GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Shewanella amazonensis SB2B

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 6937000 Sama_1174 glutamate--ammonia ligase (RefSeq)

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



>FitnessBrowser__SB2B:6937000
          Length = 455

 Score =  369 bits (947), Expect = e-106
 Identities = 191/446 (42%), Positives = 265/446 (59%), Gaps = 3/446 (0%)

Query: 12  EANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTV 71
           EA  FL +HP+V +V++ I D NG+ RGK + R  +  +Y  G  LP+++  L + G  V
Sbjct: 8   EAIDFLDKHPQVQHVEVFIIDPNGIPRGKLLHRQEVLSMYRHGRPLPSTILGLTVQGDDV 67

Query: 72  ESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLRQV 130
           E TGL  ++GDAD + +PI   L  +PW+ +PTAQ+ +TMH   G P   ADPR VL +V
Sbjct: 68  EDTGLVWEVGDADCLAFPIEGGLLMQPWRAQPTAQVHLTMHPEAGMPAAVADPRLVLSKV 127

Query: 131 VTKFDELGLTICAAFELEFYLIDQE-NVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVD 189
           +      G     A ELEF+L+DQ  + NGRPQP      G RPH TQVY I +L+    
Sbjct: 128 IDSLQADGFYPVMAAELEFFLLDQRFDANGRPQPAMQS-DGHRPHQTQVYGILELERLQP 186

Query: 190 CLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHE 249
            L D+    + QGIPA   + E AP Q E+ L H  D ++A D AV  KRL+K +A  H 
Sbjct: 187 FLDDLYHACEVQGIPARTAISEYAPGQVEITLEHRFDALQAMDEAVRYKRLVKGVAAKHG 246

Query: 250 MDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMA 309
           M   FMAKP+   AG+G+H+H+S+ D DG N FAS++PE    L  +I G++ TL     
Sbjct: 247 MQACFMAKPFGELAGSGMHMHVSLADADGNNRFASDNPEGTPELTQSIAGMMATLEDAQL 306

Query: 310 FLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLLM 369
             CPN NS+RRF +  Y P + TWG++NRTV+ RVP G A +  +EHR+ GADANPYL  
Sbjct: 307 LFCPNANSFRRFQSASYAPIAKTWGVNNRTVSFRVPGGPAPSRHVEHRICGADANPYLAA 366

Query: 370 AAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYID 429
           AA+LA  HHG+ N++ PG  + GN YE   Q+LP +   AL   + SE M   +   +  
Sbjct: 367 AAILAACHHGIRNQLSPGQAIVGNGYEGKHQTLPTDWLSALTNFERSEWMKSVLGEDFHR 426

Query: 430 IFVACKESELEEFEHSISDLEYNWYL 455
           I+   K +E +EF   +   +++WYL
Sbjct: 427 IYGRIKRAEYQEFMAEVGQQDWHWYL 452


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: 634
Number of extensions: 33
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: 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