GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Brucella inopinata BO1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_008511080.1 BIBO1_RS18765 aldehyde dehydrogenase family protein

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_000182725.1:WP_008511080.1
          Length = 510

 Score =  466 bits (1198), Expect = e-135
 Identities = 244/479 (50%), Positives = 325/479 (67%), Gaps = 4/479 (0%)

Query: 63  GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122
           G  +  + P + E IA ++  S  D E+ + +A EA++ W  +PAPKRGE++R +G+ LR
Sbjct: 30  GGDLAGFSPVSGEEIASIKTHSKEDAEKIIARADEAFRAWRTVPAPKRGELIRLLGEELR 89

Query: 123 EKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQW 182
              + LG LVSLE GKI  EG+GEVQE +DICD+AVGLSR + G  + +ER+GH ++E W
Sbjct: 90  ASKEDLGRLVSLEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERAGHRMMETW 149

Query: 183 NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLED-N 241
           +P+G+VG+I+AFNFPVAV+ WN A+A++CGN  +WK +  T L ++A   I  + L+   
Sbjct: 150 HPLGVVGVISAFNFPVAVWSWNAALAIVCGNAVVWKPSEKTLLTALACDAIFKRALKRFG 209

Query: 242 KLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNN 301
             P  I  L  G  +IG  +    +V ++S TGST++G++VG  + +RF R++LELGGNN
Sbjct: 210 DAPEGISQLLLGDREIGEVLVDSPKVPVVSATGSTRMGREVGPRLAKRFARAILELGGNN 269

Query: 302 AIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGN 361
           A I    ADL + + +  F A+GTAGQRCTT RRLF+HES++D +V RL+KAYA + VG+
Sbjct: 270 AGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDALVPRLQKAYASVSVGS 329

Query: 362 PWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGN--YVEPTIVTGLGH 419
           P + + L GPL  KQA      A++EA   GG V  G +V     N  YV P IV     
Sbjct: 330 PLETSALVGPLIDKQAFDNMQKALKEAAAHGGKVQGGERVDTGYENAYYVRPAIVEMPRQ 389

Query: 420 DASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCG 479
           +  +   ETFAPILYV K+ + ++V A +N V  GLSSSIFT +L    R+L  +GSDCG
Sbjct: 390 EGPVLE-ETFAPILYVMKYSDFDDVLASHNAVGAGLSSSIFTLNLQEAERFLSAEGSDCG 448

Query: 480 IVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLAQGIKF 538
           I NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK YMRR+T TINYSK LPLAQG+ F
Sbjct: 449 IANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTINYSKALPLAQGVSF 507


Lambda     K      H
   0.318    0.136    0.417 

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: 839
Number of extensions: 40
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: 539
Length of database: 510
Length adjustment: 35
Effective length of query: 504
Effective length of database: 475
Effective search space:   239400
Effective search space used:   239400
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 (21.7 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