GapMind for catabolism of small carbon sources

 

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

Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::P12693
         (483 letters)



>FitnessBrowser__Cola:Echvi_1497
          Length = 469

 Score =  400 bits (1029), Expect = e-116
 Identities = 213/446 (47%), Positives = 289/446 (64%), Gaps = 2/446 (0%)

Query: 39  IAERIAALNLLKETIQRREPEIIAALAADFRKPASEVKLTEIFPVLQEINHAKRNLKDWM 98
           ++ RI  L  LKE I+  + EI  AL AD RKPA+EV +TE   V+ EIN A + L  W 
Sbjct: 21  LSSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAEVAVTETSFVVMEINAALKQLPKWT 80

Query: 99  KPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVIKPSEL 158
            P +V   + + GT+A L+ EPKG  LII+PWNYPFNLS  PLVSA+AAG S  +KPSE 
Sbjct: 81  APTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEH 140

Query: 159 TPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVMEAASK 218
           +PHT+ L+  +V E F+V+ V + EG   V+ ELL  PFDHIFFTGS  VGK+VM+AA+K
Sbjct: 141 SPHTSALLRRMVTELFAVEDVTIFEGGVPVTSELLEQPFDHIFFTGSTEVGKIVMKAAAK 200

Query: 219 TLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIAQKFNE 278
            L SVTLELGGKSP II    +L  AA+ I  GKF N+GQTCIAPD++FVH    Q F E
Sbjct: 201 NLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQDFIE 260

Query: 279 ILVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKILQGGQVDATER 338
            L  ++ R+Y  +     R+ DY RI++  H  R+  +L DA+ KGA +  GG+    ++
Sbjct: 261 TLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGKNSLDQQ 320

Query: 339 LVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKPLALYVFSEDKQFV 398
            + PTV+SNV+ AMD+  EEIFGP+LPII Y  +D VI+ +    KPLA+Y F+ D + +
Sbjct: 321 FMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFTTDDRII 380

Query: 399 NNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRAFSHEKPVLIDKF- 457
             +   TSSG++ +N   + FLH  LPFGG+  SG+G +HG  GF AFS+EK +L  +  
Sbjct: 381 EQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAILKQRTG 440

Query: 458 -SITHWLFPPYTKKVKQLIGITVKYL 482
            ++   L+PPY  K   +I   +K++
Sbjct: 441 KTLPKLLYPPYGLKTSGIIKAFMKWV 466


Lambda     K      H
   0.320    0.136    0.395 

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: 506
Number of extensions: 20
Number of successful extensions: 1
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: 483
Length of database: 469
Length adjustment: 33
Effective length of query: 450
Effective length of database: 436
Effective search space:   196200
Effective search space used:   196200
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 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