GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Erythrobacter gangjinensis K7-2

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_047005389.1 AAW01_RS00220 coniferyl aldehyde dehydrogenase

Query= curated2:P39616
         (456 letters)



>NCBI__GCF_001010925.1:WP_047005389.1
          Length = 483

 Score =  322 bits (826), Expect = 1e-92
 Identities = 183/440 (41%), Positives = 251/440 (57%), Gaps = 10/440 (2%)

Query: 1   MNSIPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDL-HKSEQEA 59
           M  + S+++  KA FAA      E RL+ L +L+  +  +   L  A+  D   +S  E 
Sbjct: 13  MPDLDSLLAAQKAAFAADRMPSREVRLDRLDRLQNLLLDNRQALADAISADFCGRSPVET 72

Query: 60  YSTEIGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQ 119
              EI  +LE I +  KRL+K  KP++    LT + +++ +  +P G V ++ PWN+P+ 
Sbjct: 73  DLAEIIPLLEGIKYYRKRLKKLMKPEKRHASLTVMPARAEVRYQPKGVVGIVVPWNFPVF 132

Query: 120 LALSPLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQ 179
           LALSPLIG +AAGN  +LK SE+TP    +L  L++  F  D V +  G  +V+TA  + 
Sbjct: 133 LALSPLIGVLAAGNRAMLKMSEFTPRTGELLGGLLAEKFSDDEVVLVNGDVEVATAFTKL 192

Query: 180 PFDYIFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTN 239
           PFD++ FTGS AVG+ VM AAA+ L+PVTLELGGKSP I+H D  ++ AAKRI FGK  N
Sbjct: 193 PFDHLVFTGSTAVGRKVMAAAAENLVPVTLELGGKSPAIIHPDFPMEEAAKRIAFGKVIN 252

Query: 240 AGQTCIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLN 299
           AGQ CIAPDY+           +     +RE Y P    NP Y  I++E    RL  +L 
Sbjct: 253 AGQICIAPDYILCPRSQVDAFADAFANEVRENY-PTYRDNPDYTAIITEAQRDRLTDWLA 311

Query: 300 DG-------IPLTGGQSD-PNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEV 351
           D        + +     D     K+  TI   V DD  +MQ+EIFGPILP+  Y  + E 
Sbjct: 312 DAEAKGARLMRVNPADEDLSGTRKLPVTIALDVSDDMTIMQDEIFGPILPIVPYDTLDEA 371

Query: 352 IEKVQSRPKPLALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIG 411
           +  V  R +PLALY F  +K     VL     GG C+NDTL HV    LPFGG+G SGIG
Sbjct: 372 LAYVNERERPLALYYFDWDKSRADRVLARTHSGGACINDTLSHVTCDDLPFGGIGPSGIG 431

Query: 412 SYHGFDSFNTFTHKKSVVKQ 431
            YHG + + TF+H K+VV++
Sbjct: 432 HYHGEEGYRTFSHAKAVVRK 451


Lambda     K      H
   0.320    0.137    0.401 

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: 541
Number of extensions: 22
Number of successful extensions: 2
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: 456
Length of database: 483
Length adjustment: 33
Effective length of query: 423
Effective length of database: 450
Effective search space:   190350
Effective search space used:   190350
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 (21.8 bits)
S2: 51 (24.3 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