GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA 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)



>lcl|MicrobesOnline__882:208821 DVU3294 aldehyde dehydrogenase
           (NADP) family protein
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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