GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Dinoroseobacter shibae DFL-12

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= curated2:Q9YBY6
         (388 letters)



>FitnessBrowser__Dino:3608039
          Length = 444

 Score =  156 bits (395), Expect = 1e-42
 Identities = 124/382 (32%), Positives = 183/382 (47%), Gaps = 37/382 (9%)

Query: 19  VKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFSTPSLEE 78
           V G+  Y+ D  G++YLD   G   + LGH +PA+  A+  Q  ++  A + F T    E
Sbjct: 17  VAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAE 76

Query: 79  ALTE-FSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSFHGRT 131
            L +     AP   E++  L+ G+E+VEAALK A   +L TG   +  ++A + S+HG T
Sbjct: 77  VLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNT 136

Query: 132 LASLSVTWNP-RYRRGVPVL-DTRFLSP----------STDPG-----------EVEKLV 168
           L +L+   N  R  +  P+L +T  + P           +D             E+E+L 
Sbjct: 137 LGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLG 196

Query: 169 PEDTAAIIVEPIQGE-GGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHE 227
           PE   A I EP+ G   G         + +RE  D  G LLI DE+  G GRTG ++A E
Sbjct: 197 PETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACE 256

Query: 228 SLGVEPDIMTAGKSI-AGGLPASAVLSREGVLATLASG----RHGSTHAANPLSMAAVAA 282
             G+ PDI+T  K + AG  P  A+L+   +   +A G    +HG T+  +PL+ AA  A
Sbjct: 257 QDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGA 316

Query: 283 ASRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVELRLDPGPVLRCL 342
               LR  G   + RA GA L+  L   +     V  +RG GL  G+EL ++     R L
Sbjct: 317 VVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIEL-VEDRDTKRPL 375

Query: 343 QESERVLALRSGATVVRLLPPY 364
             + +V A    A + R L  Y
Sbjct: 376 DPARKVSARIKAAAMARGLICY 397


Lambda     K      H
   0.319    0.136    0.398 

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: 390
Number of extensions: 21
Number of successful extensions: 5
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: 388
Length of database: 444
Length adjustment: 31
Effective length of query: 357
Effective length of database: 413
Effective search space:   147441
Effective search space used:   147441
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