GapMind for catabolism of small carbon sources

 

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

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 3608113 Dshi_1518 inner-membrane translocator (RefSeq)

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Dino:3608113
          Length = 336

 Score =  174 bits (442), Expect = 2e-48
 Identities = 118/325 (36%), Positives = 181/325 (55%), Gaps = 45/325 (13%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFM---TLAAYLTWWANTS-GIN 58
           L+ ++    A GS +ALGA+G+TL YGILR SNFAHGD M   T+A  L  WA  S GI+
Sbjct: 11  LNFVVVPATAYGSQLALGALGVTLIYGILRFSNFAHGDTMAFGTMATILFTWAFQSIGIS 70

Query: 59  LW------LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGIL- 111
           L       L++  G + T   +   + L++K  R ++A     +I S+G+ +F+ N ++ 
Sbjct: 71  LGPLPTALLALPFGILVTGALLVGTDRLVYKFYRQQKAVPVIFVIASLGV-MFVTNALVR 129

Query: 112 LIWGGNNQNYRVP---IVPAQDFM-------GIKFEYYRLLVIAMAIAAMVVLHLILQRT 161
            I G ++Q +      I+ A++F        G+     + L +  A+  + +L   L RT
Sbjct: 130 FIIGPDDQRFADGERFIISAREFRNLTGLDEGLALRTTQGLTVVTAVIVVALLFWFLNRT 189

Query: 162 KVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLI 221
           + GK+MRA +DN DLA +SGIN E VVM TW++ A L  + G++YGL  + KP   + L+
Sbjct: 190 RTGKSMRAFSDNEDLALLSGINPERVVMVTWLIVAALATVAGTLYGLDKSFKPFTYFQLL 249

Query: 222 LPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW----------------------FGT 259
           LP+FA+ I+GG+G+P GAIAGG +I  + EV++ +                        T
Sbjct: 250 LPIFAAAIVGGLGSPLGAIAGGFVIAFS-EVTITYAFKKVLEYLLPEALEPDGLVQLLST 308

Query: 260 SYKMGVALLLMIIILFIRPQGLFKG 284
            YK  V+  ++II+L  +P GLFKG
Sbjct: 309 DYKFAVSFAILIIVLLFKPTGLFKG 333


Lambda     K      H
   0.329    0.143    0.450 

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: 255
Number of extensions: 17
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: 286
Length of database: 336
Length adjustment: 27
Effective length of query: 259
Effective length of database: 309
Effective search space:    80031
Effective search space used:    80031
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: 48 (23.1 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