GapMind for catabolism of small carbon sources

 

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

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__Dino:3606890
          Length = 432

 Score =  216 bits (550), Expect = 1e-60
 Identities = 139/408 (34%), Positives = 219/408 (53%), Gaps = 41/408 (10%)

Query: 4   LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVW-------------------ATTKAQ 44
           + WLR NLF +  +S+LT++ +A   WL   ++ W                         
Sbjct: 29  VNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPWMFNGVWDANSIRDCREILDGAIGGC 88

Query: 45  WAVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFN-QQKLTWRKVGLFAFI 103
           +AVI       + G +P  EYWR   VLA      A+   +FF   +K+ W   GLF FI
Sbjct: 89  FAVIAERWPQLIFGNYPNEEYWRA--VLAFVGLFVALAPVLFFKLPRKMLWF-TGLFPFI 145

Query: 104 VGLLLILFTLDLSSRLWLLLTAVL-LIPGFLLGSRLTN------LVAPWLS--LIWLLSF 154
                  + L      W+ + A++ ++ G++    L        +VA   +  L W+   
Sbjct: 146 A------YWLIWGGSAWVSVMALVGVVVGYVAFKALEERSFFGAIVAALFATLLFWIFIS 199

Query: 155 PIILWLIGG--GFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRW 212
           P+ +  +       L  V S    G ++  ++    I LS P+G+ LALGR SNLP+++ 
Sbjct: 200 PLAVNALSSVVALSLPQVESRFIGGFMINFILGTSGIALSLPLGIALALGRQSNLPIIKG 259

Query: 213 FSILYIEIVRGVPLIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGG 272
             +++IE +RGVPLI +LF+A VML  F       D VLR I  + LF++AY+AE +RGG
Sbjct: 260 VCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDLVLRVIIMITLFASAYIAEAIRGG 319

Query: 273 LQAVSRGQVEAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVE 332
           L A+ RGQ EA  +LGL+ +  + LI+LPQAL+  IP++V   IGLFKDT+L+S++ + +
Sbjct: 320 LAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIPSIVNIAIGLFKDTTLVSIISMFD 379

Query: 333 LTGIARS-ILAQPQFIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQL 379
           + G+ +  IL+  ++ G Y E+  F G+++++FCY +S  S+ LERQL
Sbjct: 380 MLGMIQGPILSSTEWFGVYWELLGFAGVLFFVFCYGISQYSQWLERQL 427


Lambda     K      H
   0.332    0.145    0.452 

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: 578
Number of extensions: 32
Number of successful extensions: 5
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: 381
Length of database: 432
Length adjustment: 31
Effective length of query: 350
Effective length of database: 401
Effective search space:   140350
Effective search space used:   140350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 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