GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Echinicola vietnamensis KMM 6221, DSM 17526

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__Cola:Echvi_1497
          Length = 469

 Score =  174 bits (440), Expect = 8e-48
 Identities = 127/422 (30%), Positives = 204/422 (48%), Gaps = 13/422 (3%)

Query: 72  SLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSK 131
           S R + L  +   IK  + E+ K    D  KP  E +A  +      E  A L +     
Sbjct: 22  SSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAE-VAVTETSFVVMEINAALKQLPKWT 80

Query: 132 QKAPISLPMDTF--KSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189
               +  P+     ++Y+  EP G V +I+PWNYPF ++   +  A+AAGC+A LKPSE 
Sbjct: 81  APTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEH 140

Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249
           +  T   L  +  E+     V  I  G G    + L   P  D I FTGS+  G  +M  
Sbjct: 141 SPHTSALLRRMVTELFAVEDV-TIFEG-GVPVTSELLEQP-FDHIFFTGSTEVGKIVMKA 197

Query: 250 AAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVE 309
           AA+ +  V+LELGGKSP ++ +  DL+  A+    G F  +GQ C A   L VHES   +
Sbjct: 198 AAKNLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQD 257

Query: 310 FVDKLVKWAENIKISD--PLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPE 367
           F++ L      +  ++    +     G I+      ++ N +  A+++GA +  GG+   
Sbjct: 258 FIETLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGKNSL 317

Query: 368 HLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMS 427
             +   F+EPT++++V+ +M + +EE+FGP+L + T+   ++ I L       L     +
Sbjct: 318 DQQ---FMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFT 374

Query: 428 NDLERCERLSKALQAGIVWINCAQPSFI--QAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
            D    E+LSK   +G + IN     F+  + P+GGI  SG GR  G  G   + + K +
Sbjct: 375 TDDRIIEQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAI 434

Query: 486 TR 487
            +
Sbjct: 435 LK 436


Lambda     K      H
   0.317    0.134    0.402 

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: 454
Number of extensions: 22
Number of successful extensions: 4
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: 503
Length of database: 469
Length adjustment: 34
Effective length of query: 469
Effective length of database: 435
Effective search space:   204015
Effective search space used:   204015
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 (21.6 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 (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