GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS05695
          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 (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