GapMind for catabolism of small carbon sources

 

Alignments for a candidate for metP in Marinobacter adhaerens HP15

Align Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized)
to candidate GFF2680 HP15_2624 sodium-dependent transporter family protein

Query= TCDB::Q8NRL8
         (579 letters)



>FitnessBrowser__Marino:GFF2680
          Length = 470

 Score =  200 bits (509), Expect = 9e-56
 Identities = 147/465 (31%), Positives = 227/465 (48%), Gaps = 50/465 (10%)

Query: 33  RREVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDF 92
           +R ++SSR  FILAA GSAVGLGNIW+FPYV  +NGGGAF++ Y + +   GIP++  + 
Sbjct: 21  QRGLWSSRLAFILAATGSAVGLGNIWKFPYVTGENGGGAFVLVYLLCIAVVGIPIMMAEV 80

Query: 93  AIGHRYRGSAPL-------AFRRFKKQTETIGWIQVGIAFFITIYYAAIIGWAGLYAFKS 145
            IG R  G +P+          R K   + +G I +   F I  +Y+ I GWA  Y   +
Sbjct: 81  MIGRR-GGRSPVKSLSLIAEHDRLKPAWKLVGAIGILAGFLILSFYSVIGGWAISYVGTT 139

Query: 146 LN-KAWGADPDTY--FFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAI-GVDKG 201
            + +  G   DT    FS  L+            P   +A   +++A ++V+ + GV  G
Sbjct: 140 ASGQLAGQSADTVGAVFSGLLS-----------DPTKLLAWHTLFMAMVMVVVVRGVRSG 188

Query: 202 IGRVSMVFMPLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFS 261
           + R   + MP L ++ LIVV  A+           LF P++  L    + + A G  FF+
Sbjct: 189 LERAVSILMPALFVLLLIVVGYAMTTGHFGQAAAFLFQPDFSKLTTSGI-LVALGHAFFT 247

Query: 262 LSVGFGIMLTYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDE 321
           LS+G  +M+ Y SYL    ++  T +     ++   +LAG+ +F  +       G     
Sbjct: 248 LSLGMAVMMAYGSYLPKNISIAKTSITVSVIDTGVALLAGLAIFPIVFANGLEPG----- 302

Query: 322 VATSGIGLAFVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLN 381
              +G GL F   P    +MP+G LFG LFF  L  A +TS  SLLE +V  ++++ G+N
Sbjct: 303 ---AGPGLIFQTLPLAFGQMPMGSLFGTLFFVLLIFAAWTSGISLLEPIVEWLEERKGMN 359

Query: 382 RKATAIGVGVV------MALLSLGLFS---------TTSGLATLDIMDKFTNNIGIVAVA 426
           R  + +G G V       ++LSL L+S            G    D++D FT NI +    
Sbjct: 360 RTVSTLGAGFVCWGLGIASILSLNLWSDFAPLGFVPMLEGKTIFDLLDFFTANIMLPLGG 419

Query: 427 LIAVVSIDWVLRRIDEFSTHLNAISAFKVNTIWRISVVNITTLVL 471
           L+  +   WV+ R  +      A+S    N +W I+V  IT + +
Sbjct: 420 LLVALFAGWVMSR--QAMERELALSPAMFN-LWLITVRFITPVAV 461


Lambda     K      H
   0.325    0.141    0.430 

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: 617
Number of extensions: 26
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: 579
Length of database: 470
Length adjustment: 35
Effective length of query: 544
Effective length of database: 435
Effective search space:   236640
Effective search space used:   236640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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