GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Herbaspirillum seropedicae SmR1

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate HSERO_RS23240 HSERO_RS23240 omega amino acid--pyruvate aminotransferase

Query= curated2:O27392
         (390 letters)



>FitnessBrowser__HerbieS:HSERO_RS23240
          Length = 442

 Score =  185 bits (469), Expect = 3e-51
 Identities = 140/425 (32%), Positives = 207/425 (48%), Gaps = 56/425 (13%)

Query: 16  QTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSS 75
           + +   P +L   +G    D  GN+ +D  AG+    +GHAHPK+  A+      L ++ 
Sbjct: 23  RNFKAAPRMLVSAEGMHYRDDAGNTILDGTAGLWCVPLGHAHPKIVSAVQKSVATLDYAP 82

Query: 76  NIYYTREQV-ELAKLLTAISPH--DRVFFANSGAEANEGAIKLARKF------TGKSEII 126
           +         ELA+ L A + +    VF+  SG+EA + A+K+A  +        ++ +I
Sbjct: 83  SFQLGHPSAFELAERLKAYTGNRFGNVFYTGSGSEAVDTALKIALAYHRAKGNATRTRLI 142

Query: 127 AAENSFHGRTLATVTATG----QKKYSEPFRPLPEGFKHVPYG-------------DIGA 169
             E  +HG     ++  G    +K +S    P   G  H+P+              + GA
Sbjct: 143 GRERGYHGVGFGGMSVGGIGGNRKTFSTALLP---GVDHLPHTHNLEKNAFTKGEPEYGA 199

Query: 170 -MADAV--------GDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQ 220
            +AD +            AA+I+EPV G  GV+IPP+GYLK ++E+  ++ +LLI DEV 
Sbjct: 200 HLADELERLVTLHDASNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHGILLIFDEVI 259

Query: 221 TGFGRTGAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGD------HG 273
           TGFGR G  FAS  F VEPDI T AK +  G  P+GAV     +  AF  G       HG
Sbjct: 260 TGFGRLGTPFASDYFDVEPDIFTTAKGLTNGVVPMGAVFVKPEIHDAFMNGPDGIELFHG 319

Query: 274 STFGGNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMI 333
            T+ G+P  CAA +A++EV   E + E A  +  YF       L G   V D+R +GL+ 
Sbjct: 320 YTYSGHPLACAAGLASLEVFQTEGVLENAQAVADYF-QEAAHALRGLPHVIDVRTIGLIA 378

Query: 334 GIEIDGECAGVVDA--------AREMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGH 385
           GIE+     G V A        A   G+LI  T G +I + PPL+I K++ID     L  
Sbjct: 379 GIEL-ASIPGRVGARAYDAFVRAFNDGILIRVT-GDIIALSPPLIINKQQIDELFGKLAA 436

Query: 386 VISDL 390
           ++  L
Sbjct: 437 ILKTL 441


Lambda     K      H
   0.320    0.138    0.404 

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: 459
Number of extensions: 21
Number of successful extensions: 6
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: 390
Length of database: 442
Length adjustment: 31
Effective length of query: 359
Effective length of database: 411
Effective search space:   147549
Effective search space used:   147549
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 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