GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Synechococcus elongatus PCC 7942

Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase

Query= SwissProt::Q9SAK4
         (528 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0489 Synpcc7942_0489 aldehyde
           dehydrogenase
          Length = 459

 Score =  167 bits (423), Expect = 8e-46
 Identities = 131/416 (31%), Positives = 203/416 (48%), Gaps = 27/416 (6%)

Query: 118 LRRWYDL--LIAHKE-ELGQLITLEQGKPLKEAIGEVAY--------GASFIEYYAEEAK 166
           L R  DL  L+A  E EL Q +  +  KP  EA     Y            +  + +  K
Sbjct: 32  LARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQIKLTCKHLRRWMQPEK 91

Query: 167 RVYGDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSEL 226
           +    +  P  + R+     +P+GVV  I PWN+P  ++   +  A+A+G   V+KPSEL
Sbjct: 92  QSISLMQQPGQAYRQA----EPLGVVLIIGPWNYPFQLLITPLIGAIAAGNCAVLKPSEL 147

Query: 227 TPLTALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAA 286
            P T+     L +     P  + V+ G+A  +  AL+T P    I FTG TA+G+K+MAA
Sbjct: 148 APATSSLIQRL-ISDRFDPDYIRVLEGDA-SVSQALITQP-FDHIFFTGGTAIGRKVMAA 204

Query: 287 AAPTVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDK 346
           AA  +  V+LELGG +P IV  D DLDVA +     KF N+GQTC+  + +LVQ  + + 
Sbjct: 205 AAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLLVQRTVAEP 264

Query: 347 FAEAFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLG 406
           F EA  + +Q+   G+  +       +++D   Q++ + + D        I  G +    
Sbjct: 265 FIEALIDNIQQF-YGEDPQQSADYARIVSDRHWQRLNSLLVDGT------IRHGGQVDRS 317

Query: 407 MTFYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSVQ 466
             +  PT+I DV+    + +EEIFGP+ P++ +   ++AI         LA Y+F+   Q
Sbjct: 318 DRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDRQ 377

Query: 467 RSWRVFEALEYGLVGVNEGLISTEV--APFGGVKQSGLGREGSKYGMDEYLEIKYV 520
              RV      G V +N+ ++   V  A FGGV  SG+G    K   + +   K V
Sbjct: 378 VQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLV 433


Lambda     K      H
   0.317    0.134    0.383 

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: 532
Number of extensions: 26
Number of successful extensions: 4
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: 528
Length of database: 459
Length adjustment: 34
Effective length of query: 494
Effective length of database: 425
Effective search space:   209950
Effective search space used:   209950
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: 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 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