GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Dinoroseobacter shibae DFL-12

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 3608408 Dshi_1808 amino acid carrier protein (RefSeq)

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__Dino:3608408
          Length = 512

 Score =  272 bits (696), Expect = 2e-77
 Identities = 165/425 (38%), Positives = 231/425 (54%), Gaps = 31/425 (7%)

Query: 50  LWQGRSKDDESSGEISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGM 109
           L +G   D + +GE+S FQAL T L+ TVG GNIAGVA A+ +GGPGA FWM    L+GM
Sbjct: 86  LVKGDYADPDDAGEVSHFQALATALSGTVGLGNIAGVAVAVGIGGPGATFWMIFAGLLGM 145

Query: 110 ATKFSEVVLAVHYREKDERNEHVGGPMYAIKNGLGKR----WAWLGAAFALFGGLAGFGI 165
           A+KF+E  L V YR +       GGPMY I  G  ++      ++   F++F  L   G 
Sbjct: 146 ASKFTECTLGVKYRNEYPDGTVSGGPMYYISKGFAEKGMPGGKFMAVLFSIFCILGALGG 205

Query: 166 GNMVQVNSMADALEVSFG-VPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYI 224
           GNM Q N     +    G  P W+TG+    V   VI+GGI+ I KV E +VPFM + Y+
Sbjct: 206 GNMFQANQAHAQISGIVGDYPGWITGIIFAAVVFAVIVGGIKSIAKVTEKVVPFMGILYV 265

Query: 225 VASVIVLVVHAEAIPGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLG 284
            A++++L+V+ + I  AF  IF  AFT +   GGF GA +      G  R  FSNEAG+G
Sbjct: 266 AAALVILLVNIDQIGWAFGQIFEGAFTGLGVAGGFVGALIQ-----GFKRAAFSNEAGVG 320

Query: 285 TAGIAQAAGTTHSAVRSGLIGMLGTFIDTLIICSLTGLAIITSG---------------- 328
           +A IA +A  T   V  G + +L  FIDT++IC++T L I  SG                
Sbjct: 321 SAAIAHSAVKTKEPVTEGYVSLLEPFIDTVVICTMTALVITISGQLMINPDTGLYMVENG 380

Query: 329 --VWTSGASGAALSSAAFEAAMPGVGHYILSLALVVFAYTTILGWSYYGERCWEYL--AG 384
             +   G SG AL+SAAF         Y+L++A+V+FA++T++ WSYYG + W YL   G
Sbjct: 381 AIMTVDGNSGVALTSAAFATGFSWF-PYVLAIAVVLFAFSTMISWSYYGLKAWTYLFGEG 439

Query: 385 TRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLIALLLLSPVVFRLTREYF 444
               L F++++ + +  GA   L      +D     MA+ N+ AL +L PVV      Y 
Sbjct: 440 RTKELVFKVIFCVFVVIGAAASLGPVIDFSDAAIFAMAVVNIAALYVLMPVVKAELASYR 499

Query: 445 AKARS 449
           A+  S
Sbjct: 500 ARLDS 504


Lambda     K      H
   0.326    0.140    0.437 

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: 609
Number of extensions: 35
Number of successful extensions: 7
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: 449
Length of database: 512
Length adjustment: 34
Effective length of query: 415
Effective length of database: 478
Effective search space:   198370
Effective search space used:   198370
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 (21.7 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:

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