GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Marinobacter adhaerens HP15

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>FitnessBrowser__Marino:GFF1405
          Length = 394

 Score =  194 bits (494), Expect = 3e-54
 Identities = 115/361 (31%), Positives = 192/361 (53%), Gaps = 11/361 (3%)

Query: 31  GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90
           G++I+ L  G+PDFDTP  I QAAI+++  G T Y  V G  AL++ I  + +R +G   
Sbjct: 31  GQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQTKYTAVDGTPALKKAIIAKFKRDNGLDY 90

Query: 91  DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150
           +A Q++V +G + + + +    LNPGDE I+  P +V+Y  +      + V +   +E  
Sbjct: 91  EANQILVSSGGKQSFFNLALATLNPGDEAIIPAPYWVSYPDMVLVAEGKPVIIETGAETR 150

Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYSE 209
           F++  E++   IT RTR   +NSP NPSG +      +A+ E+   H ++ + +D++Y  
Sbjct: 151 FKITPEQLENAITERTRLFVINSPSNPSGMAYTLEELQAIGEVLKKHPNIMIATDDMYEP 210

Query: 210 LLFDGEHVSPA--SLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCML 267
           +L+ G+       + P + DRT  LN +SK+++MTGWR+G+  GPA +   ++ +     
Sbjct: 211 ILWTGKPFCNILNATPELYDRTFVLNGVSKAYSMTGWRIGYAAGPAKIIGAMKKIQSQST 270

Query: 268 YGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVM-- 325
                  Q AA  AL+     +  M +A++ R D ++E L   PG+  L  DG  +V   
Sbjct: 271 SNPASISQAAAQAALDGDQGCVGEMVKAFKERHDWLVEALNKLPGVECLNGDGTFYVFPS 330

Query: 326 ----VDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRR 381
               +D   +  +   FA++LL   GV+++ G AFG    GH+RL      E L +A  R
Sbjct: 331 FQGAIDADSSVSTDVEFAEKLLTDAGVALVPGSAFG--CPGHMRLSFATSMENLEKAVER 388

Query: 382 I 382
           +
Sbjct: 389 L 389


Lambda     K      H
   0.322    0.136    0.411 

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: 360
Number of extensions: 15
Number of successful extensions: 3
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
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 (21.9 bits)
S2: 50 (23.9 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