GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Methanospirillum lacunae Ki8-1

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_109969430.1 DK846_RS13185 aspartate aminotransferase family protein

Query= BRENDA::P04181
         (439 letters)



>NCBI__GCF_003173355.1:WP_109969430.1
          Length = 400

 Score =  242 bits (617), Expect = 2e-68
 Identities = 145/392 (36%), Positives = 218/392 (55%), Gaps = 31/392 (7%)

Query: 60  VALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKSQVDKLTLTSRAFYNNV 119
           +++E+G G+Y+WD  G++Y DF S +     GH +P I  AL +Q  K+         N 
Sbjct: 24  LSIEKGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKKIIQNP-----NS 78

Query: 120 LGEYEEYITKLFN-YHKVLPM--------NTGVEAGETACKLARKWGYTVKGIQKYKAKI 170
              Y    ++L   +H++LP         N+G EA + A KLARK    V G    K  I
Sbjct: 79  GATYSPARSRLIQLFHEILPKHLTRIFFANSGAEANDAAIKLARK----VTG----KKNI 130

Query: 171 VFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVE 230
           +    +F GRT+S +S++      + F P MPG+  +P+ND+ A++  + D +VAA +VE
Sbjct: 131 ISTEMSFHGRTISTVSATGQDVHRNKFNPLMPGYFFVPFNDISAVKEII-DQDVAAVIVE 189

Query: 231 PIQGEAGVVVPDPGYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLL 290
           PIQGE GV +P   YL+ + E+C  H VLFIADEIQTG  RTG       +  +PDI+ +
Sbjct: 190 PIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGAKPDIITM 249

Query: 291 GKALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCRVAIAALEVLEEENLAENAD 350
            K ++GG +P SA    D+++  I+ G+HG TY GNPLGC V+ A +  L + ++  +  
Sbjct: 250 AKGIAGG-FPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSDIESHVS 308

Query: 351 KLGIILRNEL----MKLPSDVVTAVRGKGLLNAIVIKETKDWDAWKVCLRLRDNGLLAKP 406
            LGI     L     K P   +T VRG+GLL  I ++ T D  + ++  R  DNGL+   
Sbjct: 309 DLGIDTIKRLNGWKEKYPK-AITEVRGQGLL--IALELTDDLKSAEIVTRCLDNGLILNL 365

Query: 407 THGDIIRFAPPLVIKEDELRESIEIINKTILS 438
            HG IIR  P L I + E++  ++I+ K I++
Sbjct: 366 KHGHIIRIFPALTITKQEMQTGLDILEKEIVT 397


Lambda     K      H
   0.319    0.138    0.415 

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: 424
Number of extensions: 22
Number of successful extensions: 7
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: 439
Length of database: 400
Length adjustment: 32
Effective length of query: 407
Effective length of database: 368
Effective search space:   149776
Effective search space used:   149776
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