GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Calditerrivibrio nitroreducens DSM 19672

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013451176.1 CALNI_RS05270 adenosylmethionine--8-amino-7-oxononanoate transaminase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>NCBI__GCF_000183405.1:WP_013451176.1
          Length = 459

 Score =  118 bits (295), Expect = 4e-31
 Identities = 112/415 (26%), Positives = 179/415 (43%), Gaps = 65/415 (15%)

Query: 30  RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEP-ALR 88
           RG G +++D       D       N+ GH +  +   +  Q N L HV       P A+R
Sbjct: 34  RGKGVKLYDIDNNYYYDTVSSWWTNIFGHNNKHINHKIRSQLNSLDHVIFAGMTHPYAVR 93

Query: 89  LAHKLVD--ATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTL 146
           +   L +       R FF ++G+ A E A K+A +   +    EK + V   NS+HG T+
Sbjct: 94  VVELLRNFLPEKLSRFFFSDNGSTAVEVAIKMAFQYWQNIGRVEKTKFVFFENSYHGDTI 153

Query: 147 FTVNVGGQSKYSDGFGPKITGITHVP----YNDLAALKAAV--SDKTC------------ 188
             V+VGG   Y   + P +     +     YN + + +     +D  C            
Sbjct: 154 GAVSVGGIDLYHKLYKPLMFNSYQIRSPKCYNCIFSKQKMTLNADNGCNAECMDQLEKVL 213

Query: 189 --------AVVLEP-IQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLF 239
                    V++EP IQ   G+       L+  RELCD +  LL+FDEV TG GR+GK+F
Sbjct: 214 EENNGNIAGVIIEPLIQCAAGMNVYNGIVLKKIRELCDRYEVLLIFDEVATGFGRTGKMF 273

Query: 240 AYQHYGVTPDILTSAKSLGGGF-PIAAMLTTEDLAKHLV-------VGTHGTTYGGNPLA 291
           A++H  V PDI+  +K L GG+ P+A  +TTE++               HG +Y  NP++
Sbjct: 274 AFEHVDVLPDIICLSKGLTGGYLPLALTVTTEEIYSAFYDDYFSYKTFFHGHSYTANPIS 333

Query: 292 CAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKY------GLFTEVRGLGLLLGCV 345
           C+ A   ++        N +     K+K+ +    EK           +VR +G +    
Sbjct: 334 CSAAIGTLE--------NFIKKPIAKYKSGMIYFNEKVCSLKDEPYVGDVRYIGFIGAID 385

Query: 346 LSDAWKGKAKDIFNAAEREGL----------MILQAGPDVIRFAPSLVVEDADID 390
           + + + GK+   +   ER G           +IL+   D I +   + V+  DID
Sbjct: 386 IVNPYTGKS---YPEKERVGFQIYKESLKNNLILRPLGDTIYWLLPITVKKKDID 437


Lambda     K      H
   0.320    0.136    0.400 

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: 385
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 406
Length of database: 459
Length adjustment: 32
Effective length of query: 374
Effective length of database: 427
Effective search space:   159698
Effective search space used:   159698
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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