GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Nocardioides daejeonensis MJ31

Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate WP_110205265.1 DNK54_RS02005 type I glutamate--ammonia ligase

Query= reanno::MR1:200446
         (451 letters)



>NCBI__GCF_003194585.1:WP_110205265.1
          Length = 445

 Score =  182 bits (462), Expect = 2e-50
 Identities = 132/386 (34%), Positives = 185/386 (47%), Gaps = 20/386 (5%)

Query: 74  DFVCVPDENAVFMLPWTIE--ATAQVIHDCYDRMGNPIELSPRNVLKKVLSLYDEKGWEP 131
           D + +PD     +LPW  E  +TA++  D     G+P    PR VLK+ LS   EKG+  
Sbjct: 66  DMLAMPDPTTFQILPWRGEGPSTARMFCDIVMPDGSPSYADPRYVLKRTLSAAAEKGFTF 125

Query: 132 VIAPEMEFYLTSRSDDHDLPLKP-PIGRSGRPEAGRQSFSIDAANEYDPLFEDMYDWCEI 190
              PE+EFYL    D  +   +P P+ RSG  +   QS+  D   E   + E M      
Sbjct: 126 YTHPEIEFYLFK--DTPNSTAEPVPVDRSGYFDHTAQSYGSDFRREAITMLEAM------ 177

Query: 191 QGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCATFMAKPVTD 250
            G+ ++   HE GP Q EI+  + + LS AD +  F+  +RE AL   + ATFM KP T+
Sbjct: 178 -GISVEFSHHEGGPGQQEIDLRYADALSTADNIMTFRTVVREVALSQGIWATFMPKPFTE 236

Query: 251 EPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPLMAPNANSFRR 310
            PGS MH H S+   +         +   S     +IAG+  +  E   L     NS++R
Sbjct: 237 HPGSGMHTHVSLFEGDRNAFFEAGAEYQLSQTGRQFIAGVLTHASEITALTNQWVNSYKR 296

Query: 311 FLPGTSAPVNLEWGIENRTCGLRIPESSP---QNRRIENRIPGADANCYLAFAAGLLCGY 367
            L G  AP  + WG  NR+  +R+P   P   Q+ RIE R      N YLAFAA L  G 
Sbjct: 297 LLGGGEAPSYICWGHNNRSAMVRVPMYKPNKGQSTRIELRTIDPACNPYLAFAAILGAGM 356

Query: 368 IGMVEGLKPSTPVQG-----KANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFTT 422
            G+ EG +     +         E +S     LP TL EA+   E S+   E LGE    
Sbjct: 357 KGIEEGYELPREAEDDVWSLNERERQSLGIEPLPKTLYEAIRVAESSELLPEVLGEHVYE 416

Query: 423 GFVAVKQAELENFRRVVSSWEREFLL 448
            F+  K+AE + +R  VS++ER  +L
Sbjct: 417 YFLRNKRAEWDEYRVQVSAFERSRML 442


Lambda     K      H
   0.319    0.137    0.414 

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: 439
Number of extensions: 27
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: 451
Length of database: 445
Length adjustment: 33
Effective length of query: 418
Effective length of database: 412
Effective search space:   172216
Effective search space used:   172216
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 (21.7 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