GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Flavobacterium glycines Gm-149

Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate WP_066329731.1 BLR17_RS09380 family 1 glycosylhydrolase

Query= CAZy::BAD76141.1
         (470 letters)



>NCBI__GCF_900100165.1:WP_066329731.1
          Length = 465

 Score =  278 bits (710), Expect = 4e-79
 Identities = 167/473 (35%), Positives = 260/473 (54%), Gaps = 24/473 (5%)

Query: 6   KQPITYRFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFF---QGVGPEVA 62
           K+  T +    F WG A++A Q+EGA    GKG++ WD    +     F   Q     VA
Sbjct: 4   KEKTTAQEQKPFLWGVASAAYQVEGAYQADGKGESKWDFLTNKVGVTQFIIGQKQTGNVA 63

Query: 63  SDFYHR--YKEDIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANG 120
            + Y R  Y +DI LMKE+G NS+RFS+ WSR+IPDG+G VN +A+  Y+ +ID+L A G
Sbjct: 64  INMYDRTQYLKDIQLMKELGVNSYRFSLDWSRIIPDGIGAVNEKALAHYDVLIDDLKAAG 123

Query: 121 IEPFVNLYHFDMPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVP-V 179
           IEP V LYHFD P A+   GGW N E+++ Y  YA + F+ +G +VK + T NEP +   
Sbjct: 124 IEPVVTLYHFDYPFALVQKGGWGNPEMINWYKNYAQIVFKRYGKKVKHFITFNEPYIEFF 183

Query: 180 EGGYLYDFHY---PNVVDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSY 236
              +L +      P V  F R +  A+  ++A A+ +  + +  +  GKIG+  N +P  
Sbjct: 184 VAEFLMNMEQSKEPAVTRFARGMMKAHRELVASAEVIKMYHKMNL-GGKIGMTFNFSPCS 242

Query: 237 PRS-QHPADVKAAHIADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKE 295
           P    +P DV+A+ + + L N  FLD   KG YP+++++L  +Y       A+D +++  
Sbjct: 243 PLDPNNPKDVQASALQEKLLNTVFLDGYFKGTYPKEVVDLFTKYDPAFQPAADDMKILAA 302

Query: 296 NTIDLLGINYYQPRRVKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYD 355
           N  D LGIN+Y P  VK      +P  PF       +  +   K+  + G  +  + +Y 
Sbjct: 303 NKPDFLGINFYAPALVKY-----DPSEPF----EMKWMDINTDKIKSHNG-PVRPEELYK 352

Query: 356 ILINIKENYGNIECFISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGV 415
            L+ IK+ Y N E  I+ENG G EGE+     + ++ D  R ++I+ H++ V +A +EGV
Sbjct: 353 FLVKIKKEYNNPEIMITENGAGFEGED--IKATPIVKDPLRADYIKRHVEAVDKAKKEGV 410

Query: 416 NVKGYHLWTFMDNWSWTNAYKNRYGLVAVDLENGLKRTIKKSGYWFKSLAENN 468
            + GY  W+  DN+ W   Y  R+GL+ VD E   +R  K+S Y ++ + + +
Sbjct: 411 KMIGYFPWSGWDNFEWVFGYTKRFGLIYVDFET-QERIPKQSFYEYQKIIKQH 462


Lambda     K      H
   0.321    0.140    0.446 

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: 701
Number of extensions: 44
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: 470
Length of database: 465
Length adjustment: 33
Effective length of query: 437
Effective length of database: 432
Effective search space:   188784
Effective search space used:   188784
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 24 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