GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas stutzeri RCH2

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases

Query= curated2:Q2SXN9
         (487 letters)



>FitnessBrowser__psRCH2:GFF374
          Length = 480

 Score =  243 bits (619), Expect = 1e-68
 Identities = 174/470 (37%), Positives = 243/470 (51%), Gaps = 21/470 (4%)

Query: 5   FIDGAWVDGAGPVFASRNPGT-NERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63
           FIDG WV G+    A+ NP   ++ + E A A A  VE+A+A+ARRAF AW+   + AR 
Sbjct: 10  FIDGQWV-GSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWATFGIQARA 68

Query: 64  TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123
             +++    ++ R+E L T++ RE GK L EA  EVA               + GE    
Sbjct: 69  DALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLRQAGETLQS 128

Query: 124 MADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATV 182
           +  GV V +   P GV+ +  P+NFP  +P   I PAL  GN VV KP++L PG A A  
Sbjct: 129 VRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLVPGCAWAIA 188

Query: 183 EIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVL 241
           EI   AG PAGV NLV G+ ++ G A+ N + +D + FTGS   G  + +    R   V 
Sbjct: 189 EIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTCVARGAKV- 247

Query: 242 ALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLAD 301
            LEMGG NP +V +  D++ AV    QSAF S GQRCT + RI+V  G + DRFV  + +
Sbjct: 248 QLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIY-DRFVEAMVE 306

Query: 302 VASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM-----KQRDPAL 356
              KI   V  A  Q   G  +    +   +    R + +G      +     + +    
Sbjct: 307 RIKKI--KVGSALEQ---GVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGTE 361

Query: 357 GFVNAAILDV---TNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDE 413
           G+  A  L V    N+R +  EE FGP+A +V+  D D+A+A ANDT FGLSAG+     
Sbjct: 362 GYFLAPTLFVDSDPNMR-ISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420

Query: 414 QAWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462
           +  + F+R  +AG+V  N PT G     PFGG  G S   R    YA ++
Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEF 470


Lambda     K      H
   0.320    0.134    0.402 

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: 515
Number of extensions: 22
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 487
Length of database: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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: 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 (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