GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Dechlorosoma suillum PS

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= BRENDA::Q5XPV2
         (457 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  129 bits (325), Expect = 1e-34
 Identities = 126/416 (30%), Positives = 183/416 (43%), Gaps = 59/416 (14%)

Query: 47  GVWLVDAVTQKRYLDLFSFFASAPLGINPPSIVEDPAFMRELAVAAVNKPSNPDLYSVPY 106
           G WLVD    KRYLD    +A   LG   P+IVE  A      +     PS P  Y+ P 
Sbjct: 30  GSWLVDQ-QGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLI----NPS-PAFYNEPS 83

Query: 107 ARFVKTFARVLGDPRLPRLFFVDGGALAVENALKAALDWKAQKLGLAEPDTDRLQVLHLE 166
              +K  A +       R+FF   GA A E A+K A  W  +  G A       +++   
Sbjct: 84  ---LKLAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAH------EIITFA 134

Query: 167 RSFHGRSGYTMSLTNTEPSKTARFPKFGWPRISSPALQHPPAEHTGANQEAERRALEAAR 226
             FHGR+  TMS +           K GW  + +P +   P        +A+   L++  
Sbjct: 135 GGFHGRTLATMSASG----------KPGWDTLFAPQVPGFP--------KAQLNDLDSVA 176

Query: 227 EAFAAADGMIACFIAEPIQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEVQSGCGITGT 286
              A  +      + EPIQGEGG    SAEFLQ ++++C +   L ++DEVQ+G G TG 
Sbjct: 177 ---ALINERTVAIMLEPIQGEGGVVPASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGK 233

Query: 287 AWAYQQLGLQPDLVAFGKKTQVCGVMGGGRIDEVPENVFAVSSRI--------SSTWGGN 338
            +A+Q  G++PD++  GK     G+ GG     VP +       +          T+ GN
Sbjct: 234 LFAHQHAGIEPDIMTLGK-----GIGGG-----VPLSALLAKESVCCFEAGDQGGTYNGN 283

Query: 339 LADMVRATRLLETIERTQVFDTVVQRGKYFRDGLEDLAARHPSVVTNARGRGLMCAVDLP 398
                    +LE +        V  +G+Y   GL+ L+ R    +   RG+GL+ A+ L 
Sbjct: 284 PLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGLQRLSDR--LGLRGERGQGLLRALLLA 341

Query: 399 DTR--TRNEVLRLMYTEHQVIALPCGGRSLRFRPALTIAEHEIDQALQALASSVTA 452
           D R     E  R    E  ++  P     LRF P+LT++  EIDQ L  L   + A
Sbjct: 342 DERGPAIVEAARERGPEGLLLNAP-RPHLLRFMPSLTVSREEIDQMLAWLEELLRA 396


Lambda     K      H
   0.320    0.135    0.402 

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: 414
Number of extensions: 28
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: 457
Length of database: 396
Length adjustment: 32
Effective length of query: 425
Effective length of database: 364
Effective search space:   154700
Effective search space used:   154700
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