GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Marivita geojedonensis DPG-138

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_085637847.1 MGEO_RS12055 aldehyde dehydrogenase family protein

Query= BRENDA::Q65NN2
         (516 letters)



>NCBI__GCF_002115805.1:WP_085637847.1
          Length = 474

 Score =  246 bits (629), Expect = 1e-69
 Identities = 146/449 (32%), Positives = 245/449 (54%), Gaps = 20/449 (4%)

Query: 56  INPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHE 115
           I+P N EEV+ T++  +    + A+ AA +AF TW+++  +ER A+L R +    ++   
Sbjct: 25  IHPGN-EEVIATIALGSSSDVDHAVAAATEAFNTWQFSTVDERVALLERMIIAYEKRSEA 83

Query: 116 FSALLVKEAGKPWN-EADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTG 174
           F  ++ +E G   +   +      I  +E  A + ++  + +  + R G  +  +  P G
Sbjct: 84  FIKVMSQEIGTTLSFSREVQMPVGIGHLEA-AIEALKAHQFERPSLRGG--STLIDEPVG 140

Query: 175 VTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNF 234
           V  +I PWN+    +       +  G T+VLKP+  +P+ A    EV++E+G P GV N 
Sbjct: 141 VVGMITPWNWPVNQIMIKVAPALAAGCTIVLKPSEYSPLSAIMLAEVIDEAGCPPGVFNL 200

Query: 235 VPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTV 294
           V G G  VG+ +  HP   +++FTGS   G  + + AA        +K+V  E+GGK   
Sbjct: 201 VNGDGPGVGEAISAHPGIHMVSFTGSTRAGKLVTKSAAN------SIKRVTLELGGKSPN 254

Query: 295 VVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPD 354
           +   D D++ AA+    + F   GQ C A SR +V  K+YDEV++RV +I E+ KV +P 
Sbjct: 255 LFFADADLDAAARISVDACFINNGQSCDAASRLLVERKIYDEVVERVTQIVENTKVDDPM 314

Query: 355 SADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGGKGDD---SKGYFIEPTIFADLDPK 410
               ++GPV+++  F  +   I++G ++G RL +GG G     +KGY+I PT+FAD+   
Sbjct: 315 KEGSHIGPVVNKKQFEHVQRLIQVGIDDGARLAAGGLGRPAGFNKGYYIRPTLFADVTND 374

Query: 411 ARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLY 470
             + Q+E+FGPV+A     + +EA+E+AN+T YGL   + + +++ I+R  ++   G + 
Sbjct: 375 MEIAQQEVFGPVLAILPFDTEEEAIEIANDTPYGLAAYIQSTDQERIHRVSRKLRAGVIS 434

Query: 471 FNRNCTGAIVGYH-PFGGFKMSGTDSKAG 498
            N    G +  Y  PFGG+K SG   +AG
Sbjct: 435 VN----GKVGDYDVPFGGYKESGNGREAG 459


Lambda     K      H
   0.315    0.133    0.382 

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: 613
Number of extensions: 32
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: 516
Length of database: 474
Length adjustment: 34
Effective length of query: 482
Effective length of database: 440
Effective search space:   212080
Effective search space used:   212080
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