GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ppa in Azospirillum brasilense Sp245

Align Phenylacetate permease, Ppa (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease

Query= TCDB::O50471
         (520 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS02940 AZOBR_RS02940 actetate
           permease
          Length = 572

 Score =  694 bits (1790), Expect = 0.0
 Identities = 349/539 (64%), Positives = 428/539 (79%), Gaps = 24/539 (4%)

Query: 2   NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61
           N++AI MF+VFV  TL +T WAA RT+SA DFY AGGG+TG QNGLAIAGD +SAASFLG
Sbjct: 38  NFSAIVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLG 97

Query: 62  ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121
           I+ +++ +G+DGL++++G L GWPIILFL+AERLRNLGKYTFADV SYR  QTP+R  +A
Sbjct: 98  IAGLVYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAA 157

Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181
            G+L     YL+AQMVGAGKLI+LLFG+ YL+AV++VGVLM+AYVTFGGMLATTWVQIIK
Sbjct: 158 CGSLATVTFYLIAQMVGAGKLIQLLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIK 217

Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241
           AV+LLSG SFMAF VL  FGFS EAMF++AV VH K   IMAPG L+++PV AISLG+ +
Sbjct: 218 AVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMAL 277

Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301
           MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY+L  +IGFGAIV++       D
Sbjct: 278 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAIVLLLAP----D 333

Query: 302 ATGA--------------------IIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAV 341
           ATGA                    IIGG NM A+H A AVGG+LF GFISAVAFATILAV
Sbjct: 334 ATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGGDLFFGFISAVAFATILAV 393

Query: 342 VAGLALSGASAVSHDLYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAF 401
           VAGL L+GASAVSHDLYA VI +G+A+E +E+RVS+I T++IG++++ LG+ FE+QN+AF
Sbjct: 394 VAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVIIGIVSIFLGIAFENQNVAF 453

Query: 402 LSGLVLAVAASVNFPVLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHE 461
           + GL   +AAS NFPVLL+SMFW  +TTRGAV G   GL S+V L+++GP VW +VL + 
Sbjct: 454 MVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNP 513

Query: 462 KALFPYSNPALFSMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
            ALFPY NP +F++ L+FL+ W FS+TD+S+ A +ER  Y AQ+IRS TG+GA GAS H
Sbjct: 514 AALFPYDNPGVFTIPLSFLAIWFFSITDNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572


Lambda     K      H
   0.328    0.139    0.407 

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: 970
Number of extensions: 34
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: 520
Length of database: 572
Length adjustment: 35
Effective length of query: 485
Effective length of database: 537
Effective search space:   260445
Effective search space used:   260445
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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