GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Herbaspirillum seropedicae SmR1

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate HSERO_RS05695 HSERO_RS05695 D-amino acid oxidase

Query= BRENDA::O59089
         (382 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05695 HSERO_RS05695 D-amino
           acid oxidase
          Length = 441

 Score =  154 bits (389), Expect = 5e-42
 Identities = 117/422 (27%), Positives = 186/422 (44%), Gaps = 61/422 (14%)

Query: 3   PEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANVR 62
           P  +++VVIGGGI+G+  A+ LAKRG  V V+EK  IG+  + R     RQQ  D   + 
Sbjct: 15  PASADVVVIGGGIIGIFTAYFLAKRGISVAVVEKGRIGAEQSSRNWGWCRQQNRDARELP 74

Query: 63  VMKRSVELWKKYSEEYG--FSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPE 120
           +  +S++LW+++S E G    F + G L+L  D+EE+  +    +     GV T ++  +
Sbjct: 75  MATKSIDLWEQFSAETGEDTGFNRCGLLYLSNDEEEIARWAAWGDFAKTAGVTTYMLDSK 134

Query: 121 EAKEIVPLLDISEVIAASW-----NPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGF 175
           +A E             +W     +PTDG ADP +A  A A    + G  +++    +G 
Sbjct: 135 QAAE------RGHATGRAWKGGVFSPTDGTADPGKAAPAVARAIMKLGGHVIQQCAARGI 188

Query: 176 LIENNEIKGVKTNKGIIKTGIVVNATNAWANLINAMAGIK-----------TKIPIEPYK 224
             E   + GV T  G+IKT + V A  AWA+      GI+           +  P+E   
Sbjct: 189 DTEGGRVSGVITEAGVIKTKVAVMAGGAWASSFCHQLGIRFPQASVRQSIMSVAPMEAPL 248

Query: 225 HQAVITQPIK---------------RGTINPMVISFKYGHAYL---TQTFHGGIIGGI-- 264
             A+ T  +                R  ++P +   ++   +L    + +     GG+  
Sbjct: 249 PGALYTSGVAVTRRSDGSYALAISGRARVDPTMQFLRFSPQFLPMFAKRWRSLSPGGLEA 308

Query: 265 ---GYEI-------GPT-------YDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAGY 307
              G+E         PT        D +     +R       +++P L    +  TWAGY
Sbjct: 309 WRSGHETLSRWRMDAPTPMERMRILDASADPASIRATHRRAVELLPQLAQAKVTHTWAGY 368

Query: 308 YAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPY 367
              TPD  P IG + +     +AAGFSGHGF + P  G ++A+L +     +    Y P 
Sbjct: 369 VDSTPDGVPGIGELPQTPGLILAAGFSGHGFGIGPGAGHLIADLASGAAPIVDPRPYHPN 428

Query: 368 RF 369
           RF
Sbjct: 429 RF 430


Lambda     K      H
   0.318    0.138    0.405 

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: 365
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 382
Length of database: 441
Length adjustment: 31
Effective length of query: 351
Effective length of database: 410
Effective search space:   143910
Effective search space used:   143910
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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