GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS02940
          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:

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