GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ppa in Pseudomonas stutzeri RCH2

Align Phenylacetate permease, Ppa (characterized)
to candidate GFF2882 Psest_2938 transporter, SSS family

Query= TCDB::O50471
         (520 letters)



>FitnessBrowser__psRCH2:GFF2882
          Length = 551

 Score =  739 bits (1907), Expect = 0.0
 Identities = 358/519 (68%), Positives = 435/519 (83%)

Query: 2   NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61
           N+TAI MF+VF+ FT+ +T+WAA R  S +D+YTAGG +TG QNGLAIAGD +SAASFLG
Sbjct: 33  NYTAIIMFVVFIAFTMGITKWAAKRNTSTADYYTAGGSITGFQNGLAIAGDFMSAASFLG 92

Query: 62  ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121
           ISA+++ +GYDGL+Y++G L GWPIILFL+AERLRNLGK+TF+DV SYRL QT +RL SA
Sbjct: 93  ISALVYTSGYDGLIYSIGFLVGWPIILFLMAERLRNLGKFTFSDVASYRLGQTQIRLLSA 152

Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181
           FG+L+V   YL+AQMVGAGKLI+LLFG+ Y  AV+LVGVLMV YV FGGMLATTWVQIIK
Sbjct: 153 FGSLIVVAFYLIAQMVGAGKLIQLLFGLDYYVAVVLVGVLMVMYVLFGGMLATTWVQIIK 212

Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241
           AV+LLSG SFMA MV+K  GF   ++FA AV +H KG  IM+PGGL+S+P+ AISLGL +
Sbjct: 213 AVLLLSGASFMAIMVMKSVGFDFGSLFAEAVKIHEKGAQIMSPGGLVSDPISAISLGLAL 272

Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301
           MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY+L  +IGFGAI++V T P ++D
Sbjct: 273 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAILLVSTNPEFKD 332

Query: 302 ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361
            TGAI+GG NM+A+HLA AVGGNLFLGFISAVAFATILAVVAGL L+GASAVSHDLYACV
Sbjct: 333 VTGAIVGGTNMVAIHLASAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYACV 392

Query: 362 IRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421
           I+QGKA E++EMRV+++ TL +G++A+LLG++FE QNIAF+ GL  ++AAS NFPVL LS
Sbjct: 393 IKQGKAREEDEMRVTKLTTLTLGVVAILLGIIFEKQNIAFMVGLAFSIAASCNFPVLFLS 452

Query: 422 MFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFLS 481
           M+WKGL+TRGA+ G   GL +A+LL ++ P VWV+V    +A+FPY  PALFSM+ AF  
Sbjct: 453 MYWKGLSTRGALFGGSLGLFTALLLTIISPTVWVDVFGFAEAIFPYKYPALFSMAAAFAG 512

Query: 482 AWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
            W FSVTD S+RA EER R+ AQF+RS TG+GA GA  H
Sbjct: 513 IWFFSVTDKSKRAGEERERFFAQFVRSQTGLGATGAVAH 551


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: 946
Number of extensions: 42
Number of successful extensions: 1
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: 551
Length adjustment: 35
Effective length of query: 485
Effective length of database: 516
Effective search space:   250260
Effective search space used:   250260
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.

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