
           +    +  G  A  +GW A  +  +++  +  W E  L  +LR G ++      G    V
Sbjct: 217 EDRDRHFGGGEA--EGWQAYAINTESKAPI-PWDEQSLAFYLRNGWHEFHGVSRGPMAEV 273

Query: 267 EHSLQHLSDDDITAIARYLKSL----------------GAKDASQTVFTQDDQVAKALWK 310
             +L  L D DI AIA Y++S+                 A +  +     D Q +     
Sbjct: 274 TGNLAFLPDSDIAAIATYVRSIMGAPTPEREQRAAQLREAFEGQRPEQAADSQRSPVSAS 333

Query: 311 GDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQPGG---------AGEPDPTSLIHI 361
           G  SQ G ++Y+ +CA+CH+           G   QP G            P+P +++++
Sbjct: 334 G--SQPGEAIYLAACASCHE-----------GGRRQPFGGLNFELSTAVNAPNPQNIVNV 380

Query: 362 VLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIR 400
           VL G  LP   G  +A+ MPAF   LNDQQVAD++ ++R
Sbjct: 381 VLFG--LPPADGEASAV-MPAFRHLLNDQQVADLLAYMR 416


Lambda     K      H
   0.317    0.133    0.409 

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: 590
Number of extensions: 36
Number of successful extensions: 9
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: 441
Length of database: 462
Length adjustment: 33
Effective length of query: 408
Effective length of database: 429
Effective search space:   175032
Effective search space used:   175032
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.

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