GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas stutzeri RCH2

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate GFF2537 Psest_2587 Aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__psRCH2:GFF2537
          Length = 336

 Score =  230 bits (587), Expect = 3e-65
 Identities = 122/330 (36%), Positives = 191/330 (57%), Gaps = 1/330 (0%)

Query: 7   VAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDWSQ 66
           VA+ G+   VGE ++EVL+ER FP+ EL LL +    G T  +NG+ +RV   + FD+++
Sbjct: 7   VAVVGSVSLVGEALVEVLEERAFPLSELHLLDAGEGVGHTVPYNGRNLRVSAADRFDFAR 66

Query: 67  VHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNRNI 126
           V +        L +     A+ AG  ++D +     D + P +VPEVN   +    +R  
Sbjct: 67  VQLVFLVGASALVSACHVAASAAGCRIVDLSGSISVD-EQPCLVPEVNGAVLDSSSDRRA 125

Query: 127 IANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYPAE 186
           +A+P  +++ + +AL P+   +G+  + VT    VS  G AG+ ELA QT +LLN  P E
Sbjct: 126 VASPLPASVALALALAPVRHQLGLLGVTVTACLPVSSRGVAGVKELARQTTELLNARPLE 185

Query: 187 TNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYGHA 246
              F +Q+AFN + Q ++   +GY  +E ++V E +++  +P + V  T ++ PVF+G +
Sbjct: 186 PRVFGRQMAFNLLAQTEEVDSHGYGAQERRLVDELRQLLQNPELAVAVTFIQAPVFFGES 245

Query: 247 EAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVRNDISHHS 306
             V +     +D + +   LE   G+E+  G D+PT V DA G+D + VGRVR  I    
Sbjct: 246 LVVSLRCSLEVDPQALSAALEAAPGVEVVGGDDYPTAVGDAVGQDVIYVGRVRCGIGDPR 305

Query: 307 GINLWVVADNVRKGAATNAVQIAELLVRDY 336
            +NLW+V+DNVRKGAA NAVQ  ELL++DY
Sbjct: 306 QVNLWIVSDNVRKGAALNAVQSGELLIKDY 335


Lambda     K      H
   0.319    0.135    0.395 

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: 268
Number of extensions: 12
Number of successful extensions: 2
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: 337
Length of database: 336
Length adjustment: 28
Effective length of query: 309
Effective length of database: 308
Effective search space:    95172
Effective search space used:    95172
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: 49 (23.5 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