GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Sinorhizobium meliloti 1021

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate SMa0244 SMa0244 Dehydrogenase, FAD-dependent

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



>FitnessBrowser__Smeli:SMa0244
          Length = 481

 Score =  172 bits (436), Expect = 2e-47
 Identities = 150/476 (31%), Positives = 233/476 (48%), Gaps = 43/476 (9%)

Query: 20  EIVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYG 79
           E+   L  +L E  ++S+   +  F  D         +AV+ P +T+ VAA +K C   G
Sbjct: 15  ELRLALRQMLGEDIVLSETEEMLRFCRDWHGDVTTGTVAVIRPRSTQQVAAAVKACRELG 74

Query: 80  IPIVPRGAGTSLSGGAIPQ--EDAIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAV 137
           + IVP+G  T L  GAIP   E  +V+ LS+M+R   ID  + +A V++G     + DA+
Sbjct: 75  LSIVPQGGNTGLVLGAIPDAPERQVVLSLSRMNRIRKIDPADFSAVVESGCILSELKDAI 134

Query: 138 SADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGG 196
           +  G F+     +Q +C IGGN+  N+GG + L+YG+T   +LG+++VL DG+++E L  
Sbjct: 135 AKMGMFFPLALGAQGSCQIGGNVSTNAGGVNVLRYGMTRELVLGLEVVLPDGSILEGLST 194

Query: 197 KALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESA--------G 248
              D  G DL  L  G+EG LGI+T  ++ L   P+     L G AS E A         
Sbjct: 195 LRKDNRGIDLKQLFIGAEGTLGIITAVSITLTPYPDHVATALLGLASLEDAIRLYRRARR 254

Query: 249 SCVADIIGSGIIPVAIEFMDRPAIEIC-EAFAQAGYPLDVE--ALLIVEVEGSE-AEMDA 304
            C  D++       A EFM   A  +  EA      P+  E  A +++E+ GS   ++D 
Sbjct: 255 DC-CDLMS------AFEFMPPLAFTLAQEAMPDLPIPISAEYPAYVLMEISGSGLVDVDD 307

Query: 305 TLAGIIEIARRHGVM---TIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQ 361
            +   +E A   G++   TI  SQ+  +A  +W  R+       +   ++  D +VPLSQ
Sbjct: 308 LMQRFLEGAMEEGLVLDGTIAASQT--QARNLWLIREGMNEGQAKRGTHMRTDISVPLSQ 365

Query: 362 LSHVLRRTGEIV--AGYGLRVANVFHAGDGNMHPLILYNI-NDPEEAA----RAEAAGND 414
           L+  +    + V  A  G    +  H GDGN+H  +L    + PEE      +A+   N+
Sbjct: 366 LASFVEEAEKAVSEALPGAVSVSYGHVGDGNVHLNVLPPAGSTPEERIQLIYKAKTVVNE 425

Query: 415 ILKLCVEAGGCLTGEHGVGIEKR---DLMLHQYSRADLGQQMAARAAFDPQWLMNP 467
           +L       G ++ EHG+G  KR   D  L    R  L    A + A DP+ +MNP
Sbjct: 426 VLD---RYTGSISAEHGIGRLKRPDFDARLPATRRKLL---TALKHAVDPEMIMNP 475


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: 560
Number of extensions: 26
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: 481
Length adjustment: 34
Effective length of query: 445
Effective length of database: 447
Effective search space:   198915
Effective search space used:   198915
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