GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Kocuria flava HO-9041

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_083529261.1 AS188_RS05075 PLP-dependent aminotransferase family protein

Query= SwissProt::H3ZPL1
         (417 letters)



>NCBI__GCF_001482365.1:WP_083529261.1
          Length = 412

 Score =  266 bits (679), Expect = 1e-75
 Identities = 144/404 (35%), Positives = 229/404 (56%), Gaps = 8/404 (1%)

Query: 13  APTL-DYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEV 71
           AP L D    F+ +A G + S +R + ++     +ISLAGG P     P  ++      +
Sbjct: 12  APGLPDPAALFARRAEGFRPSPVRAVFEIAMRPGMISLAGGNPDTGALPHAVLAGTAARL 71

Query: 72  LEKHAAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVD---IMTTSGSQQALDLIGRV 128
           L +  ++ LQYG+  G   L   +   M    D+  +  D   I  T+GSQ  +DL+ ++
Sbjct: 72  LAERGSEVLQYGSGAGIERLPELVCRLM----DLEGAATDPGRIQITAGSQAGIDLVVKL 127

Query: 129 FINPGDIIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKI 188
           F +PGD++V E PTY+ AL  F  YE     + +DD+G++ + + E++  L   G+ VK+
Sbjct: 128 FCDPGDVVVAEGPTYVGALGVFGSYEVAVSHVDVDDDGLDPEAVAERIDALRATGRTVKL 187

Query: 189 VYTIPTFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEG 248
           VYT+PTF NP GVT+ E+RR+RL+ + ++   +++ED+PYG L +  E   P     +  
Sbjct: 188 VYTVPTFHNPTGVTLGEERRRRLVAVCAERGVVVLEDDPYGLLGFDREHRLPSLYSLDPE 247

Query: 249 RVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLD 308
            V++LG+FSKI +PG R+GWIAA P    +L+IA ++V +  +   Q +A +YV G +  
Sbjct: 248 TVVHLGSFSKIFSPGLRVGWIAASPAVRARLQIAAEAVTIHPSVLGQELAAEYVGGEHWR 307

Query: 309 KHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAK 368
             + + +  Y+ R  AM+ ALEE MP+GV+WT+P GG F W  L        +L +A+  
Sbjct: 308 PALDRAVARYRSRCAAMMAALEEHMPEGVRWTRPAGGFFTWLDLDPARAHGDLLHRAIDH 367

Query: 369 GVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIK 412
           GV  VPG A +A      ++RL F+   EE I EG++RL   ++
Sbjct: 368 GVVVVPGGACYADGRPSTSLRLAFSAAAEEDIAEGVRRLGRMLR 411


Lambda     K      H
   0.318    0.137    0.398 

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: 432
Number of extensions: 16
Number of successful extensions: 2
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: 417
Length of database: 412
Length adjustment: 31
Effective length of query: 386
Effective length of database: 381
Effective search space:   147066
Effective search space used:   147066
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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