GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Dechlorosoma suillum PS

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_0378 Dsui_0378 FAD/FMN-dependent dehydrogenase

Query= reanno::Smeli:SMc00832
         (479 letters)



>FitnessBrowser__PS:Dsui_0378
          Length = 465

 Score =  219 bits (559), Expect = 1e-61
 Identities = 131/423 (30%), Positives = 214/423 (50%), Gaps = 10/423 (2%)

Query: 55  MPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLD 114
           +P  VV  E+TE VAAV++ C  Y +P++P G G+S+ G  +     I + LS M+R L 
Sbjct: 45  LPDGVVFAESTEEVAAVVRLCREYRVPVIPYGVGSSVEGHVLAVHGGISIDLSGMNRVLS 104

Query: 115 IDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGV 174
           I   +   TVQAGVT   ++D +   G F+  DP +    T+GG     + G + ++YG 
Sbjct: 105 IHAEDLDVTVQAGVTRKQLNDELKGTGLFFPIDPGAD--ATLGGMAATRASGTNAVRYGT 162

Query: 175 TTNNLLGVKMVLFDGTVIELGGKAL-DAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEG 233
              N+L + +V  +G ++  G +A   + GYDL  L  GSEG LGI+TE TV+L   PE 
Sbjct: 163 MRENVLSLTVVTPEGKIVRTGSRARKSSAGYDLTRLFVGSEGTLGIITELTVKLYPIPEA 222

Query: 234 ARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEA-LLI 292
               +  F S ++A   V   I  G+    +E +D   ++    +++   P   EA  L 
Sbjct: 223 MSAAVCAFPSVDAAVDTVIQTIQLGVPVARVELLDALTLQAINRYSKTTLP---EAPTLF 279

Query: 293 VEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRI---AD 349
            E  GS++ +        EIA+ +G    + +    + + +W+ R  A+ A  ++   A 
Sbjct: 280 FEFHGSDSGVQEQAELTQEIAQGNGGQDFQWATRQEDRSRLWQARHDAYFACLQLKPGAR 339

Query: 350 YICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAE 409
               D  VP+S+L+  +  T E +A   L +A   H GDGN H ++L + ++P+E A  E
Sbjct: 340 CFPTDVCVPISRLAECIHATNEDIAQVSLPIALFGHVGDGNFHLVVLVDTDNPKEMAEGE 399

Query: 410 AAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSK 469
                +++  +   G  TGEHG+G+ K+  +L ++    +      + A DP  LMNP K
Sbjct: 400 WISQRVVERAIAMEGTCTGEHGIGLGKQHYLLQEHGEDGVALMRTLKTALDPLNLMNPGK 459

Query: 470 VFP 472
           + P
Sbjct: 460 ILP 462


Lambda     K      H
   0.320    0.138    0.404 

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: 559
Number of extensions: 31
Number of successful extensions: 5
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: 479
Length of database: 465
Length adjustment: 33
Effective length of query: 446
Effective length of database: 432
Effective search space:   192672
Effective search space used:   192672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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