GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maeN in Pseudomonas fluorescens GW456-L13

Align Na(+)-malate symporter; Sodium-dependent malate transporter (characterized)
to candidate PfGW456L13_3595 Citrate-sodium symport

Query= SwissProt::O05256
         (448 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3595
          Length = 448

 Score =  530 bits (1365), Expect = e-155
 Identities = 250/424 (58%), Positives = 333/424 (78%), Gaps = 1/424 (0%)

Query: 24  QKIWSWEIGVIPLPLYTVLAVIIILAAYYNELPANMLGGFAIIMILGVFLGDIGQRIPIL 83
           + + ++EIGVIPLP++  +AVI+ L+A+   LP NM+GG A+IM +GVF G +G R+PIL
Sbjct: 24  RSLCAYEIGVIPLPIFLGIAVIVYLSAHLGFLPKNMIGGLAVIMTMGVFFGQMGSRLPIL 83

Query: 84  KDIGGPAILSLFVPSFLVFYNVLNSTSLDAVTNLMKTSNFLYFYIACLVVGSILGMNRIV 143
           K+IGG AIL L +PS LVFY      ++DA   LMK +NFLYF IA LVVGSILGM+R +
Sbjct: 84  KEIGGGAILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIASLVVGSILGMSRFI 143

Query: 144 LIQGFIRMFVPLVAGTIAAVAAGILVGFIFGYSAYDSFFFVVVPIIAGGIGEGILPLSIA 203
           L+QG +RMF+PL+ GT+AAVA+G++VG + GYS + +FFF++VPII GGIGEGILPLS+A
Sbjct: 144 LVQGMLRMFIPLLVGTLAAVASGLIVGKLVGYSFHHTFFFIIVPIIGGGIGEGILPLSLA 203

Query: 204 YSQILGSSADVFVSQLVPAAIIGNVFAIICAALMKKLGDKRPDLNGNGRLVKSKKANEIF 263
           YS ILG + D++V+QL PAA++GN+ AIICA  + +L  KRP +NG G L+++K  N+ F
Sbjct: 204 YSAILGGTPDIYVAQLAPAAVVGNIVAIICAGYLARLALKRPTINGEGSLIRAKDENDQF 263

Query: 264 NQKEAEAKI-DFKLMGAGVLLACTFFIFGGLLEKFIFIPGAILMIISAAAVKYANILPKK 322
             KE    I DF++MGAGVL+ C FF+ GGLLEK + IPG ++MI++A   KY  +LP+K
Sbjct: 264 LVKEDTGTIVDFRVMGAGVLVICAFFVLGGLLEKVVGIPGPVMMILAAVLFKYLRVLPEK 323

Query: 323 MEEGAYQLYKFISSSFTWPLMVGLGILFIPLDDVASVISIPFVIICISVVIAMIGSGYFV 382
           +E+GA   YK +SS+F WP+M+GLG+L++PLD V  V S+ +V++C+SVV++M  +G+F+
Sbjct: 324 LEKGANSFYKLVSSAFIWPVMIGLGMLYVPLDSVVKVFSVGYVLVCVSVVVSMTVAGFFI 383

Query: 383 GKLMNMYPVESAIVTCCHSGLGGTGDVAILSASGRMGLMPFAQISTRLGGAGTVICATVL 442
           G LM MYP+ESAIVTCCHSGLGGTGDVAILSAS RM LMPFAQISTR+GGA TVI AT+L
Sbjct: 384 GNLMKMYPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQISTRIGGASTVILATIL 443

Query: 443 LRFF 446
           LR F
Sbjct: 444 LRLF 447


Lambda     K      H
   0.328    0.145    0.427 

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: 876
Number of extensions: 43
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: 448
Length of database: 448
Length adjustment: 33
Effective length of query: 415
Effective length of database: 415
Effective search space:   172225
Effective search space used:   172225
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 (21.7 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:

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