GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Lentibacillus jeotgali Grbi

Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate WP_010530711.1 ON01_RS09045 type I glutamate--ammonia ligase

Query= reanno::Koxy:BWI76_RS10710
         (472 letters)



>NCBI__GCF_000224785.1:WP_010530711.1
          Length = 445

 Score =  148 bits (374), Expect = 3e-40
 Identities = 138/448 (30%), Positives = 205/448 (45%), Gaps = 51/448 (11%)

Query: 36  NTQYVDVLLTDLNGCFRGKRIPVSGLSK-LEKGCYFPASVFAMDILGNV-VEEAGLGQEM 93
           N +++ +  TD+ G  +   IP+S L K L+    F  S     I G V +EE+ +  + 
Sbjct: 18  NVRFIRLQFTDMLGNIKNVEIPLSQLDKALDNKMMFDGS----SIEGFVRIEESDMYLQ- 72

Query: 94  GEPDRTCVPVLGTLTPSAADPEYIGQVLLTMVDEDGAPFDVEPRNVLNRLWQQLRQRGLF 153
             PD     V     P  ++   + + +  + + DG PF   PR  L R  Q++ + G  
Sbjct: 73  --PDLDSFVVF----PWTSEKGKVARFICDIYNPDGTPFAGCPRYNLKRKLQKMEELGFN 126

Query: 154 PV-VAVELEFYLLDRKRDAEGYLQPPCAPGTGDRNTQSQVYSVD-NLNHFADVLNEIDEI 211
              +  E EF+L   K D +G  QP       D      +   D   N   D++ E++E+
Sbjct: 127 AFNIGTEPEFFLF--KLDEKG--QPSME--LNDHGGYFDLAPTDLGENCRRDIVLELEEM 180

Query: 212 AQLQLIPADGAVAEASPGQFEINLHHTDNVLDACDDALALKRLVRLMAEKHKMHATFMAK 271
                   + +  E +PGQ EI+  ++D V  A DD    K +VR +A KH +HATFM K
Sbjct: 181 G----FEIEASHHEGAPGQHEIDFKYSDAVKHA-DDIQTFKLVVRTIARKHNLHATFMPK 235

Query: 272 PYEEHAGSGMHIHISMQNNKGENVLADADGED--SAMLKRALAGMIDLMPASMALLAPNV 329
           P     GSGMH+++S+  N GEN   D DGE   S +  +  AG+I       A+  P V
Sbjct: 236 PLFGVNGSGMHVNMSLFRN-GENAFFDKDGEMQLSDVAYQFTAGVIKHATNFTAVTNPTV 294

Query: 330 NSYRRFQPGMYVPTQASWGHNNRTVALRIPCGDRHNHRVEYRVAGADANPYLVMAAIFAG 389
           NSY+R  PG   P   +W   NR+  +RIP     + R+E R     ANPY+ M+ + A 
Sbjct: 295 NSYKRLVPGYEAPCYVAWSGTNRSPLVRIPYSRGLSTRIEVRSVDPAANPYMAMSVLLAS 354

Query: 390 ILHGLDNPLPLQEEVEGN-------GLEQEGL-PFPIRQSDALWEFMQNDHLRERLGERF 441
            L G++N L   E V+ N         E+ G+   P    DAL    Q++ + E LGE  
Sbjct: 355 GLDGVENKLTPPESVDQNIYDMDKKEREENGVKDLPATLMDALEVMQQDETIVEALGE-- 412

Query: 442 CHVYHACKNDELLQFERLITETEIEWML 469
            H+Y           E  +    IEW L
Sbjct: 413 -HLY-----------EHFVEAKTIEWDL 428


Lambda     K      H
   0.319    0.136    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: 535
Number of extensions: 37
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: 472
Length of database: 445
Length adjustment: 33
Effective length of query: 439
Effective length of database: 412
Effective search space:   180868
Effective search space used:   180868
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