GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argF' in Desulfovibrio vulgaris Miyazaki F

Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq)

Query= BRENDA::Q8P8J2
         (339 letters)



>FitnessBrowser__Miya:8499267
          Length = 300

 Score =  123 bits (308), Expect = 7e-33
 Identities = 102/330 (30%), Positives = 147/330 (44%), Gaps = 41/330 (12%)

Query: 4   KHFLNTQDWSRAELDALLTQAALFKRNK-LGSELKGKSIALVFFNPSMRTRTSFELGAFQ 62
           +HF   +D        LL +A   K     G  ++GK+  L+F   S RTR SFE+    
Sbjct: 3   RHFTRIRDLGYEGAWKLLQRAKEMKDTAHRGKIMEGKTAILIFEKASTRTRVSFEMAVRH 62

Query: 63  LGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSK 122
           LGG  + + P       E  LG        E + + ARVL RY D + VR F +      
Sbjct: 63  LGGSTIFMTPA------ESQLGR------SEPLRDTARVLSRYADCMVVRTFGQ------ 104

Query: 123 DREDQVLKSFAKYSPVPVINMETIT-HPCQELAHALALQEHFGTPDLRGKKYVLTWTYHP 181
                 +   A+Y  +PVIN  T   HPCQ +   L + E   TPDL   +  + W    
Sbjct: 105 ----SKITELAEYGSIPVINALTDEGHPCQVMGDVLTMYER--TPDLSTVR--VAWVGD- 155

Query: 182 KPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDS 241
                 +ANS +  A     ++ +  P   Y  D   + +A      +G  + ++HD   
Sbjct: 156 ---GNNMANSWIEAAVYFPFELFMAFPE-GYEPDRDLLGYALN----AGAKIFLTHDPRM 207

Query: 242 AYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTN-NGVFSHCLPLRRN 300
           A  GA  V    W ++   G  E +K     ++ + +D   MAL   +  F HCLP  R 
Sbjct: 208 AVEGAHYVNTDVWASM---GQEEEQKKREAAFKGYCIDTEMMALAAPDAKFMHCLPAHRG 264

Query: 301 VKATDAVMDSPNCIAIDEAENRLHVQKAIM 330
            + TD VM+SP  I  D+AENRLH+QKAI+
Sbjct: 265 EEVTDEVMESPASIIFDQAENRLHIQKAIL 294


Lambda     K      H
   0.320    0.134    0.412 

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: 257
Number of extensions: 18
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: 339
Length of database: 300
Length adjustment: 28
Effective length of query: 311
Effective length of database: 272
Effective search space:    84592
Effective search space used:    84592
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: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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