GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella oneidensis MR-1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 199807 SO0619 succinylglutamic semialdehyde dehydrogenase (NCBI ptt file)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__MR1:199807
          Length = 487

 Score =  582 bits (1500), Expect = e-170
 Identities = 283/487 (58%), Positives = 369/487 (75%)

Query: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60
           MT +I G W TG+G      NP +GE++W+G  A A QV  A  AAR A   W  L F  
Sbjct: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120
           R  +VE + + LE+NKAEL   IA+ETGKP+WE ATEV AMI KI +S  AY+ RTG + 
Sbjct: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120

Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180
           ++ P G A LRH+PHGV+AVFGPYNFPGHLPNGHIVPALLAGN+++FKPSELTP   E +
Sbjct: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180

Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240
           + LW+++GLP GVLNLVQG  +TG+AL++   LDGL FTGS+ TG+ LH+Q +G P KIL
Sbjct: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300
           ALEMGGNNPLII  VADI AAVH  +QSA++++GQRCTCARRL ++ G QGDA +A+LV 
Sbjct: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300

Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
             +++  G W+ +PQPF+G +ISE AA+ +V A   L ++GG PL+    LQAGT L++P
Sbjct: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           G+I++T V+ +PDEE FGPLL++ RY  FD+AI++AN TR+GLS G+++  RE ++  L 
Sbjct: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480
             RAGIVNWNK +TGA+  APFGG+GASGNHR SA+YAADYCA+P+AS+E+D+++LPATL
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480

Query: 481 NPGLDFS 487
           +PGL  S
Sbjct: 481 SPGLTLS 487


Lambda     K      H
   0.318    0.134    0.412 

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: 744
Number of extensions: 25
Number of successful extensions: 1
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: 492
Length of database: 487
Length adjustment: 34
Effective length of query: 458
Effective length of database: 453
Effective search space:   207474
Effective search space used:   207474
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