GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Pseudomonas fluorescens FW300-N2C3

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate AO356_10720 AO356_10720 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q8ZPV0
         (492 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10720 AO356_10720
           succinate-semialdehyde dehydrogenase
          Length = 480

 Score =  189 bits (480), Expect = 2e-52
 Identities = 143/463 (30%), Positives = 223/463 (48%), Gaps = 14/463 (3%)

Query: 4   WINGDWITGQ-GERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62
           +I+G W+    G+  + TNP + E+L       AA+   A +AA  A P W       R 
Sbjct: 14  FIDGAWVDADNGQTIKVTNPATGEVLGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73

Query: 63  AIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIA-ISIKAYHARTGAQKS 121
             + ++  LL  ++ +L  ++  E GKP  EA  E+    + I   + +A          
Sbjct: 74  NKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPG 133

Query: 122 ELVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVI 181
              D    +  +P GV A   P+NFP  +      PAL AG T++ KP+  TP++   ++
Sbjct: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALV 193

Query: 182 KLWERAGLPAGVLNLVQGGR-ETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKIL 240
           +L  RAG+P GVL++V G   + G  L+S   +  L FTGS   G QL  + +   +K+ 
Sbjct: 194 ELAHRAGIPQGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKV- 252

Query: 241 ALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVD 300
           +LE+GGN P I+ D A++D AV   + S +   GQ C CA RL + Q +  DAF  +L  
Sbjct: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYI-QDSVYDAFAEKLKV 311

Query: 301 VAGRLQPGRWDDD---PQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTSL 357
              +L+ G   DD     P I G   A+  +H+ +A  +     G T+L+  K  EG   
Sbjct: 312 AVAKLKIGNGLDDGTTTGPLIDGKAVAKVQEHIADAVSK-----GATVLSGGKAMEGNFF 366

Query: 358 LTPGIIELTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQ 417
               +  +   A V  EE FGPL  ++R+    E I ++N+T FGL+    + D  +  +
Sbjct: 367 EPTILTNVPKNAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFR 426

Query: 418 LLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAAD 460
           +      G+V  N  L  +   APFGG+ ASG  R  + Y  +
Sbjct: 427 VAEALEYGMVGVNTGLI-SNEVAPFGGIKASGLGREGSKYGIE 468


Lambda     K      H
   0.319    0.134    0.411 

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: 531
Number of extensions: 30
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: 492
Length of database: 480
Length adjustment: 34
Effective length of query: 458
Effective length of database: 446
Effective search space:   204268
Effective search space used:   204268
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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