GapMind for catabolism of small carbon sources

 

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

Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate PfGW456L13_3582 Aspartate-proton symporter

Query= SwissProt::O07002
         (520 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3582
          Length = 548

 Score =  673 bits (1736), Expect = 0.0
 Identities = 301/512 (58%), Positives = 410/512 (80%), Gaps = 1/512 (0%)

Query: 1   MSKQGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGL 60
           MS QG F+K +SL DL  IG+GAIFGS WLFA S+V++ AGP+G FSW+LGG  +LL+G+
Sbjct: 1   MSGQGKFKKQLSLIDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIFSWLLGGFAVLLLGI 60

Query: 61  VYAELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPG 120
           VY ELGAALPR GG++RYPVYSHG L+GYL+ F+T++A++SL++IEV A RQY A WFP 
Sbjct: 61  VYCELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVAARQYAAAWFPA 120

Query: 121 LTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFH 180
           LT  GS +PT  GW++QF LLCLFF+LNY+SVKTFAKAN +IS+FK+IVP+ +I VL   
Sbjct: 121 LTQAGSSNPTAIGWLVQFGLLCLFFMLNYYSVKTFAKANNLISMFKFIVPLLVIGVLFTF 180

Query: 181 FQPENLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICI 240
           F+PEN   QGF PFG +G++ A+S GG++FAYLGL PI+SVA EV+NP+R IPIALI+ +
Sbjct: 181 FKPENFQSQGFMPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIALILSV 240

Query: 241 IVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAIL 300
           ++ST IY +LQV F+G +PTE L +GW  + +E +LP++DIA+ LG+GWLA LV+ DA++
Sbjct: 241 LLSTAIYVLLQVAFLGGVPTEMLANGWAGVAKELALPYRDIALALGVGWLAYLVVADAVI 300

Query: 301 SPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPS 360
           SP G GNI+MN T R++Y WA+ GT F +F+++++ +G PR +LWL+FALS+FWTLPFPS
Sbjct: 301 SPSGCGNIYMNATPRVIYGWAQTGTFFKVFTRIDEKSGIPRPALWLTFALSVFWTLPFPS 360

Query: 361 WNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWS 420
           W AL+NV S AL+LSYA+AP+S AALR NA D+ RPF +K M ++GP+SFI  A IVYWS
Sbjct: 361 WEALINVVSAALVLSYAVAPVSVAALRRNAPDMPRPFKVKRMGVLGPVSFIIAALIVYWS 420

Query: 421 GWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFG 480
           GW TVSWLLG Q++MF++YL   ++ P + +SLAQQ++S+ WLIGFY + ++ S++GSFG
Sbjct: 421 GWSTVSWLLGLQILMFVVYLLCGRFVPTQHLSLAQQVRSSAWLIGFYAVTIVLSWLGSFG 480

Query: 481 HGLGIISNPVDLILVAIGSLAIYYWAKYTGLP 512
            G+G++++P D ++VA  ++ IYYW   TG+P
Sbjct: 481 -GMGVLTHPFDTVVVAACAMGIYYWGAATGVP 511


Lambda     K      H
   0.328    0.143    0.451 

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: 1043
Number of extensions: 47
Number of successful extensions: 3
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: 548
Length adjustment: 35
Effective length of query: 485
Effective length of database: 513
Effective search space:   248805
Effective search space used:   248805
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: 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