GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgl in Magnetospirillum magneticum AMB-1

Align Rpal_1936 (EC 3.2.1.21) (characterized)
to candidate WP_050750700.1 AMB_RS11280 beta-glucosidase

Query= CAZy::ACF00459.1
         (458 letters)



>NCBI__GCF_000009985.1:WP_050750700.1
          Length = 449

 Score =  501 bits (1290), Expect = e-146
 Identities = 240/449 (53%), Positives = 300/449 (66%), Gaps = 11/449 (2%)

Query: 14  AGLPVLSHIRKDFIWGVSTASFQIEGAANEDGRGQSIWDVYCR-SGYVANNDTGDVACDH 72
           AG   ++ +R DF+WGVST++FQ+EGA  EDGRG SIWD  CR  G V      DVACDH
Sbjct: 3   AGNKNITSLRPDFVWGVSTSAFQVEGATKEDGRGLSIWDTRCRLQGGVWTGANADVACDH 62

Query: 73  YHRYQEDVALMKTLGIQAYRFSIAWPRIFPQGTGAINEPGLAFYDRLIDALEAAGIEPWI 132
           YHR+ EDV L+K LG+ AYRFSIAWPR+ P+G G +N+ GL FYDRLID +  AGI PW+
Sbjct: 63  YHRWPEDVGLIKDLGVDAYRFSIAWPRLLPKGKGPVNQKGLDFYDRLIDGVLEAGITPWV 122

Query: 133 CLYHWDLPQAMEERGGWMNRDIVGWFADYARVIGERYGKRVKRFATFNEPGIFSLFSRSF 192
           CLYHWDLPQA+++ GGW NRD  GWFADYA +  +RYG RVK FATFNE  +F++F  + 
Sbjct: 123 CLYHWDLPQALDDLGGWTNRDCAGWFADYAVLAAKRYGDRVKHFATFNEFSVFTMFGYAI 182

Query: 193 -----GARDRSADEKLHRWIHHVNLAHGAAVDVLRETVADAKIGLVTNYQPVYPSSDKPE 247
                G  DR+A  K    IHHVNLAHG  VDVLR+ V D  IG + N Q V P     E
Sbjct: 183 DWAAPGVTDRAAHMKA---IHHVNLAHGMGVDVLRDHVKDVSIGAIHNRQIVRPEGGLAE 239

Query: 248 DVAEAKLISDYWNRAFADPQYRGEYPGLIRDAVKPYIQPGDMERIHRPLDWFGLNHYSPV 307
           + A A L+  +WN  F DPQ+ G YP ++   V+PY+Q GD+ RI RP DW GLNHY P+
Sbjct: 240 NQAAADLLDAHWNGVFCDPQHLGHYPEIMARDVEPYVQAGDLARICRPTDWMGLNHYGPI 299

Query: 308 YINSDPNAIVGLGWGPKPEGIPRSPIDWTIEPDAFRDTLIEISRRYGKPVYVTENGY--G 365
           Y  +DP    G GWG  PE      + W I P+ F+D L+ ++RRYG PVYVTENG   G
Sbjct: 300 YAKADPATTWGYGWGAPPESANHPEVGWPIFPEVFKDELLTLTRRYGLPVYVTENGCGGG 359

Query: 366 SNIEKPDANGEVVDPGRIGFLRDYITALDQAVAAGADVRGYMVWSLLDNFEWESGYSVRF 425
           +  + PD NG V D  R+ + R+Y  A+  AVA GADVRGY VW+LLDNFEW SGY  RF
Sbjct: 360 AGSDTPDENGVVDDTHRLAYFREYQQAMLDAVAEGADVRGYFVWALLDNFEWGSGYGPRF 419

Query: 426 GLIYIDYATLRRIPKASFKWFADVIRHAR 454
           GL ++D+ + +R  K S KW+ D+I+  R
Sbjct: 420 GLYHVDFDSQKRTLKNSGKWYRDMIKGQR 448


Lambda     K      H
   0.321    0.140    0.451 

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: 831
Number of extensions: 43
Number of successful extensions: 4
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: 458
Length of database: 449
Length adjustment: 33
Effective length of query: 425
Effective length of database: 416
Effective search space:   176800
Effective search space used:   176800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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