GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctM in Pseudomonas stutzeri RCH2

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate GFF4197 Psest_4270 TRAP transporter, DctM subunit

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



>lcl|FitnessBrowser__psRCH2:GFF4197 Psest_4270 TRAP transporter,
           DctM subunit
          Length = 426

 Score =  518 bits (1333), Expect = e-151
 Identities = 268/459 (58%), Positives = 345/459 (75%), Gaps = 35/459 (7%)

Query: 1   MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60
           MTI  LF +LF+ M +G+P+A++LG +  LTI++FS DS+ S+A+KL+E TSEHYTLLAI
Sbjct: 1   MTILFLFAALFVLMFIGVPVAVSLGLAGSLTIMIFSQDSVRSLAIKLFE-TSEHYTLLAI 59

Query: 61  PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120
           PFF+L+ AF++TGGVARR+IDFA   VGHIRGGLA+ +V+ACMLFAA+SGSSPATVAA+G
Sbjct: 60  PFFLLAGAFMTTGGVARRLIDFANACVGHIRGGLAIGAVLACMLFAALSGSSPATVAAVG 119

Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180
           SI I GMVR+GYP+ F AG++  +GTLGILIPPS+VM+VYAAATE S  ++FMAG++PG+
Sbjct: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSVVMVVYAAATETSVGKLFMAGVVPGI 179

Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240
           ++G  LM+AIYI+A  K LP+ P   FR    ++ KA+ GL L+VI+LG IY G+ +PTE
Sbjct: 180 LLGGALMIAIYIIAVKKNLPALPRASFREWLSAARKAIWGLLLMVIILGGIYSGMFTPTE 239

Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300
           AAAVA VY+ F+A+F Y+DI      S RD  + L+                        
Sbjct: 240 AAAVAAVYSAFVALFVYKDI------SLRDCPKVLL------------------------ 269

Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360
               +  K+SIML+FIIANAMLFAHVLTTE+IP  I   ++  GL  W FL++VN++LL 
Sbjct: 270 ----ESGKLSIMLMFIIANAMLFAHVLTTEQIPQAITAWVIEAGLQPWMFLLVVNIVLLI 325

Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420
           AG FMEPSAI+LI+APILFPIA QLGIDPIHLGIIMVVNMEIG++TPPVGLNLFV + +T
Sbjct: 326 AGAFMEPSAIILILAPILFPIAIQLGIDPIHLGIIMVVNMEIGLITPPVGLNLFVASAVT 385

Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459
           G  +  VI + +PWLAL+L FL +ITY+P ISL LP  +
Sbjct: 386 GMPVTQVIRAVLPWLALMLSFLVIITYVPSISLALPNML 424


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: 676
Number of extensions: 25
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: 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.

Links

Downloads

Related tools

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 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