GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Amantichitinum ursilacus IGB-41

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_053936829.1 WG78_RS05700 glutamate--ammonia ligase

Query= reanno::pseudo1_N1B4:Pf1N1B4_2254
         (426 letters)



>NCBI__GCF_001294205.1:WP_053936829.1
          Length = 469

 Score =  129 bits (325), Expect = 1e-34
 Identities = 111/405 (27%), Positives = 183/405 (45%), Gaps = 35/405 (8%)

Query: 51  ADRICYPIPDTLCNEPWQKRPTAQLLMTMHE-LEGDPFFADPREVLRQVVAKFDEMGLTI 109
           +D +  P   T   +P+   PT  +   + E  +G  +  DPR + ++  A     GL  
Sbjct: 64  SDMLLAPDTTTAKLDPFYDEPTVFITCDVIEPSDGKGYDRDPRSIAKRAEAYLKSSGLGD 123

Query: 110 CAAF--ELEFYLID-----------------QENVNGRPQPPRSPISGKRPHSTQVYL-I 149
            A F  E EF++ D                 +E      +      +G RP     Y  +
Sbjct: 124 TAYFGPEPEFFIFDGVTWGADMSGCFVKIKSEEGAWSSAEDYEGGNTGHRPTVKGGYFPV 183

Query: 150 DDLDEYVDCLQDILEGAKEQGIPADAIVKESAPA-QFEVNLHHVADPIKACDYAVLLKRL 208
             +D + D    ++   +E G+P +    E A A Q E+     +  ++  D+  +LK +
Sbjct: 184 PPVDSHQDIRASMVLVLEELGVPVEVFHHEVATAGQNEIGTKF-SSLVQRADWTQILKYV 242

Query: 209 IKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASED-PEQNAALRHAIGG 267
           + N+A+ +    TFM KP  G  G+G+HVH S+  KDGKN+FA       +    + IGG
Sbjct: 243 VHNVAHQYGKTATFMPKPIVGDNGSGMHVHQSVW-KDGKNLFAGNGYAGLSEFALYYIGG 301

Query: 268 VLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSD-AVRIEHRV 326
           +++   A  A   P  NSY+R    +  P    +   NR+ +IR+P   SD A RIE R 
Sbjct: 302 IIKHAKALNAITNPGTNSYKRLVPHYEAPVKLAYSARNRSASIRIPHVQSDKARRIEARF 361

Query: 327 AGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYE---QNEQSLPN---NLRDALRE 380
               ANPYL  +++L     G+ NKI PG P + N Y+   + ++ +P    +L +AL  
Sbjct: 362 PDPLANPYLCFSALLMAGLDGVQNKIHPGDPADKNLYDLPPEEDKLIPTVCASLDEALDA 421

Query: 381 LD-DSEVMAK--YIDPKYIDIFVACKESELEEFEHSISDLEYNWY 422
           LD D E + +       +ID ++  K  E+     +   +E++ Y
Sbjct: 422 LDKDREFLTRGGVFSNDFIDAYIELKMVEVNRTRMTTHPVEFDMY 466


Lambda     K      H
   0.318    0.137    0.411 

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: 532
Number of extensions: 30
Number of successful extensions: 3
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: 426
Length of database: 469
Length adjustment: 33
Effective length of query: 393
Effective length of database: 436
Effective search space:   171348
Effective search space used:   171348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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