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

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources