GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Desulfovibrio vulgaris Hildenborough

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 208921 DVU3392 glutamine synthetase, type I

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



>MicrobesOnline__882:208921
          Length = 447

 Score =  171 bits (433), Expect = 4e-47
 Identities = 125/393 (31%), Positives = 190/393 (48%), Gaps = 30/393 (7%)

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

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

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

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

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

Query: 358 ATLAAGYLGMTQKLEATEPLLSDGYELPYQ---------LPRNLEEGLTLMGACEPIAEV 408
             L AG  G+    E  + + ++ + +  +         LP +L E    +     + E+
Sbjct: 352 VMLGAGLEGIENNYELPKAVEANIFHMGEEDLGKHGIGSLPGSLYEAAMELRNSNLMKEI 411

Query: 409 LGEKFVKAYLALKETEYEAFFRVISSWERRHLL 441
           LGE      +  K  E++ +   IS +E +  L
Sbjct: 412 LGEHTHANIVGNKLIEWDDYRTHISEFELKRYL 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: 536
Number of extensions: 21
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: 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:

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