GapMind for catabolism of small carbon sources

 

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

Align N-acetylglucosamine transporter nagP (characterized)
to candidate CA265_RS04675 CA265_RS04675 L-fucose:H+ symporter permease

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



>lcl|FitnessBrowser__Pedo557:CA265_RS04675 CA265_RS04675 L-fucose:H+
           symporter permease
          Length = 436

 Score =  197 bits (501), Expect = 5e-55
 Identities = 134/432 (31%), Positives = 216/432 (50%), Gaps = 32/432 (7%)

Query: 9   KSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPS 68
           K    P+ +V +LFF  GF   L+  L+P+L++  QLN F+++L+  S +IA    ALP+
Sbjct: 19  KGYLFPLILVTSLFFFWGFVHNLDPVLIPHLRKAFQLNVFESTLVDSSVFIAYFLLALPA 78

Query: 69  AWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPY 128
            +++RK GYK+G+ LG+ +  +  LLFIPAA T  +  FL A  ++  G T L+TA NPY
Sbjct: 79  GYIMRKYGYKSGIILGLVLFAIGCLLFIPAANTAQYIFFLGALFIIACGLTFLETAANPY 138

Query: 129 VVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQID------ 182
           V  LGP E+A  R++     N  A  +AP++    I    K         + ++      
Sbjct: 139 VTVLGPPETATQRLNFSQSFNGLAAFLAPVLGGKFIFTEVKYTDAQLAKMLPLEKQAYML 198

Query: 183 EMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGV 242
           E A+++  PYL + I I V+A+    + LP++  E+   E   K      L H +L + +
Sbjct: 199 EEASTVKAPYLILGILIIVVAILFIFTKLPDIKEEENAQE---KSSFSHVLGHSHLRWAI 255

Query: 243 IALFVYVAVEVIAGDTIGTFAL-SLGVEHYGV--MTSYTMVCMVLGYTLGIILIPRFISQ 299
           I  F YV  +V       +F   S G+             +  ++G   G   + R+++ 
Sbjct: 256 IGQFFYVGAQVCVLSLFISFVTSSAGISQDAAKWYAGAAGLAFMVGRFAGTFFM-RYVAA 314

Query: 300 PTALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWP 359
              LM+ A++  +LTL  +F                 G+     L+ ++F     +I++P
Sbjct: 315 HKLLMLYALISAVLTLVSIFA---------------SGMITVYALIGVSFF---MSIMFP 356

Query: 360 AVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFI 419
            ++ L ++GLGK T  GS+L++M I GGAF P   GL S AT    Q GY+V   C+L +
Sbjct: 357 TIFSLGIAGLGKDTKLGSSLIVMSIVGGAFLPPVLGLISDATH-NIQYGYLVPFVCFLVV 415

Query: 420 LFYAVKGHKMRH 431
            ++  KG K  H
Sbjct: 416 FYFGWKGWKPNH 427


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: 524
Number of extensions: 25
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: 436
Length adjustment: 32
Effective length of query: 400
Effective length of database: 404
Effective search space:   161600
Effective search space used:   161600
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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