GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Desulfoscipio geothermicus DSM 3669

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_900115975.1:WP_092481894.1
          Length = 453

 Score =  198 bits (504), Expect = 2e-55
 Identities = 136/404 (33%), Positives = 205/404 (50%), Gaps = 32/404 (7%)

Query: 10  FDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAG 69
           F E+   V      +  +  GS   D  GKE+ID  GG  +  +GH HP+++KA+ +Q  
Sbjct: 48  FLEYRKSVSTDYTSVEWKDSGSTFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQ 107

Query: 70  KFWHTGNGYTNEPVLRLAKQLIDATFADR--VFFCNSGAEANEAALKLARKYAHDRFGSE 127
           +         +     LAK L   T  D    FF NSG E+ EA +K A+ Y   R    
Sbjct: 108 RQALHSQELLDPLRAFLAKLLGSITPGDLQYAFFVNSGTESVEAGIKFAKMYTGRR---- 163

Query: 128 KSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAK------ALID 181
               ++   AFHG++L ++SA  +  + + F PL P   H  Y + ++ +      A + 
Sbjct: 164 --SFISTTRAFHGKSLGSLSATAKGVFRKPFLPLIPGFHHVPYGNAEAVEMMLESCAFVG 221

Query: 182 DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHY 241
           ++  AVIVEP+QGEGGV+    D+L  LRELCD + ALLI DEVQTG+GRTG+++A  H 
Sbjct: 222 EDVAAVIVEPVQGEGGVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHS 281

Query: 242 GVTPDLLSTAKALGGG-FPIGALLASERCASVMTVG--THGTTYGGNPLACAVAGEVFAT 298
            V PD+L  AKA GGG  PIGA +A +     +      H TT+GGNP+ CA A      
Sbjct: 282 NVVPDILCLAKAFGGGIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINV 341

Query: 299 INTREVLNGVKQRHQWFCERLNAINARY-GLFKEIRGLGLLIGCVLKDEYAGKAKAISNQ 357
           +    +     +   +   +L  +  +Y  + +E+RG GL+IG    ++  G   A    
Sbjct: 342 LLEENLPQRSAESGVYMLGKLRELAEKYPAVVQEVRGKGLMIGIEFFNDELGYEVA---- 397

Query: 358 AAEEGLM---ILIAG----ANVVRFAPALIISEDEVNSGLDRFE 394
              +GL    +L+AG    A  +R  P L IS ++ +  ++R +
Sbjct: 398 ---KGLFARGVLVAGTLINAKSIRIEPPLTISREQQDQVIERLD 438


Lambda     K      H
   0.321    0.137    0.412 

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: 463
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: 406
Length of database: 453
Length adjustment: 32
Effective length of query: 374
Effective length of database: 421
Effective search space:   157454
Effective search space used:   157454
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 Apr 09 2024. 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