GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Pseudomonas litoralis 2SM5

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::WCS417:GFF4238
         (406 letters)



>NCBI__GCF_900105005.1:WP_090271605.1
          Length = 417

 Score =  217 bits (553), Expect = 4e-61
 Identities = 130/401 (32%), Positives = 210/401 (52%), Gaps = 36/401 (8%)

Query: 30  RGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVS-NVFTNEPALR 88
           RGEG  +    G+  +DF  GI V   GH HP +V A  EQ  KL H      T++P L 
Sbjct: 18  RGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQPMLD 77

Query: 89  LAHKLIDAT--FAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTL 146
           LA +L+       + V F N+G+EA E A +LAR        + +  +I     FHGRT+
Sbjct: 78  LAERLVGKMPDGIDSVAFSNAGSEAVEMALRLARHA------TRRANVIVFNGGFHGRTM 131

Query: 147 FTVNVGGQ-SKYSDGFGPKITGITHVPYN------------------DLDAL--KAAVSD 185
              ++    +K  + + P + G+   P+                   +LD +       +
Sbjct: 132 GAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQTAPE 191

Query: 186 KTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYG 245
            T A+V+EP+QGE G  P   A++QG  + C  +  LLV DE+Q G GRSG  +++QH+G
Sbjct: 192 DTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQHFG 251

Query: 246 VTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTP 305
           +TPDI+ +AK L  GFP++AM  ++ L    + G+ G TYG N ++CA A A + V++  
Sbjct: 252 ITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVMDNE 311

Query: 306 EVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDA----FKGKAKDVFNAA 361
            ++A   A+       L+ + +QY    ++RG GL+LG  ++ +        A  +  A+
Sbjct: 312 NLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPDKPLADLAASLTTAS 371

Query: 362 EKENLMILQAGPD--VVRFAPSLVVEDADIKEGLDRFERAV 400
           E+E L++L+ G D  ++R+ P LVV +A++ + + RF R +
Sbjct: 372 EEEGLLLLRCGTDSQIIRWLPPLVVSEAEVDDAVQRFTRVL 412


Lambda     K      H
   0.320    0.137    0.400 

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: 372
Number of extensions: 17
Number of successful extensions: 6
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: 406
Length of database: 417
Length adjustment: 31
Effective length of query: 375
Effective length of database: 386
Effective search space:   144750
Effective search space used:   144750
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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