GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Desulfovibrio vulgaris Miyazaki F

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 8501367 DvMF_2099 glutamine synthetase, type I (RefSeq)

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>lcl|FitnessBrowser__Miya:8501367 DvMF_2099 glutamine synthetase,
           type I (RefSeq)
          Length = 447

 Score =  176 bits (446), Expect = 1e-48
 Identities = 127/393 (32%), Positives = 194/393 (49%), Gaps = 30/393 (7%)

Query: 65  TGVTDPDMVCVPDASTIRMIPWAV--DPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYK 122
           T + + DMV  PDA+T ++  W     P A++  D  + DGTP    PR +LR++ E   
Sbjct: 66  TRIEESDMVAFPDATTFQICAWRPMERPVARMFCDVRNPDGTPYEGDPRYILRKLTEKAA 125

Query: 123 AKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIY 182
            KG+   + PELEF+L   ++ P      PI   G        +    ++  + +  DI 
Sbjct: 126 QKGYTYYVGPELEFFLFASSQCPQ-----PIDAGGY-------FDAPPLDLGNDVRRDII 173

Query: 183 EYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMA 242
              +   + V+   HEV  +Q EI+  + + +K+AD V  +K  V+E A +H +YATFM 
Sbjct: 174 FALQRMGIPVEYSHHEVAPSQHEIDLRYNEAMKMADVVMTYKVVVKEMARKHGVYATFMP 233

Query: 243 KPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKP--TSLFTSYIAGLQKYTPALMPIFAP 300
           KP+ G+ GS MH+HQSL     G N F  P+     +    SYIAGL K+      +   
Sbjct: 234 KPIFGQNGSGMHVHQSLF--RNGRNAFFDPNDPHHLSGECRSYIAGLLKHAREFCCVTNQ 291

Query: 301 YINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGP---AARRIENRIPGVDCNPYLAIA 357
           +INSY+RL     AP+ +AW   NR+   R+P   P   AA RIE R P   CNPYLA +
Sbjct: 292 WINSYKRLVPGYEAPVYLAWAQRNRSALIRVPMYKPGKEAATRIELRSPDPACNPYLAFS 351

Query: 358 ATLAAGYLGMTQKLEATEPLLSDGYELPYQ---------LPRNLEEGLTLMGACEPIAEV 408
             LAAG  G+ +  E  + + ++ + +  +         LP +L E    +     + EV
Sbjct: 352 VMLAAGLEGIEKSYELPKAVEANIFHMGEEDLTKHGIGSLPGSLYEAAMELKGSALMQEV 411

Query: 409 LGEKFVKAYLALKETEYEAFFRVISSWERRHLL 441
           LGE      +  K  E++A+   +S +E +  L
Sbjct: 412 LGEHTHANLVGNKLIEWDAYRTHVSEFELQRYL 444


Lambda     K      H
   0.321    0.138    0.418 

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: 529
Number of extensions: 24
Number of successful extensions: 6
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: 444
Length of database: 447
Length adjustment: 32
Effective length of query: 412
Effective length of database: 415
Effective search space:   170980
Effective search space used:   170980
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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