GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Phaeobacter inhibens BS107

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC

Query= CharProtDB::CH_122352
         (572 letters)



>lcl|FitnessBrowser__Phaeo:GFF3174 PGA1_c32250
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
           PuuC
          Length = 494

 Score =  159 bits (402), Expect = 2e-43
 Identities = 158/500 (31%), Positives = 240/500 (48%), Gaps = 46/500 (9%)

Query: 71  VIAGKEVKSSSSLTQS--NPASHGPVATYSNATAKDVQAAIESALEA--RKSWASTPFAD 126
           +I G++V +S   T    +P     +   +  T +D++ AI SA  A   + WA  P A 
Sbjct: 20  LIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAA 79

Query: 127 RASVFLKAADLISTKYRYDVMALTMHGQGKN------AWQAEIDSAAELCDFFRFGVKYA 180
           R  V +K A+LI      D + L + G   N      A +AE  SAA      R+  +  
Sbjct: 80  RKKVLMKWAELIEA----DALNLAVLGVRDNGTEITMALKAEPGSAAAT---IRYYAEAL 132

Query: 181 EDLYAQQPVHHAPGVWNRVEYRPLEGFVYAISPFNFTAIGGNLAGAPAL-MGNVVVWKPS 239
           + +Y +     +  V   V   P+ G V AI P+NF  + G    APAL MGN VV KPS
Sbjct: 133 DKIYGEI-APTSSDVLGMVHKEPV-GVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPS 190

Query: 240 PSAIASNWLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLY 299
            +A  S   + ++ LEAGLP  V+  V GE   V + +    D   L FTGS        
Sbjct: 191 ETASLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGS-------- 242

Query: 300 GQISTRVAAGKYRS-YPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSAT 357
           GQ   R+     RS   R+  E GGK+ +++   A D+ +AA  T  G F   GQ C A 
Sbjct: 243 GQTGRRLMEYAARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAG 302

Query: 358 SRVYVASSIADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPE 417
           SR+ V +SI D+F+E+VA  A+ ++VG P       G +  EA   +  + +  A+ +  
Sbjct: 303 SRLLVEASIHDAFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGG 362

Query: 418 LELLAGGS--YDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIA 475
            +++ GG      + G Y+ PT+     PD  L   E+FGP+L V   P  T+A+  RIA
Sbjct: 363 -QIITGGQRLLSETGGSYMAPTIVTGVTPDATLAQEEVFGPVLAV--TPFETDAEALRIA 419

Query: 476 QKIDATGEYGLTGSVFAQDREALAVANDVLRNA-AGNFYINCKSTGAVVGQQPFGGARAS 534
              +AT  YGL G+V+      L  A+ +++    G  ++N  + G   G  P GG   S
Sbjct: 420 ---NAT-VYGLAGAVWT---SGLTRAHRMVQGVRTGVMHVN--TYGGADGTVPLGGVGQS 470

Query: 535 GTNDKAGSGNLLSRFVSLRS 554
           G N    S + + ++++L++
Sbjct: 471 G-NGADKSLHAIDKYINLKT 489


Lambda     K      H
   0.316    0.130    0.379 

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: 577
Number of extensions: 27
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: 572
Length of database: 494
Length adjustment: 35
Effective length of query: 537
Effective length of database: 459
Effective search space:   246483
Effective search space used:   246483
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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