GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Sinorhizobium meliloti 1021

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor

Query= reanno::WCS417:GFF2133
         (447 letters)



>FitnessBrowser__Smeli:SM_b20402
          Length = 462

 Score =  234 bits (597), Expect = 4e-66
 Identities = 152/428 (35%), Positives = 213/428 (49%), Gaps = 33/428 (7%)

Query: 5   RFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVA 64
           R  R A  +A   LVAA     +  R    P +   A A F   LV++G  +A L +C+A
Sbjct: 2   RALRVAIGIAAVILVAAAAFFLFAWRSEI-PEDTTAAEARFAAELVAKGAQLAALGNCIA 60

Query: 65  CHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLY 124
           CH++ G+  FAGGL + TP G I++TNITPD+ TGIG +S A F+RA+R GV   G  LY
Sbjct: 61  CHTVPGRPAFAGGLALPTPFGTIYSTNITPDRETGIGGWSEAAFERAMREGVDREGSHLY 120

Query: 125 PAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTA 184
           PA PY  + ++S DD +ALYAF M  +       + +D+P+PL  R  +A W  +F  + 
Sbjct: 121 PAFPYEHFTRVSADDNRALYAFLMTRV-AVKAEALENDLPFPLKFRPLLAGWKLLFLDSG 179

Query: 185 TYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAP 244
                P Q   WNRG Y+ +G GHCG+CHTPR   F  +  D        G   +GW A 
Sbjct: 180 EREPDPGQSDAWNRGRYLAEGLGHCGACHTPRN-PFGAEDRDR----HFGGGEAEGWQAY 234

Query: 245 SLRQDPNTGLGRWSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYL 303
           ++  +    +  W E  +  +L+ G    H V  G M E   N   F+ D D+AAIA Y+
Sbjct: 235 AINTESKAPI-PWDEQSLAFYLRNGWHEFHGVSRGPMAEVTGN-LAFLPDSDIAAIATYV 292

Query: 304 KSLPGDP-------------------QRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGL 344
           +S+ G P                       A  Q   V+A    PG   Y   CASCH  
Sbjct: 293 RSIMGAPTPEREQRAAQLREAFEGQRPEQAADSQRSPVSASGSQPGEAIYLAACASCHE- 351

Query: 345 DGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEI 404
            G+ QP        +T+  A    + +N+ L G     A G   A  MPAFR  L+D ++
Sbjct: 352 GGRRQPFGGLNFELSTAVNAPNPQNIVNVVLFGLP--PADGEASAV-MPAFRHLLNDQQV 408

Query: 405 AEVLSYVR 412
           A++L+Y+R
Sbjct: 409 ADLLAYMR 416


Lambda     K      H
   0.318    0.133    0.423 

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: 617
Number of extensions: 28
Number of successful extensions: 7
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: 447
Length of database: 462
Length adjustment: 33
Effective length of query: 414
Effective length of database: 429
Effective search space:   177606
Effective search space used:   177606
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: 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