GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Herbaspirillum seropedicae SmR1

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate HSERO_RS05745 HSERO_RS05745 NADP-dependent malic enzyme oxidoreductase

Query= BRENDA::P41790
         (338 letters)



>FitnessBrowser__HerbieS:HSERO_RS05745
          Length = 758

 Score =  142 bits (358), Expect = 3e-38
 Identities = 112/336 (33%), Positives = 175/336 (52%), Gaps = 20/336 (5%)

Query: 1   MIIERARELAVRAPARVVFPDALDERVLKAAHYLQQYGLARPVLVASPFA----LRQFAL 56
           M ++     A  AP RVV+ D  DERVL+A  ++   GLA P+LV +P A    +++  L
Sbjct: 435 MFMQPVFNTAKVAPQRVVYADGQDERVLRAVQFVADEGLAAPILVGAPAAIEAGIKKAGL 494

Query: 57  SHRMAMDGIQVIDPHSNLSMRQRFAQRWLARAGEKTPPDAVEKLSDPLMFAAAMVSAGEA 116
             ++  + +QVIDP ++  + Q  AQ        K   +A  + S  L+ AA MV AG+A
Sbjct: 495 RIKIGQN-VQVIDPATDARVAQYAAQ-------YKDGGEADVRASGSLL-AALMVKAGDA 545

Query: 117 DVCIAGNLSSTANVLRAGLRVIGLQPGCKTLSSI-FLMLPQYAGPALGFADCSVVPQPTA 175
           D  + G   +    L    +VIGL+ G +  +++  ++LP      L   D  V   P A
Sbjct: 546 DAMLCGLDGNYDGHLAHVEKVIGLKQGAQEFAALNAVLLPD---QTLFITDTYVNDTPDA 602

Query: 176 AQLADIALASADTWRAITGEEPRVAMLSFSSNGSARHPNVANVQQATELVRERAPQLLVD 235
            QLA IA A+A+   A  G  P+VA LS S+ GS+  P+   +  A E  ++ AP++   
Sbjct: 603 EQLARIAQAAAEE-VARFGVPPKVAFLSHSNRGSSSRPSARKMAAAHEAFKKLAPEVESA 661

Query: 236 GELQFDAAFVPEVAAQKA-PDSPLQGRANVMIFPSLEAGNIGYKITQRLGGY-RAVGPLI 293
           GEL  DAA   ++       DS L G ANV++ P+L+A NI + + +   G    +GP++
Sbjct: 662 GELHGDAALSEKIRNNAGLADSGLTGAANVLVCPNLDAANILFNVLKTSSGQGTTIGPIL 721

Query: 294 QGLAAPLHDLSRGCSVQEIIELALVAAVPRQADVSR 329
            G AAP+H L+   +V+ +I +  +AA   Q   S+
Sbjct: 722 LGAAAPVHVLTPSSTVRRVINMTALAAAKAQDGKSK 757


Lambda     K      H
   0.321    0.134    0.384 

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: 525
Number of extensions: 30
Number of successful extensions: 4
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: 338
Length of database: 758
Length adjustment: 34
Effective length of query: 304
Effective length of database: 724
Effective search space:   220096
Effective search space used:   220096
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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