GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Pseudomonas simiae WCS417

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease

Query= uniprot:I7DRS6
         (467 letters)



>FitnessBrowser__WCS417:GFF2912
          Length = 426

 Score =  499 bits (1284), Expect = e-146
 Identities = 259/457 (56%), Positives = 336/457 (73%), Gaps = 35/457 (7%)

Query: 1   MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60
           M V+ LF ++   + +GVPIA++LGLS  + +L++S  S++S+A  LFE  +  +T LAI
Sbjct: 1   MAVLCLFLLLFVFMFLGVPIAISLGLSGAVSILMFSQDSVSSLAIKLFETSDA-YTFLAI 59

Query: 61  PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120
           PFF+L+ +FMTTGGVA+R+I F+ ACVGH+ GGLAIA V ACMLFAALSGSSPATV A+G
Sbjct: 60  PFFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119

Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180
           SI +AGM + GY K F AG+ICNAGTLGILIPPSIVMVVY+AA E SVG++F+AGVIPGL
Sbjct: 120 SIAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGL 179

Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240
           + GLMLM+ IY++A++K LP      + E   SA  A  GLLL+ IILGGIY G+FTPTE
Sbjct: 180 LLGLMLMIAIYIVARIKKLPAQPRATFREWLTSARRAFWGLLLLVIILGGIYSGMFTPTE 239

Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300
           AAAVA+VY+ FVA F+Y+DM  L+  PK                                
Sbjct: 240 AAAVAAVYSAFVALFIYKDM-QLRDCPK-------------------------------- 266

Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360
             L E+G+L + L+F+IANA++  HVLT EQ+PQ+I   +LS G  P+ FLI+VNV+LLI
Sbjct: 267 -VLLESGRLAIMLMFIIANAMLFAHVLTTEQIPQEITAWVLSEGLTPIGFLIMVNVVLLI 325

Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420
            G FMEPS +++I+AP+ FPIA++LGIDPIHLGI+MVVNMEIG++ PPVGLNLFVTS V 
Sbjct: 326 AGSFMEPSAIVLILAPIFFPIAMKLGIDPIHLGIVMVVNMEIGLVHPPVGLNLFVTSAVT 385

Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPN 457
           G+ +   +RAALP+L +L VFLIM+TY+P+IS  LP+
Sbjct: 386 GLTLGQTIRAALPWLMILLVFLIMVTYLPFISLALPH 422


Lambda     K      H
   0.329    0.144    0.421 

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: 667
Number of extensions: 22
Number of successful extensions: 4
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: 467
Length of database: 426
Length adjustment: 32
Effective length of query: 435
Effective length of database: 394
Effective search space:   171390
Effective search space used:   171390
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