GapMind for catabolism of small carbon sources

 

Aligments for a candidate for potE in Pseudomonas fluorescens GW456-L13

Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate PfGW456L13_3775 Putrescine/proton symporter, putrescine/ornithine antiporter PotE

Query= SwissProt::P0AAF1
         (439 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3775
           Putrescine/proton symporter, putrescine/ornithine
           antiporter PotE
          Length = 461

 Score =  587 bits (1513), Expect = e-172
 Identities = 288/431 (66%), Positives = 350/431 (81%), Gaps = 2/431 (0%)

Query: 1   MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60
           MS AK  KM V QLT+LT VNM+GSGI++LPTKLAEVG ISI+SWL+TA GS+ALA+AFA
Sbjct: 1   MSVAK--KMSVGQLTMLTAVNMLGSGIVLLPTKLAEVGAISILSWLITATGSLALAYAFA 58

Query: 61  KCGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGASLS 120
           +CGM SRK+GGMGGYAEY FGK+GN++ NYTYG+SLLIANVAI+I+AVGY   L G  L 
Sbjct: 59  RCGMLSRKTGGMGGYAEYTFGKAGNYITNYTYGLSLLIANVAISITAVGYIQVLFGIELD 118

Query: 121 PVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDS 180
            +Q+GLATI +LWI T ANFGGA ITG+I ++TVWGVI PVV +  +GWFWF  ++Y   
Sbjct: 119 SLQVGLATIALLWITTFANFGGASITGRIGAVTVWGVIAPVVLVSTVGWFWFDSSVYAAG 178

Query: 181 WNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIV 240
           WNPH   +F A G+S+A+TLWAFLGLESACANTD VENPERNVPIAVLGGTLGAAVIYIV
Sbjct: 179 WNPHDKGWFEAAGASVAITLWAFLGLESACANTDAVENPERNVPIAVLGGTLGAAVIYIV 238

Query: 241 STNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVF 300
           STNVI GIV N ELA STAPFGL FA+MFTP VG ++MA MV++C GSLLGWQFTIAQV+
Sbjct: 239 STNVIFGIVGNEELAASTAPFGLVFAKMFTPMVGDIVMAAMVLACIGSLLGWQFTIAQVY 298

Query: 301 KSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTN 360
           KSS+D GYF  IF++  K   P+ GML ++  Q+ LAL+TISP L+ QF+ LVNLAVVTN
Sbjct: 299 KSSADTGYFLPIFAKGNKAGTPIVGMLVLLAAQTALALLTISPDLSKQFDTLVNLAVVTN 358

Query: 361 IIPYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFL 420
           ++PYILSMAAL+ +QKV+NVP  KA   N +A + A YS+ ALYSSGE+A++ G + T +
Sbjct: 359 LVPYILSMAALMTMQKVSNVPEGKALATNVIALIAAAYSYLALYSSGEQALMLGGVATIV 418

Query: 421 GWTLYGLVSPR 431
           G+TL+G V+ R
Sbjct: 419 GYTLFGFVNNR 429


Lambda     K      H
   0.323    0.136    0.411 

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: 726
Number of extensions: 27
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: 439
Length of database: 461
Length adjustment: 33
Effective length of query: 406
Effective length of database: 428
Effective search space:   173768
Effective search space used:   173768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 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 preprint 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