GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Collimonas arenae Ter10

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_061534526.1 CAter10_RS18190 aldehyde dehydrogenase family protein

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_001584165.1:WP_061534526.1
          Length = 506

 Score =  487 bits (1254), Expect = e-142
 Identities = 245/485 (50%), Positives = 333/485 (68%), Gaps = 10/485 (2%)

Query: 63  GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122
           G  + +  P +   IA +R  +VA+ E  +K A++A++ W  +PAP RGE+VR +G+ LR
Sbjct: 20  GNDLHSRSPRDGAAIASLRAHTVAETEAAIKNAQQAYEKWRVVPAPVRGELVRILGEVLR 79

Query: 123 EKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQW 182
           E  + LG LV+LE GKIL EG+GEVQE +DICD+AVGLSR + G  + SER GH ++E W
Sbjct: 80  ENREPLGKLVTLESGKILSEGIGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMMETW 139

Query: 183 NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVL---- 238
           +P+G+ G+ITAFNFPVAV+ WN A+A++CGN  +WK +  T ++++AV  +  K +    
Sbjct: 140 HPLGVCGVITAFNFPVAVWAWNAALALVCGNAVIWKPSEKTPVVALAVHALYEKAVARFS 199

Query: 239 --EDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLE 296
               + LP  +C +  G A+IG  ++    V L+S TGS ++G++V   V ER GRSLLE
Sbjct: 200 QQRPDLLPSNLCQVVLGRAEIGATLSASPLVPLISATGSVRMGRKVATTVAERLGRSLLE 259

Query: 297 LGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQ 356
           LGGNN +I    ADLSL + +  F+AVGTAGQRCT+ RRLF+H SI+D+VVNR+++ YA 
Sbjct: 260 LGGNNGMIVTPTADLSLALRAITFSAVGTAGQRCTSLRRLFVHSSIYDDVVNRIERIYAS 319

Query: 357 IRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGN---YVEPTI 413
           ++VG+P D   L GPL  +Q+      A+++AK EGG V  G +V    G    YV P +
Sbjct: 320 VKVGDPLDAGTLVGPLVDQQSFEAMQTALQQAKAEGGVVTGGERVAVGDGENAYYVRPAL 379

Query: 414 VTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGP 473
           V  +   + I H ETFAPILYV +++N ++    NN V QGLSS+IFT D+     ++  
Sbjct: 380 VR-MSQQSDIVHHETFAPILYVLRYENFDDAVRMNNAVPQGLSSAIFTNDVREAEAFMSA 438

Query: 474 KGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLA 533
            GSDCG+ NVNI TSGAEIGGAFGGEK TGGGRESGSD+WK YMRR+T TINYS+ LPLA
Sbjct: 439 SGSDCGLANVNIGTSGAEIGGAFGGEKETGGGRESGSDSWKTYMRRATNTINYSRTLPLA 498

Query: 534 QGIKF 538
           QG+KF
Sbjct: 499 QGVKF 503


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: 806
Number of extensions: 29
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: 506
Length adjustment: 35
Effective length of query: 504
Effective length of database: 471
Effective search space:   237384
Effective search space used:   237384
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