GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dinoroseobacter shibae DFL-12

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Dino:3609503
          Length = 492

 Score =  211 bits (536), Expect = 6e-59
 Identities = 145/448 (32%), Positives = 222/448 (49%), Gaps = 10/448 (2%)

Query: 14  ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQ 73
           AD+G T  V NP+ G+ +  VP   R    +AI AA AA   W       RAQVL R+  
Sbjct: 31  ADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVLRRWFD 90

Query: 74  LLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGPNIDAW 133
           L+  N + + ++++ E GK + +A GE+  G   VE+     + L GE      P+    
Sbjct: 91  LIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPGHLPDARIQ 150

Query: 134 SDFQPIGVVAGITPFNFP-AMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAG 192
              QPIGVV  ITP+NFP AM+     P A+A G  F+ KP+E  P S L +A L   AG
Sbjct: 151 VIRQPIGVVGAITPWNFPIAMITRKAAP-ALAAGCAFLSKPAEDTPLSALALAVLAERAG 209

Query: 193 LPKGVLNVV-HGDKGAV-DALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAK 250
           +P G+  V+   D  A+     E   V+ L+F GST +   + ++   + K+     G  
Sbjct: 210 IPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSMELGGN 269

Query: 251 NHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKI 310
              ++  DADLD AV   M   + + G+ C+  +  + V D + DA  +KL   ++ LK+
Sbjct: 270 APFIVFDDADLDKAVEGAMACKFRNAGQTCVCAN-RIYVQDGVYDAFAEKLAAAVEELKV 328

Query: 311 GAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFD 370
           G G + G+ +GPL+   A +KV  ++D   A+G  +V  G  + +     G F   T+  
Sbjct: 329 GDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPL----GGTFFTPTVVT 384

Query: 371 RVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIE 430
            VT EM + +EE FGPV  + R    +E + + ND  +G     + RD        + +E
Sbjct: 385 GVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALE 444

Query: 431 VGMVGVNVPLPVPVAYHSFGGWKRSLFG 458
            G+VG+N  + +      FGG K+S  G
Sbjct: 445 YGIVGINTGI-ISTEGAPFGGVKQSGLG 471


Lambda     K      H
   0.319    0.137    0.411 

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: 591
Number of extensions: 32
Number of successful extensions: 5
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: 498
Length of database: 492
Length adjustment: 34
Effective length of query: 464
Effective length of database: 458
Effective search space:   212512
Effective search space used:   212512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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