GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Cupriavidus basilensis 4G11

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate RR42_RS13660 RR42_RS13660 aldehyde dehydrogenase

Query= SwissProt::Q8CHT0
         (562 letters)



>FitnessBrowser__Cup4G11:RR42_RS13660
          Length = 490

 Score =  148 bits (373), Expect = 6e-40
 Identities = 126/430 (29%), Positives = 191/430 (44%), Gaps = 37/430 (8%)

Query: 115 WDLKPMADRAQVFLKAADMLSGPRRAEVLAKTM-VGQGKTVIQAEIDAAAELIDFFRFNA 173
           W  +   +RA V  + AD++    RAE LA+   +  GK + +      A     F+F A
Sbjct: 60  WAQRKPHERAAVLHRVADLIRA--RAEPLAQRQRLDNGKPISETRA-LVASAAGTFQFFA 116

Query: 174 KFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALM-GNVVLWK 232
                LE     +       +V+  + G VAAI+P+N          APAL  GN V+ K
Sbjct: 117 AACETLEEALTPARGDFLTMSVHEAM-GVVAAITPWNSPIASEAQKLAPALAAGNAVVIK 175

Query: 233 PSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKH 292
           P++   L +  +  I  EAG+P  +I  +P  G   GD +T    +  ++FTG   T +H
Sbjct: 176 PAEITPLMALELAAICEEAGVPKGLISVLPGKGSVIGDAITKHPLVRRVSFTGGTTTGRH 235

Query: 293 LWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSR 352
           +    A  +        ++ E GGK+   V   AD+D  V+G L   F   G+ C A SR
Sbjct: 236 IAHIAADKM------MPVSLELGGKSPTMVFDDADLDHAVNGVLYGIFSSSGESCIAGSR 289

Query: 353 LYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSL 412
           L+V +SL+     RL E  +R++VGDPA++       + D        +  +   S  +L
Sbjct: 290 LFVARSLYEPFMDRLAEGAARLRVGDPADERTQMGPLISD--------RHRDSIESYVAL 341

Query: 413 SILAGGQCNE----------SVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKY 462
            +  GGQ               GY+  P IIE  D    + +EEIFGPVL    + D+  
Sbjct: 342 GVSEGGQLRTGGIRPAVAGCENGYFYTPTIIEGLDNSARVCQEEIFGPVLVAMAFDDE-- 399

Query: 463 RETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGA 522
            + L    + + Y L   V+ +D        R ++  AGN +IN     S+    PFGG 
Sbjct: 400 -DDLIAQANDSVYALAAGVWTRDYKRAWRFARAVQ--AGNVWINTYKQFSI--STPFGGW 454

Query: 523 RASGTNDKPG 532
           R SG   + G
Sbjct: 455 RDSGLGREKG 464


Lambda     K      H
   0.319    0.135    0.411 

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: 619
Number of extensions: 26
Number of successful extensions: 3
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: 562
Length of database: 490
Length adjustment: 35
Effective length of query: 527
Effective length of database: 455
Effective search space:   239785
Effective search space used:   239785
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 (21.8 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 (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