GapMind for catabolism of small carbon sources

 

Alignments for a candidate for padH in Shewanella loihica PV-4

Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate 5208217 Shew_0729 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)

Query= SwissProt::Q8L3B0
         (421 letters)



>FitnessBrowser__PV4:5208217
          Length = 566

 Score =  117 bits (292), Expect = 1e-30
 Identities = 101/336 (30%), Positives = 157/336 (46%), Gaps = 37/336 (11%)

Query: 11  LIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPER--IFLRD 68
           +I G +  A  A  A R+ +    I +  R  ++ ++   LPY +SG+ A     +    
Sbjct: 6   IIGGVAGGASAAARARRLSET-AEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTP 64

Query: 69  DDFFARNKVAYRPKAALKALHADR-----NTAELADGSSVV--YEKLLLATGASPAIPPI 121
           + F AR  V  R K  + A+  DR         L DGS     Y+ LLL+ GA+P +PPI
Sbjct: 65  ESFKARFNVEVRVKHEVVAI--DRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPI 122

Query: 122 PGIDTVSYHVLRTLDDALKLRGAIAES--KQAVVLGAGLVGMHAAENLVKAGATVTIVEM 179
           PG+D    H LR + D  ++   I  +  + A V+G G +G+   E+L   G   T++E+
Sbjct: 123 PGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLEL 182

Query: 180 SEQLTSGYFDKVAADMIEQAFRDAGGKIMTGSRV--------VRLEPTAAGA-------- 223
           ++Q+ +   D+  A    QA RD G  +  G+ +          +   AAG         
Sbjct: 183 ADQVMTPV-DREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIK 241

Query: 224 ---KLTLENGTTLEADLLLVATGVKPEMDYLNGSGVEHAQ--GILVDDRMQTTAENVWAA 278
               LTL NG  LE DLL++A GV+PE      +G+   +  GI V+  MQT+   ++A 
Sbjct: 242 GHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAV 301

Query: 279 ATA-QARGFFTGTKVMNAILPDATIQGRVAGMAMAG 313
             A + + F TG   +  +   A  QGR+A   M G
Sbjct: 302 GDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFG 337


Lambda     K      H
   0.318    0.134    0.382 

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: 492
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 421
Length of database: 566
Length adjustment: 34
Effective length of query: 387
Effective length of database: 532
Effective search space:   205884
Effective search space used:   205884
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 (21.7 bits)
S2: 52 (24.6 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