GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Sinorhizobium meliloti 1021

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate SMc01973 SMc01973 glutamine synthetase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_925
         (458 letters)



>FitnessBrowser__Smeli:SMc01973
          Length = 455

 Score =  331 bits (849), Expect = 3e-95
 Identities = 171/445 (38%), Positives = 255/445 (57%), Gaps = 3/445 (0%)

Query: 15  AFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVEST 74
           ++L+++  +  +  +I D+NG++RGKR+      KV   GI +P S+  +D+ G  +  +
Sbjct: 13  SWLEQNGPIESIQAVICDLNGIMRGKRVPVEQARKVLGGGIRMPLSIVGVDVWGEDIIGS 72

Query: 75  GLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLANVVRKF 134
                 GD D IC           W  RP+A + + +    G PF ADPR+ LA ++R++
Sbjct: 73  AQVFATGDRDGICGVTGRGALPVNWTSRPSALVPLWLFVENGRPFLADPRQALAAIMREY 132

Query: 135 DEMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVDCLQDI 194
            E+GL    A ELEFYLID E  +    PP SP +GKR  S  +  ID+LD++ +   D+
Sbjct: 133 RELGLRPVVATELEFYLIDPEPDSA--VPPISPYTGKRLDSDAILSIDELDDFGEFFSDV 190

Query: 195 LEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTF 254
                 Q +PADA + E+   QFE+NL H  DP+KA D A+  KR++K +A  H +  TF
Sbjct: 191 YRECARQNVPADAAIAENGIGQFEINLLHSDDPLKAADDAIFFKRIVKGVARKHGLAATF 250

Query: 255 MAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPN 314
           MAKPY  ++GNG+HVH S+LD++G N+F     E +A L+HA+ G+L  +        P+
Sbjct: 251 MAKPYGTRSGNGMHVHFSLLDEEGNNVFDDGSDEGSAVLKHAVAGLLRGMAETTLMFAPH 310

Query: 315 VNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLMASVLA 374
            NSYRR     + P S  WG +NRT AIR+P G+  A RIEHRVAGADANPYL++A++L 
Sbjct: 311 FNSYRRLRPDTHAPTSISWGYENRTSAIRIPGGNPAARRIEHRVAGADANPYLVIAAILG 370

Query: 375 GVHHGLTNKIEPGAPVEGNSYEQNE-QSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVA 433
               G+ NK +P  PVEG +Y   +   +P +   A+   +   + A+  DP    + +A
Sbjct: 371 AALVGIRNKWKPPVPVEGRAYAAEKLPKIPADWGQAVDAFEAGPIAAEIFDPVLRSMLIA 430

Query: 434 CKESELEEFEHSISDLEYNWYLHTV 458
           CK  E+  F   ++D E++ YL  V
Sbjct: 431 CKRQEIAGFAEQVTDYEFSAYLEIV 455


Lambda     K      H
   0.318    0.137    0.409 

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: 607
Number of extensions: 23
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: 458
Length of database: 455
Length adjustment: 33
Effective length of query: 425
Effective length of database: 422
Effective search space:   179350
Effective search space used:   179350
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:

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