GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Corynebacterium deserti GIMN1.010

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_053543863.1 CDES_RS00960 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_001277995.1:WP_053543863.1
          Length = 504

 Score =  208 bits (530), Expect = 3e-58
 Identities = 154/475 (32%), Positives = 239/475 (50%), Gaps = 36/475 (7%)

Query: 56  NPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRKHEF 115
           NPA  + V G V  A+QE  +  I +A KA + W   S  +R AV+F     +  RK E 
Sbjct: 28  NPATGQ-VTGNVVLANQEEIDATIASATKAAKAWGRLSIAKRQAVIFNFRELLNARKEEL 86

Query: 116 SALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYT----- 170
           +A++  E GK  ++A  +            ++++ELA G P +  +G  ++ V T     
Sbjct: 87  AAIITAEHGKVLSDALGEILRG--------QEVVELATGFP-HLLKGAFSENVSTGVDVY 137

Query: 171 ----PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGL 226
               P GV  +I P+NF   +        I  GN V+LKP+   P  A    ++ +E+GL
Sbjct: 138 SLKQPLGVVGIISPFNFPAMVPMWFFPIAIAAGNAVILKPSEKDPSAALWMAQLWKEAGL 197

Query: 227 PKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAE 286
           P GV N + G    V D L++ P+ S I+F GS  +   I+E +AK      + KRV A 
Sbjct: 198 PDGVFNVLQGDKLAV-DGLLNSPEVSAISFVGSTPIAQYIYETSAK------NGKRVQAL 250

Query: 287 MGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITES 346
            G K+ ++V  DAD++L A     S FG AG++C A S  +  + + D+++E++ E  ++
Sbjct: 251 GGAKNHMLVLPDADLDLVADQAINSGFGAAGERCMAISVVLAIDSIADELIEKIKERIDT 310

Query: 347 KVT---AKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG----TGDDSKGYFI 398
                 A  D  +  MGP+I     DK+  Y++I + +G R+V  G         +G+F 
Sbjct: 311 LRIGNGAGDDQGEPDMGPLITDVHRDKVSGYVDIAEADGARIVVDGRNYAVAGHEEGFFF 370

Query: 399 KPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIER 458
            PT+  D+   +R   EEIFGPV++  +VS FDEA+E+ N+ E+G   A+ TN+     R
Sbjct: 371 GPTLIDDVPLTSRAYTEEIFGPVLSVVRVSSFDEAIELINSGEFGNGTAIFTNDGGAARR 430

Query: 459 AKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMS-GTDSKAGGPDYLALHMQAKTIS 512
            + E  VG +  N       V YH FGG+K S   D+KA G        + K I+
Sbjct: 431 FQNEIQVGMIGINVPIP-VPVAYHSFGGWKNSLFGDAKAYGTQGFDFFTREKAIT 484


Lambda     K      H
   0.316    0.133    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: 556
Number of extensions: 38
Number of successful extensions: 7
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: 515
Length of database: 504
Length adjustment: 34
Effective length of query: 481
Effective length of database: 470
Effective search space:   226070
Effective search space used:   226070
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 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