GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_0489
          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:

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