GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Herbaspirillum seropedicae SmR1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= BRENDA::Q88RB9
         (425 letters)



>FitnessBrowser__HerbieS:HSERO_RS17580
          Length = 440

 Score =  166 bits (419), Expect = 2e-45
 Identities = 116/378 (30%), Positives = 186/378 (49%), Gaps = 23/378 (6%)

Query: 36  VIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKIN 95
           +ID +G+  ID +GG AV   GH HP+V+ A+++Q+ ++++         P  EL   + 
Sbjct: 24  LIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHTSFFTTAPAEELAAMLA 83

Query: 96  KLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAG------VIAFTGGYHGRTMMTLGL 149
              PG  +    L + GSEAVE A+K+AR      G      +IA    YHG T+  L +
Sbjct: 84  DAAPGSLNHVYFL-SGGSEAVEAALKLARQYYVEVGQPQRRHIIARRQSYHGNTLGALAI 142

Query: 150 TGKVVPYSAGMGLM-------PGGIFRALFPSELHGISVDDAIASVERIFKNDAEPRDIA 202
            G        M ++       P   +R     E     V      +E+   +    + IA
Sbjct: 143 GGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADELEQKILSLGADQVIA 202

Query: 203 AIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAP 262
            +    V    G +P   +  +++RA+CD++G+LLI DEV +G GRTG  FA E+ GV P
Sbjct: 203 FVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGRTGYLFACEEDGVVP 262

Query: 263 DLTTFAKSIAGGF-PLAGVCGKAEYMDAIAPGG----LGGTYAGSPIACAAALAVIEVFE 317
           D+   AK +  G+ P+  +       DA+  G      G TY G   ACAAA+AV +  +
Sbjct: 263 DIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHTYIGHATACAAAVAVQKTIQ 322

Query: 318 EEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTH----TPNAAAV 373
           EE+LL+  +  GE+L + LR+       +GD+RG G  + VE+  + +     +P+    
Sbjct: 323 EERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVELVAERSSKLPLSPDLRTH 382

Query: 374 GQVVAKAREKGLILLSCG 391
            +V A+A ++GL++   G
Sbjct: 383 ARVKAEAMKRGLLVYPMG 400


Lambda     K      H
   0.320    0.138    0.395 

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: 481
Number of extensions: 30
Number of successful extensions: 5
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: 425
Length of database: 440
Length adjustment: 32
Effective length of query: 393
Effective length of database: 408
Effective search space:   160344
Effective search space used:   160344
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: 51 (24.3 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