GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Desulfovibrio vulgaris Hildenborough

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::Q72IB9
         (516 letters)



>MicrobesOnline__882:208821
          Length = 464

 Score =  152 bits (383), Expect = 3e-41
 Identities = 129/435 (29%), Positives = 190/435 (43%), Gaps = 19/435 (4%)

Query: 65  VGTTAKAGKAEAEAALEAAWKAF-KTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYE 123
           VG      +AEA AALE A           P  +R  +L + A LMR     L    V E
Sbjct: 15  VGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLMRTHAEALVRDAVRE 74

Query: 124 VGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYV---PLGAGVVI 180
            GK W ++  +V  AID + + AR   +     V +   P       +    P G  + I
Sbjct: 75  GGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLAFTVREPRGVVLAI 134

Query: 181 APWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVG 240
           + +N PV +     +   A G  V+ KPA    +    V  + HEAG P      LP   
Sbjct: 135 SAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAGVPEAWATMLP-CA 193

Query: 241 EEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDET 300
                 LV  PR  F++F GS  VG   +    +LAPG T      +E GG   +++D +
Sbjct: 194 AATAEKLVADPRVAFLSFIGSSRVG---WHLRSKLAPGAT----CALEHGGAAPVVLDAS 246

Query: 301 ADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPD 359
           AD D A   ++   +   GQ C +  R+           ER+   A +L  G P   +  
Sbjct: 247 ADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGDPMRHDTA 306

Query: 360 LGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKRLEGEGYFIAPTVFTEVPPKARIAQEEI 418
           +GP++   +  +V  ++E  +  G  VL GG  L    Y  +PTV  + P   R+A+ E+
Sbjct: 307 VGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSETLY--SPTVVYDPPQGCRLARNEV 364

Query: 419 FGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE-HLEWARREFHVGNLYFNRKITG 477
           FGPV++V   +D  EA+  AND P+     V++R  +  L+ ARR    G +  +   T 
Sbjct: 365 FGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVNDH--TA 422

Query: 478 ALVGVQPFGGFKLSG 492
             V   PFGG   SG
Sbjct: 423 FRVDWMPFGGRGESG 437


Lambda     K      H
   0.319    0.137    0.403 

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: 517
Number of extensions: 24
Number of successful extensions: 5
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: 464
Length adjustment: 34
Effective length of query: 482
Effective length of database: 430
Effective search space:   207260
Effective search space used:   207260
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 (21.7 bits)
S2: 52 (24.6 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