GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ppa in Pseudomonas fluorescens FW300-N2C3

Align Phenylacetate permease, Ppa (characterized)
to candidate AO356_19665 AO356_19665 cation/acetate symporter ActP

Query= TCDB::O50471
         (520 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19665 AO356_19665
           cation/acetate symporter ActP
          Length = 552

 Score =  713 bits (1841), Expect = 0.0
 Identities = 349/520 (67%), Positives = 424/520 (81%)

Query: 1   MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60
           +N  AI MF+ FV  TL +T WA+ +  SA+D+Y AGG +TG QNGLAIAGD +SAASFL
Sbjct: 33  LNVAAILMFVAFVGATLYITYWASKKNNSAADYYAAGGKITGFQNGLAIAGDYMSAASFL 92

Query: 61  GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120
           GISA++F +GYDGL+Y++G L GWPIILFLIAERLRNLGKYTFADV SYRL QT +R  S
Sbjct: 93  GISALVFTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVASYRLGQTQIRTLS 152

Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180
           A G+LVV   YL+AQMVGAGKLI+LLFG+ Y  AV+LVG+LM  YV FGGMLATTWVQII
Sbjct: 153 ASGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVGILMCLYVLFGGMLATTWVQII 212

Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240
           KAV+LLSG SFMA MV+KH  F    +FA AV VH KG+AIM+PGGL+ +P+ A SLGL 
Sbjct: 213 KAVLLLSGASFMALMVMKHVNFDFNMLFAEAVKVHPKGEAIMSPGGLVKDPISAFSLGLA 272

Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300
           +MFGTAGLPHILMRFFTVSDAKEARKSV YATGFIGYFY+L  +IGFGAI++V T P+++
Sbjct: 273 LMFGTAGLPHILMRFFTVSDAKEARKSVLYATGFIGYFYILTFIIGFGAILLVSTNPAFK 332

Query: 301 DATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360
           DA GA++GG NM AVHLA AVGG++FLGFISAVAFATILAVVAGL L+GASAVSHDLYA 
Sbjct: 333 DAAGALLGGNNMAAVHLANAVGGSIFLGFISAVAFATILAVVAGLTLAGASAVSHDLYAS 392

Query: 361 VIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420
           VI++GKA E++E+RVS+I T+ + +LA+ LG++FE QNIAF+ GL  ++AAS NFPVLLL
Sbjct: 393 VIKKGKANEKDEIRVSKITTIALAVLAIGLGILFEKQNIAFMVGLAFSIAASCNFPVLLL 452

Query: 421 SMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFL 480
           SM+WK LTTRGA+ G   GL SAV L++LGP +WV ++ HEKA+FPY  PALFSM++AF+
Sbjct: 453 SMYWKKLTTRGAMIGGWLGLVSAVGLMILGPTIWVQIMGHEKAIFPYEYPALFSMAIAFV 512

Query: 481 SAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
             W FS+TD S   + ER  +  QF+RS TG+GA+GA  H
Sbjct: 513 GIWFFSITDKSAEGANERALFFPQFVRSQTGLGASGAVNH 552


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: 920
Number of extensions: 39
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: 552
Length adjustment: 35
Effective length of query: 485
Effective length of database: 517
Effective search space:   250745
Effective search space used:   250745
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