GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Jannaschia aquimarina GSW-M26

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_043917824.1 jaqu_RS04905 TRAP transporter large permease

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_000877395.1:WP_043917824.1
          Length = 476

 Score =  689 bits (1778), Expect = 0.0
 Identities = 363/478 (75%), Positives = 413/478 (86%), Gaps = 13/478 (2%)

Query: 1   MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60
           M+VVLLF+M+IGLLL+GVPIAV+LG SS +FLL +SD+SLAS+A + ++A  GH+TLLAI
Sbjct: 1   MEVVLLFTMIIGLLLVGVPIAVSLGFSSIIFLLAFSDTSLASIAQSFYQAMAGHYTLLAI 60

Query: 61  PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120
           PFFILASSFM+TGGVARRIIRFSIACVGHL GGLAIAGVFACM+FAALSGSSPATVVAIG
Sbjct: 61  PFFILASSFMSTGGVARRIIRFSIACVGHLRGGLAIAGVFACMMFAALSGSSPATVVAIG 120

Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180
           +IVIA M+Q GY+K+FAAGVICNAGTLGILIPPSIVMVVYA+A +VSVGRMFLAGV+PGL
Sbjct: 121 TIVIAAMKQAGYTKDFAAGVICNAGTLGILIPPSIVMVVYASATDVSVGRMFLAGVVPGL 180

Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIY------GG 234
           MAGLMLM+TIYV+A++K++PKGE+ GWGEV AS  +A  GL+LI II+ GIY      G 
Sbjct: 181 MAGLMLMITIYVIARIKDMPKGEFAGWGEVGASFRDAFWGLMLIVIIMIGIYGIPGVTGA 240

Query: 235 IFTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKP-KDMGQFLT----MLPKMLGQTVVY 289
           IFTPTEAAAVASVYAF VA F+YRD+GPL  AP+P + +G  +       PK L      
Sbjct: 241 IFTPTEAAAVASVYAFIVAMFIYRDIGPL--APRPAQSVGAAVAGPVEGTPKSLFSAPWA 298

Query: 290 FIPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVM 349
            + +F H DTR  LFEAGKLT+ L+F+IANALILKHVLTDEQ+PQ IA AMLSAG GP+ 
Sbjct: 299 LLTAFVHRDTRDTLFEAGKLTIMLMFIIANALILKHVLTDEQIPQHIAEAMLSAGLGPIT 358

Query: 350 FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV 409
           FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV
Sbjct: 359 FLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPV 418

Query: 410 GLNLFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMGPEIITK 467
           GLNLFVTSGVAGM MMAVVRAALPFLAVLFVFLI++TYIP IS  LP+A+MGPE I +
Sbjct: 419 GLNLFVTSGVAGMSMMAVVRAALPFLAVLFVFLILVTYIPAISLTLPHAIMGPETIIR 476


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: 844
Number of extensions: 24
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: 467
Length of database: 476
Length adjustment: 33
Effective length of query: 434
Effective length of database: 443
Effective search space:   192262
Effective search space used:   192262
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 24 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