GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Shewanella sp. ANA-3

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 7023062 Shewana3_0300 glutamine synthetase (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7023062 Shewana3_0300 glutamine synthetase
           (RefSeq)
          Length = 469

 Score =  140 bits (352), Expect = 1e-37
 Identities = 131/423 (30%), Positives = 184/423 (43%), Gaps = 51/423 (12%)

Query: 54  VTGDYPEDGTL---------TGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGT 104
           V  D+ EDG +          G+ + DMV +PD +T  + P+  + TA +  D +   GT
Sbjct: 39  VDADFFEDGKMFDGSSIAGWKGINESDMVLMPDPTTFVLDPFTEETTALIRCDILE-PGT 97

Query: 105 PVAIS--PRRVLRRVLELYKAKGWKP--VIAPELEFYLVD-MNKDPDLP----------- 148
                  PR + ++  E  ++ G     ++ PE EF+L D +    D+            
Sbjct: 98  MTGYDRDPRSIAKKAEEYLRSTGIADTVLVGPEPEFFLFDDVRFGTDMSGCFVKIDAKEA 157

Query: 149 -----LQPPIGRTG-RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA 202
                     G TG RP      + +  V+    L   +    E     V+   HEV  A
Sbjct: 158 AWNSGTSYEGGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATA 217

Query: 203 -QMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVD 261
            Q EI        K AD + + K  V   A  +   ATFM KP+ G+ GS MH+HQSL  
Sbjct: 218 GQNEIATRFNTLTKKADEIQILKYVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSL-- 275

Query: 262 EETGHNLFTGPDG---KPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINV 318
            + G NLF G        T+L+  YI G+ K+  AL     P  NSY+RL     AP+ +
Sbjct: 276 SKDGVNLFAGDKYAGLSETALY--YIGGIIKHARALNAFTNPSTNSYKRLVPHFEAPVML 333

Query: 319 AWGYDNRTVGFRIPH-SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPL 377
           A+   NR+   RIP    P  RRIE R P    NPYL  AA L AG  G+  K+   E +
Sbjct: 334 AYSARNRSASIRIPVVPSPKGRRIETRFPDPHANPYLGFAALLMAGIDGIQNKIHPGEAM 393

Query: 378 LSDGYELPY-------QLPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLALKETEYEA 427
             D Y+LP        Q+  +LE  L  + A         V  E F+++Y+ALK  E E 
Sbjct: 394 DKDLYDLPAEEAAEIPQVATSLENALENLQADHEFLTRGGVFSEDFIQSYIALKSAEAER 453

Query: 428 FFR 430
             R
Sbjct: 454 VSR 456


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: 509
Number of extensions: 32
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: 444
Length of database: 469
Length adjustment: 33
Effective length of query: 411
Effective length of database: 436
Effective search space:   179196
Effective search space used:   179196
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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