GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella loihica PV-4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  515 bits (1327), Expect = e-150
 Identities = 257/478 (53%), Positives = 345/478 (72%), Gaps = 3/478 (0%)

Query: 46  LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105
           L++  S++ GRW      F V +PAS   +  V D  + + + A+ AA  A   W + S 
Sbjct: 9   LIKLSSYIDGRWTVGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSA 68

Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165
            ER++L+RKW++LM++++++L +++T E GKPL EA+GEI Y A F++WF+EE +RVYGD
Sbjct: 69  NERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGD 128

Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225
            I   A DKR LV+KQPVGV + ITPWNFP+AMI RK  AALAAGCT V +P+  TP SA
Sbjct: 129 TIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSA 188

Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285
           LA+A+LA +AGIP GV+N++      A  +G+VL   P V+K +FTGSTA GKILL   A
Sbjct: 189 LAMAELAERAGIPAGVFNIV--VGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCA 246

Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345
            SVK+VSMELGG APFIVFD A++D AV GA+ SK+RNAGQTCVC+NR  VQ+G+  +F 
Sbjct: 247 TSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFT 306

Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGG 405
            KF  A+  +L++G+G  +G T GP+I++ AV+ V K V+D VA GA +VTGG+  + G 
Sbjct: 307 EKFTAAV-ANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGE 365

Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465
           +F  P ++++VT +M     E FGPV P+I FD E EA+A+AN  + GLA YFY++D  +
Sbjct: 366 SFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGR 425

Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           I+RVAE LE GMVGVNEG+IS+   PFGGVKQSG GREGSKYG+D+YLE+KY+C GGL
Sbjct: 426 IFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCLGGL 483


Lambda     K      H
   0.318    0.135    0.400 

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: 627
Number of extensions: 26
Number of successful extensions: 3
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: 523
Length of database: 485
Length adjustment: 34
Effective length of query: 489
Effective length of database: 451
Effective search space:   220539
Effective search space used:   220539
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