GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Dyella japonica UNC79MFTsu3.2

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

Query= reanno::Smeli:SM_b20891
         (477 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2488 N515DRAFT_2488
           succinate-semialdehyde dehydrogenase /
           glutarate-semialdehyde dehydrogenase
          Length = 463

 Score =  236 bits (601), Expect = 2e-66
 Identities = 154/461 (33%), Positives = 231/461 (50%), Gaps = 11/461 (2%)

Query: 19  ANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILARK 78
           A INP  T + V  +  A+  +   A+  A+A F AW   G+  R  +L+K AD +    
Sbjct: 4   ATINPY-TGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESH 62

Query: 79  DELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRL-AGEVVPSVRPGIGVE-ITRE 136
            +  ++L+ E GK + E  GE     QI E++A    +L A E + S  P      +   
Sbjct: 63  TQYAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHV 122

Query: 137 PAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKG- 195
           P G++  + PWNFP        AP L  GN ++ K A  VP C+ A   +   AGLP+G 
Sbjct: 123 PQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGG 182

Query: 196 VLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVV 255
             NL   +  +  +A+++ P VQ +  TGS   G  VA  + +  +K  +E+GG + FVV
Sbjct: 183 FTNLYATRDQL--KAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVV 240

Query: 256 LDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKP 315
           L DADL  AV+ AV    ++ GQ C +S RIIV + I+D F+      +  L   D ++P
Sbjct: 241 LADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEP 300

Query: 316 GTHIGPVVDQSQLNQDTDYIAIGKQEGAKL-AFGGEVISRDTPGFYLQPALFTEATNEMR 374
            T + P+  +  ++     +      GAK+   G EV SR   G + +P L +  +++  
Sbjct: 301 STTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSR---GAFFRPVLLSHVSDDNP 357

Query: 375 ISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVN 434
               E FGPV+ VIR +D  +A+ +AND+PFGL   + TT +KH     +    GMV +N
Sbjct: 358 ARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYIN 417

Query: 435 LPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYT 475
            PT GV   +PFGG + S YG    G    EF  +   A T
Sbjct: 418 HPT-GVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAVT 457


Lambda     K      H
   0.317    0.134    0.391 

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: 520
Number of extensions: 25
Number of successful extensions: 6
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: 477
Length of database: 463
Length adjustment: 33
Effective length of query: 444
Effective length of database: 430
Effective search space:   190920
Effective search space used:   190920
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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