GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Pseudomonas fluorescens FW300-N2E2

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Pf6N2E2_2730 glutamine synthetase family protein

Query= reanno::pseudo5_N2C3_1:AO356_13135
         (458 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2730 glutamine synthetase
           family protein
          Length = 460

 Score =  382 bits (980), Expect = e-110
 Identities = 197/449 (43%), Positives = 276/449 (61%), Gaps = 3/449 (0%)

Query: 10  LNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGS 69
           +  A AFL ++P++   +L I D NGV RGK + R  L  V+E G  LP+++  L +NG 
Sbjct: 11  VQHAEAFLAQNPDIELFELFILDNNGVPRGKLLHRDELLAVFESGRPLPSTILGLTVNGD 70

Query: 70  TVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLR 128
            VE++GL  DIGD D   YP+  +L   PW+  PTA + ++MH  EG P   ADPR +L 
Sbjct: 71  DVENSGLVWDIGDIDCRAYPLSGSLQRMPWRLIPTAAVQVSMHPQEGMPATIADPRYLLS 130

Query: 129 QVVTKFDELGLTICAAFELEFYLID-QENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEY 187
           QV+      G     A ELEFYL+D Q +  GRPQP R    G RP +TQVY + +L++ 
Sbjct: 131 QVIEALQADGYYPVMAAELEFYLLDAQRDSQGRPQPARDA-DGGRPRATQVYGLRELEQI 189

Query: 188 VDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYD 247
              L D+    K QGI A   + E AP Q E+ L H +D ++A D AV  KRL+K +A+ 
Sbjct: 190 EPFLADLYAACKLQGIAARTAISEYAPGQVEITLEHRSDALQAMDEAVRYKRLVKGVAHK 249

Query: 248 HEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQ 307
           H M   FMAKP+   AG+G+H+H+S+ D+DG N+FASE  +    LRHA+GG+L+TL   
Sbjct: 250 HGMQACFMAKPFDHLAGSGMHMHVSLADRDGHNLFASEAADGTPLLRHAVGGMLDTLLDS 309

Query: 308 MAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYL 367
           +   CPN NSYRRF +  Y P + TWG+DNRTV+LRVP G A +  +EHR+ GADANPYL
Sbjct: 310 LLMFCPNANSYRRFQSNSYAPLAATWGVDNRTVSLRVPGGPALSRHIEHRICGADANPYL 369

Query: 368 LMAAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKY 427
             AA+LAG+H GL  + +PG PVEGN Y Q  + LP +    LR L+ S    +    ++
Sbjct: 370 AAAAILAGIHRGLREQCDPGKPVEGNGYAQAAELLPTDWLTTLRALEASAWAREAFGDEF 429

Query: 428 IDIFVACKESELEEFEHSISDLEYNWYLH 456
           + +++A K +E  +F   + + ++ WYL+
Sbjct: 430 LGVYLAVKRAEYRQFMAEVGEQDWRWYLN 458


Lambda     K      H
   0.318    0.137    0.408 

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: 593
Number of extensions: 25
Number of successful extensions: 3
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: 458
Length of database: 460
Length adjustment: 33
Effective length of query: 425
Effective length of database: 427
Effective search space:   181475
Effective search space used:   181475
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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