GapMind for catabolism of small carbon sources

 

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

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::P42236
         (488 letters)



>FitnessBrowser__Cola:Echvi_0535
          Length = 514

 Score =  258 bits (659), Expect = 3e-73
 Identities = 158/467 (33%), Positives = 250/467 (53%), Gaps = 18/467 (3%)

Query: 14  INGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAERG 73
           I GEW+ S S        P D  ++ G VQ +T E  E+ +  A +A  AWRK+   +RG
Sbjct: 32  IKGEWLSSYS--------PVDGKEL-GKVQMTTRESYEKVLDQAEKAFKAWRKVPAPQRG 82

Query: 74  QYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDVIPS 133
           + + +    +  +   +    + EMGK+  E  GE    I I  +  G   +  G  + S
Sbjct: 83  EVVRQIGIELRNKKSLLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHS 142

Query: 134 TDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT---CA 190
                 M+    PLG+VGVIS +NFPVA+  W    A V G+  V KP+ +T +T   C 
Sbjct: 143 ERPSHRMYEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQ 202

Query: 191 KIIA-CFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARG 249
            I A  F   G P G+ +L+ G G+ VG  L +   V  ++ TGS Q+GK +G+    R 
Sbjct: 203 LIAADVFNRNGFPEGITSLLIG-GANVGAFLTQDPRVALISATGSTQMGKSVGETVGGRL 261

Query: 250 AKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKL 309
            K  LE+GG N +I+ + ADL+ A    + GA  + GQ+CT+T R+I+   ++E  KE++
Sbjct: 262 GKVLLELGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERM 321

Query: 310 LQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNG 369
           +     +TIG+ L ED  +GP+  K+ + N L+ IE+ K EG   ++ G  LE  +Y +G
Sbjct: 322 VAAYSKLTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYVSG 381

Query: 370 YYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGR 429
            YV+P++F+   +   I Q+E FGP++ L+K    +EA+ + N+V  GLS++I T N+  
Sbjct: 382 CYVRPSVFE-AENHFQIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMRE 440

Query: 430 MLSFI--DEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAA 474
              ++  +  D G+  +N  ++G E+   FGG K++    RE G  A
Sbjct: 441 AERYLSSEGSDCGISNVNIGTSGAEIGGAFGGEKETGG-GRESGSDA 486


Lambda     K      H
   0.315    0.132    0.374 

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: 563
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 488
Length of database: 514
Length adjustment: 34
Effective length of query: 454
Effective length of database: 480
Effective search space:   217920
Effective search space used:   217920
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 (21.5 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