GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Shewanella oneidensis MR-1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__MR1:200453 SO1275 succinate-semialdehyde
           dehydrogenase (NCBI ptt file)
          Length = 482

 Score =  297 bits (761), Expect = 5e-85
 Identities = 177/472 (37%), Positives = 263/472 (55%), Gaps = 8/472 (1%)

Query: 21  RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80
           + +ING++ DA S ET    +P  G  +A V     A+   A+  A A   +  W  L  
Sbjct: 12  QCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPA--WRALTA 69

Query: 81  AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140
            +R AKL R+ +LL +N ++LALL T + GKP+ ++   ++  AA  I W AE   ++Y 
Sbjct: 70  KERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKG-EVTYAASFIEWFAEEAKRIYG 128

Query: 141 EVAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLT 199
           +  P    D+  +V ++PVGV  AI PWNFP  M   K  PALA G ++V+KP+ ++P T
Sbjct: 129 DTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFT 188

Query: 200 AIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGES 259
           A+ +A LA  AGIPAGV +V+ G    +G  +  +  V  L FTGST +  +LM     +
Sbjct: 189 ALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAPT 248

Query: 260 NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFL 319
            +K++ LE GG +P IVF DA ++ AA E A  A   N G+ C   +R+ V+  + D+F 
Sbjct: 249 -LKKLSLELGGNAPFIVFDDA-NIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFA 306

Query: 320 PMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG 379
             +  A+   K G  +    T G L++   +  V S++E   K GA +LAGGK  + E G
Sbjct: 307 EKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGK--VHELG 364

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
           G + EPT+      +MR+A+EE FGP+  +  F+  ++ +  ANDT +GLAA  +  DIS
Sbjct: 365 GNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDIS 424

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
              K A ++  G V VN        APFGG K SG GR+ S + +E+Y E+K
Sbjct: 425 LVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476


Lambda     K      H
   0.316    0.132    0.390 

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: 36
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: 497
Length of database: 482
Length adjustment: 34
Effective length of query: 463
Effective length of database: 448
Effective search space:   207424
Effective search space used:   207424
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 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, the preprint 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