GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Pseudomonas fluorescens FW300-N2E2

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate Pf6N2E2_1302 TRAP-type C4-dicarboxylate transport system, large permease component

Query= reanno::PV4:5208943
         (465 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1302
          Length = 426

 Score =  221 bits (562), Expect = 5e-62
 Identities = 132/453 (29%), Positives = 242/453 (53%), Gaps = 35/453 (7%)

Query: 1   MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60
           MT+     SL   M LGMPIA AL   S+  ++ + D   A +  +   + ++ + L+A+
Sbjct: 1   MTLVIFLGSLVGSMALGMPIAFALLVVSV-ALMFYLDLFDAQIIAQNLLNGADSFPLMAV 59

Query: 61  PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120
           PFF+L+   ++ GG+++RI++ AM  VGH RGGL   +++A  L A++SGS+ A  AA+ 
Sbjct: 60  PFFMLAGEIMNVGGLSKRIVNIAMALVGHKRGGLGYVAIIASCLLASLSGSAVADAAALA 119

Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180
           ++++  MV AG+    +AG+I     +  +IPPSI  +V+  A+ VS +++F+AG++PGL
Sbjct: 120 ALLVPMMVLAGHNRGRSAGLIAAGSIIAPVIPPSIGFIVFGVASGVSISKLFLAGIVPGL 179

Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240
           M+G  L +A + ++R + + + P      +  +       + L +I++  +  GI +PTE
Sbjct: 180 MLGASLAVAWWYISRSENVETPPKRSRAEVLRTLLDGSWAMGLPLIIILGLKFGIFTPTE 239

Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300
           AA VA VY+ F+++  YR++     VS                              ++ 
Sbjct: 240 AAVVAAVYSLFVSLVIYREM----KVS------------------------------QLY 265

Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360
            V+   AK + +++ ++A AM+ + ++T   +P  +AE +          L+++  L++ 
Sbjct: 266 EVILSSAKTTSVVMLLVAAAMVSSWLVTIADLPGQLAEMLAPFMDNQTLLLLVMMTLIIL 325

Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420
            G  M+ +  +LI+ P+L P   Q GIDP++ G++ ++N  IG++TPPVG  L V  G+ 
Sbjct: 326 VGTVMDMTPTILILTPVLMPAVIQAGIDPVYFGVLFLINTAIGLITPPVGTVLNVVCGVA 385

Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISL 453
                 ++    P++      L L+   PQ+ L
Sbjct: 386 KLDFEEIVRGVWPFMFAQFVVLFLLVLFPQLVL 418


Lambda     K      H
   0.330    0.144    0.424 

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: 530
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 465
Length of database: 426
Length adjustment: 32
Effective length of query: 433
Effective length of database: 394
Effective search space:   170602
Effective search space used:   170602
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: 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