GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Magnetospirillum magneticum AMB-1

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein

Query= curated2:O27392
         (390 letters)



>NCBI__GCF_000009985.1:WP_011384093.1
          Length = 459

 Score =  197 bits (500), Expect = 7e-55
 Identities = 144/408 (35%), Positives = 206/408 (50%), Gaps = 55/408 (13%)

Query: 22  PIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRL--IHSSNIYY 79
           P+V++ G+G  V+D  G  YI+  AG+   S+G    ++  A   Q ++L   H  +   
Sbjct: 33  PLVITRGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAARQMRQLPFYHLFSHKT 92

Query: 80  TREQVELAKLLTAISP--HDRVFFANSGAEANEGAIKL------ARKFTGKSEIIAAENS 131
               VEL   L A++P    +VF A SG+EAN+ AIKL      A     K +IIA E +
Sbjct: 93  HDVGVELCARLLAMAPVPMSKVFLAGSGSEANDTAIKLIHYRANALGTPDKKKIIAREKA 152

Query: 132 FHGRTLATVTATGQKKYSEPFR-PLP--------------------EGFKHVPYGDIGAM 170
           +HG T+AT + TG       F  P+P                    E F     G++ AM
Sbjct: 153 YHGVTVATASLTGLVNNQRSFDLPIPGVLRAACPHHYRFAKDGESEEDFSTRLAGELEAM 212

Query: 171 ADAVGDET-AAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAM 229
             A G +T AA   EPV G GGVI+PP GY   +Q +  + DVLL++DEV  GFGRTG M
Sbjct: 213 ILAEGPDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVLLVVDEVICGFGRTGKM 272

Query: 230 FASQLFGVEPDITTVAKAMGGGY-PIGAVLANERV--AMAFEPG-----DHGSTFGGNPW 281
           F ++ FG+ PD+ T+AK +  GY PI A++ NERV   +A E G      HG T+GG+P 
Sbjct: 273 FGTETFGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESGRIGVFGHGYTYGGHPV 332

Query: 282 GCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGEC 341
             A A+ T+ +  +  +  + A++G      LR  L G   V + RGVGL+  +E+  + 
Sbjct: 333 SAAVALETLNIYAERDILAQVAEVGPVLQDGLR-ALRGHPLVGEARGVGLIGAVELVADK 391

Query: 342 AG-------------VVDAAREMGVLINCTAGKVIRIVPPLVIKKEEI 376
           A              VV  A+  GV++    G  +   PPLVI K +I
Sbjct: 392 ANRAPFPPELAVGARVVAKAQAKGVILR-AMGDAVAFAPPLVISKADI 438


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: 476
Number of extensions: 27
Number of successful extensions: 7
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: 459
Length adjustment: 32
Effective length of query: 358
Effective length of database: 427
Effective search space:   152866
Effective search space used:   152866
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