GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Catellicoccus marimammalium M35/04/3

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_009488515.1 C683_RS01225 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>NCBI__GCF_000313915.1:WP_009488515.1
          Length = 473

 Score =  217 bits (552), Expect = 9e-61
 Identities = 146/463 (31%), Positives = 230/463 (49%), Gaps = 20/463 (4%)

Query: 36  RHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQ 95
           + Y   + GEW  T + +    P+   E+ GT     + E E  +++A +A K W+    
Sbjct: 2   KSYLNLVNGEWKGTSQTITIKEPATGKEL-GTVPAMEEKEIEEVMQSARQAQKEWQALAV 60

Query: 96  EDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYP 155
            +R+++L +AA L+++   E+   L  E+ K+   +  +V    D I Y A    R    
Sbjct: 61  VERAQILHQAAQLLKKEAVEIGTLLSKEIAKSRAASIQEVERTADLIAYTAEEGCRMEGQ 120

Query: 156 AVEVVPYPGED-NESFYV---PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAED 211
            +E   +  +D N+  +V    +G  + IAP+N+PV +    I   +  GNTV+ K    
Sbjct: 121 ILEGGSFSKKDQNKIAFVHKEAMGVVLAIAPFNYPVNLAASKIAPALIGGNTVVFKTPTQ 180

Query: 212 AVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEA 271
             + G ++  IFHEAG P GV+N + G G  +G  LV HP    INFTGS E+G  I E 
Sbjct: 181 GAISGLQLARIFHEAGVPAGVLNTVTGRGSVIGDALVTHPEVDAINFTGSTEIGTHIAEL 240

Query: 272 AGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILT 331
           AG         K   +E GGKDA +V E AD + AA+ +V  A+ + GQ+C+A  R+ +T
Sbjct: 241 AG--------MKPCIMELGGKDAALVLEDADLENAAKEIVAGAFQYSGQRCTAIKRVFVT 292

Query: 332 QGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQL--VLGG 389
           +   + ++  + K  E LSVG  EEN D+ P++    +R V  +IE    +  L   +  
Sbjct: 293 EKNADALVAAIQKEMETLSVGLPEENADITPLI----DRFVADHIEFLIEDALLKGAVAK 348

Query: 390 KRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449
            + + E   I P +  +V     +A EE FGPVL ++RVKD  E + +AN + YGL   +
Sbjct: 349 TKYQRERNLIWPMLLDQVTVDMDLAWEEPFGPVLPILRVKDVEEMIRLANASEYGLQSAI 408

Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSG 492
           ++          +   VG ++ N + T       PF G K SG
Sbjct: 409 FTNNYPLAMEIGKALKVGTVHMNHR-TQRGADHFPFLGIKNSG 450


Lambda     K      H
   0.319    0.137    0.403 

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: 492
Number of extensions: 23
Number of successful extensions: 4
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: 516
Length of database: 473
Length adjustment: 34
Effective length of query: 482
Effective length of database: 439
Effective search space:   211598
Effective search space used:   211598
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 24 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