GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagP in Pedobacter sp. GW460-11-11-14-LB5

Align N-acetylglucosamine transporter nagP (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease

Query= reanno::ANA3:7025962
         (432 letters)



>FitnessBrowser__Pedo557:CA265_RS08575
          Length = 422

 Score =  176 bits (447), Expect = 9e-49
 Identities = 132/438 (30%), Positives = 204/438 (46%), Gaps = 32/438 (7%)

Query: 4   DKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTF 63
           D S  K   LP  +V +LFF+ G A  L+  L+P+LK+   LN  Q++LI  S + A   
Sbjct: 6   DSSSGKKYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFL 65

Query: 64  TALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQT 123
            A+P+  +++K GYK  M  G+        LF+PAA    +  FL A  ++G G T+L+T
Sbjct: 66  MAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLET 125

Query: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQV---- 179
           + NPY   LG    A +R+++    N  A ++AP++    IL S K      L  +    
Sbjct: 126 SANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFIL-SGKSHTKEELAAMTDAG 184

Query: 180 ---QIDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHP 236
                 E A S+  PY+ + I + V+A       LPE+  +    E   KG    AL H 
Sbjct: 185 RNSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGE--AKGSFFGALRHK 242

Query: 237 NLAFGVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGII---LI 293
           +L + V+A F YV  +V         A   G        SY  +  +L +T+G      I
Sbjct: 243 HLKWAVVAQFFYVGAQVCVTSFFIRMAQQGGGFDEKTAASYLAIYGLL-FTVGRFAGTAI 301

Query: 294 PRFISQPTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLA 353
            +F+S    L I A++ +LL L  + G   SY +                   +  +G  
Sbjct: 302 LQFVSSHKLLAIYAVISILLCLVAILG-KGSYVV-----------------YALGAIGFF 343

Query: 354 NAIVWPAVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVML 413
            +I++P ++ L + G+G  T  GS+ LIM I GGA  P   G          Q GY + L
Sbjct: 344 MSIMFPTIFALGIDGIGDDTKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPL 403

Query: 414 PCYLFILFYAVKGHKMRH 431
            C+L IL++ ++G+K+ H
Sbjct: 404 VCFLVILYFGLRGYKIAH 421


Lambda     K      H
   0.327    0.141    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: 506
Number of extensions: 27
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: 432
Length of database: 422
Length adjustment: 32
Effective length of query: 400
Effective length of database: 390
Effective search space:   156000
Effective search space used:   156000
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.

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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