GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Desulfoscipio geothermicus DSM 3669

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_245779653.1 BM299_RS04985 aspartate aminotransferase family protein

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_900115975.1:WP_245779653.1
          Length = 471

 Score =  244 bits (622), Expect = 5e-69
 Identities = 155/411 (37%), Positives = 218/411 (53%), Gaps = 62/411 (15%)

Query: 32  ALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKD--------QADKITLTSRAFH 83
           A G  V D EGN Y+D L  Y ++N GH HP++I+A++         QA   T+T+   H
Sbjct: 57  AEGTRVWDSEGNAYLDFLGGYGSLNIGHNHPRVIEAVEQVRELPNILQASIPTITAALLH 116

Query: 84  NDQLGPFYEKTAKLT-GK-EMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIACV 141
           N          A +T GK +     N+GAEAVE A+K AR         A  +   I C 
Sbjct: 117 N---------LAVITPGKLKRSFLCNSGAEAVEGALKLAR--------AATGRKTFIYCR 159

Query: 142 GNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITP-NTAAFLFEPIQG 200
            +FHG++  A+S++  E+Y+  F P+L   + +P+GD++ALR+A+     AAF+ EP+QG
Sbjct: 160 NSFHGKSFGALSVTGREKYRELFEPLLFDCREVPFGDIDALRKALRKYQAAAFIVEPVQG 219

Query: 201 EAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKAL 260
           E GI +PP G+L EAA  C++   LFIADEIQTG GRTG  FAC  + + PD+  L K+L
Sbjct: 220 EGGINMPPRGYLSEAARACRDAGTLFIADEIQTGFGRTGAMFACQHENVEPDVMCLAKSL 279

Query: 261 GGGVFPISCIAADREIL-----GVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRS 315
           GGG+ PI     + +I       V     H STFGGN  A A  IA++EVL  EKL   +
Sbjct: 280 GGGIMPIGAFITNDDIWQKAYGSVEKATLHTSTFGGNTWAAAAGIAAIEVLVKEKLPAAA 339

Query: 316 LELGEYFKSELESIDS--PVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETHD-- 371
            E G YF S L  +    P+++EVRG+GL IG+EL +            GL  K +H+  
Sbjct: 340 AEKGTYFISGLRDLQKKYPLLQEVRGQGLLIGIELAQPGG--LTNKATMGLASKLSHEYL 397

Query: 372 -----------------------TVIRFAPPLIISKEDLDWAIEKIKHVLR 399
                                   VIR  PPL ++ E+LD+ +  +  VL+
Sbjct: 398 GSMVAGELLNRHRIITAYTLNNPNVIRMEPPLTVTGEELDYVLNALDDVLK 448


Lambda     K      H
   0.318    0.136    0.401 

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: 467
Number of extensions: 26
Number of successful extensions: 7
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: 401
Length of database: 471
Length adjustment: 32
Effective length of query: 369
Effective length of database: 439
Effective search space:   161991
Effective search space used:   161991
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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