GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Pedobacter sp. GW460-11-11-14-LB5

Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase

Query= CharProtDB::CH_007936
         (497 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS24850 CA265_RS24850 aldehyde
           dehydrogenase
          Length = 454

 Score =  244 bits (624), Expect = 4e-69
 Identities = 151/456 (33%), Positives = 238/456 (52%), Gaps = 6/456 (1%)

Query: 37  QVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSERGILINKLADLMERDI 96
           Q+INP+  ++ITS+ E     + +   A + A +  W   T  ER  +I   +DL+E +I
Sbjct: 2   QIINPATAEIITSLEEDNLSTLQLKFDALQKA-QPQWAGKTLQERIAVITHFSDLLEVEI 60

Query: 97  DTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTIDTN-PETLTYTRHEPV 155
           + LA++ + + GK    ++ ++  +   +++    A+K     + T+ P      ++EP+
Sbjct: 61  EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL 120

Query: 156 GVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSALYAAKLIKEAGFPAGVIN 215
           GV   I  WN+P L+      PA+ +GNTV+ K +E   L+ +   KL+K+AG P  V +
Sbjct: 121 GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH 180

Query: 216 VISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNLKKVTLELGGKSPNIVFD 275
           +  G   T  A ++  MD +   FTGS   G+ I +  A + +    LELGGK P  + D
Sbjct: 181 IAIGAKETGSALLN--MDFNGYFFTGSYKTGKLIYEKVA-AKMVPCQLELGGKDPLYITD 237

Query: 276 DA-DIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARFKERAQKNKVGNPFEQD 334
           D  D+  A      G F+N+GQ CCA  RI VQE  YD +   F    +  K G P  + 
Sbjct: 238 DVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEG 297

Query: 335 TFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGNEGYFIQPTVFTDVTSDMKIAQE 394
            + G    + Q   +   +      GA + TGG     +GY+ +PTV TDVT+DM + QE
Sbjct: 298 VYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQE 357

Query: 395 EIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTAIRVSNALKAGTVWINNYNM 454
           E FGP++ I K KD+AEA+K+   TDYGL A+V+T +   A ++   L AG+ + N  + 
Sbjct: 358 ESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDR 417

Query: 455 ISYQAPFGGFKQSGLGRELGSYALENYTQIKTVHYR 490
           +S   P+ G K SG+G  L    +  +T+ K  H R
Sbjct: 418 VSAALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLR 453


Lambda     K      H
   0.318    0.134    0.397 

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: 496
Number of extensions: 27
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: 497
Length of database: 454
Length adjustment: 33
Effective length of query: 464
Effective length of database: 421
Effective search space:   195344
Effective search space used:   195344
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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