GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Methylocystis bryophila S285

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_085770042.1 B1812_RS01610 aldehyde dehydrogenase family protein

Query= BRENDA::Q65NN2
         (516 letters)



>NCBI__GCF_002117405.1:WP_085770042.1
          Length = 474

 Score =  218 bits (556), Expect = 3e-61
 Identities = 147/462 (31%), Positives = 232/462 (50%), Gaps = 22/462 (4%)

Query: 56  INPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHE 115
           INPA  E V G ++  +    ++A+ AA +AF+++  T   ER  +L R V ++ ++  +
Sbjct: 25  INPAT-EAVCGHIALGSATDVDRAVAAAGEAFKSFSRTSRRERLELLQRIVVELEKRHED 83

Query: 116 FSALLVKEAGKP-WNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTG 174
            +  + +E G P W    A  A+A     +++   IE+ K      R G     V  P G
Sbjct: 84  MARAITEEMGAPVWL---AQRAQARMGAAHFSTA-IEVLKRYEFEERRGA-TIIVKEPIG 138

Query: 175 VTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNF 234
           V   I PWN+    MA      + TG  +VLKP+  AP       E LE +G P GV N 
Sbjct: 139 VCGFITPWNWPLNQMACKIAPALATGCAMVLKPSEIAPFSGIVLAEALEAAGTPPGVFNL 198

Query: 235 VPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTV 294
           V G G  VG  +  HP  S+++FTGS   G  + + AA        +K++  E+GGK   
Sbjct: 199 VNGDGPTVGAAISSHPGVSMVSFTGSTRAGVEVAKNAAPT------VKRICQELGGKSPN 252

Query: 295 VVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPD 354
           ++ ED D++ A  +   +    +GQ C+A +R +   K  +EV+       E+  VG+P 
Sbjct: 253 ILLEDADMKAAVTAGVNAVMLNSGQSCNAPTRMLAPRKRMEEVIGFARSAAEATTVGDP- 311

Query: 355 SADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGGKGDD---SKGYFIEPTIFADLDPK 410
           + +  MGPV+ +A +NK+   I+ G EEG  LV+GG G      KGY+++PT+FA++   
Sbjct: 312 NGNAQMGPVVSEAQWNKVQGLIQKGLEEGASLVAGGLGKPEGLEKGYYVKPTVFANVTND 371

Query: 411 ARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLY 470
             + +EEIFGPV++        +A+E+AN+TEYGL+  V   +   +         G + 
Sbjct: 372 MTIAREEIFGPVLSILAYDRVADAIEIANDTEYGLSAYVSGADPARLMETASRLRAGQVQ 431

Query: 471 FNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 512
            N      +    PFGG+KMSG + +  G    A  ++ K I
Sbjct: 432 LNSAPMDLMA---PFGGYKMSG-NGREWGDHAFAEFLETKAI 469


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: 586
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