GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Desulfovibrio vulgaris Hildenborough

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  211 bits (538), Expect = 7e-59
 Identities = 145/433 (33%), Positives = 213/433 (49%), Gaps = 24/433 (5%)

Query: 55  DLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIG 114
           ++ DA  A + A  T     W   +PA R A L R AD+ RK + EL+  + +++GK   
Sbjct: 549 EIDDAIAAAKKAALT-----WRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQ-W 602

Query: 115 DSSSIDIPGAAQAIHWTAEAIDKVYDEV----APTPHDQLGLVTREPVGVVGAIVPWNFP 170
           D +  D+      + + A  + ++        AP  H+ L     +P G+   I PWNFP
Sbjct: 603 DQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEHNHLFY---QPKGIAAVIAPWNFP 659

Query: 171 LLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKA 230
             +A      A+ TGN V+ KPS  S      +A++  EAG+P GV N  PG    +G  
Sbjct: 660 FAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGDY 719

Query: 231 LALHMDVDTLVFTGSTKIA-----KQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQA 285
           L  H D+  + FTGS ++      K   V  G+   KR+  E GGK+  I+  DA   +A
Sbjct: 720 LVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEA 779

Query: 286 AAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALV 345
             +   SA  F QG+ C+A SR++V  +I D+F+  +V+A      G   DP   +G + 
Sbjct: 780 VLQVLYSAFGF-QGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVA 838

Query: 346 DTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGP 405
           D      V  YI    ++G  LL   KRT     G YV  TI   +    RIAQEEIFGP
Sbjct: 839 DATLQKNVSDYIRIAEEEGRVLL---KRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGP 895

Query: 406 VLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMT- 464
           VL+V+   T +EA++IAN T + L   +++       K  R  R G++++N+   G +  
Sbjct: 896 VLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVE 955

Query: 465 -APFGGFKQSGNG 476
             PFGGF  SG G
Sbjct: 956 RQPFGGFAMSGVG 968


Lambda     K      H
   0.316    0.132    0.390 

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: 1019
Number of extensions: 47
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: 497
Length of database: 1006
Length adjustment: 39
Effective length of query: 458
Effective length of database: 967
Effective search space:   442886
Effective search space used:   442886
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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