GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200453
          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 (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