GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Acidovorax sp. GW101-3H11

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          Length = 398

 Score =  270 bits (689), Expect = 7e-77
 Identities = 156/365 (42%), Positives = 208/365 (56%), Gaps = 9/365 (2%)

Query: 30  RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPALRL 89
           RG G RVWD +G+E ID  GGIAVN LGH H  LV AL +Q  KL H SN +      +L
Sbjct: 25  RGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKLIHTSNYYHVPLQEKL 84

Query: 90  AHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFTV 149
           A KLV+ +  + VFFCNSG EANEAA K+AR+   D+ G  K EIV    +FHGR++ T+
Sbjct: 85  ATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVDK-GIAKPEIVVYEKAFHGRSIATM 143

Query: 150 NVGGQSKYSDGFGPKITGITHVPYNDLAALKAAV--SDKTCAVVLEPIQGEGGVLPAELS 207
           +  G  K  +GFGP + G   VP ND+ A+K A   +    AV  E IQGEGG+    + 
Sbjct: 144 SATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQATEGNPNVVAVFFETIQGEGGINGMRIE 203

Query: 208 YLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGFPIAAML 267
           YLQ  R+LCD    L++ DEVQ GMGR+GK FA+Q  G+ PD++  AK LG G PI A++
Sbjct: 204 YLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWAGIVPDVMPLAKGLGSGVPIGAVV 263

Query: 268 TTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLE-QIG 326
                A  L  G HGTT+GGNPLA       I ++    +L+      D  +  L+ ++G
Sbjct: 264 AGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEEDGLLHNAAQVGDHLRAALQRELG 323

Query: 327 EKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVED 386
              G+  E+RG GL+LG  L+         +   A   GL++      VIR  P L++  
Sbjct: 324 SLPGV-KEIRGQGLMLGIELNK----PCGALIGRAAEAGLLLSVTADSVIRLVPPLILTT 378

Query: 387 ADIDA 391
           A+ DA
Sbjct: 379 AEADA 383


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: 395
Number of extensions: 19
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: 406
Length of database: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 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