GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Caulobacter crescentus NA1000

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate CCNA_03240 CCNA_03240 glutamine synthetase

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



>FitnessBrowser__Caulo:CCNA_03240
          Length = 460

 Score =  384 bits (985), Expect = e-111
 Identities = 198/450 (44%), Positives = 278/450 (61%), Gaps = 4/450 (0%)

Query: 10  LNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGS 69
           + E   FL  HP+V +V++    M GV RGKR+    L  +YE G  LP S+  +D NG+
Sbjct: 8   IQECRDFLAAHPQVKFVEVFFTSMTGVPRGKRLRVHELEAIYEYGRFLPGSVLVVDTNGA 67

Query: 70  TVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQ 129
             E TGL  + GDADR   P+P TL   PW     AQ++++++EL+G P   DPR VL++
Sbjct: 68  DCEDTGLVWEDGDADRRARPVPGTLTLAPWLGPDVAQVMLSLYELDGTPNDLDPRHVLQR 127

Query: 130 VVTKFDELGLTICAAFELEFYLID-QENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYV 188
           V+ ++   GLT  AA ELE+YL+D Q   NG   P +S  +G RP   QVY + +L+ + 
Sbjct: 128 VLDRYAADGLTPVAACELEYYLVDLQRGPNGELLPAKSLQTGLRPTGIQVYGLPELEAHA 187

Query: 189 DCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDH 248
             L+++ + A   G+P +  + E APAQ E+ L H  D ++A D AVL KR  K +A  H
Sbjct: 188 PFLRELWDVADTLGVPLEGAISEFAPAQVELTLKHKPDALRAADDAVLYKRAAKGVALRH 247

Query: 249 EMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQM 308
            M+ TFMAKP+  +AGNG HVH+S+ D  G N+ ASED E +  L+HAIGG+   L   M
Sbjct: 248 GMEATFMAKPWSDRAGNGFHVHLSVNDAAGNNLCASEDIEGSDLLKHAIGGMKVLLGEGM 307

Query: 309 AFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLL 368
           A L PN NSYRRF A  Y P +PTWG++NRTV+LRVP G      +EHRVAGAD NPYL+
Sbjct: 308 AILAPNANSYRRFKANSYAPVAPTWGVNNRTVSLRVPAGPPKTRHVEHRVAGADGNPYLV 367

Query: 369 MAAVLAGVHHGLVNKIEPGAPVEGNSY---EQNEQSLPNNLRDALRELDDSEVMAKYIDP 425
           +A +LA  HHG+ NKI+PG  V G+ Y    +    LPNN   A+   + S V+  Y+  
Sbjct: 368 LAVLLASAHHGITNKIDPGPAVIGDGYAAAAKENIRLPNNWFAAVDLFEQSSVLRDYLGD 427

Query: 426 KYIDIFVACKESELEEFEHSISDLEYNWYL 455
           +++D+FV+ K +E   F   +++L+++WYL
Sbjct: 428 RFVDMFVSVKRTEQARFFEVVTELDFDWYL 457


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: 629
Number of extensions: 30
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:

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