GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Desulfovibrio vulgaris Miyazaki F

Align Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (uncharacterized)
to candidate 8501044 DvMF_1780 Aldehyde Dehydrogenase (RefSeq)

Query= curated2:O32507
         (477 letters)



>FitnessBrowser__Miya:8501044
          Length = 560

 Score =  148 bits (373), Expect = 5e-40
 Identities = 138/461 (29%), Positives = 192/461 (41%), Gaps = 24/461 (5%)

Query: 21  YTGETVKTFPFLESAEIPALIERADQAYRE----WGQRPVTERAAIMRRAAELMLERTDE 76
           +T   +   P L+ A     ++ AD A+ +    W    V ER   +   A  M  R  E
Sbjct: 80  FTPRLLGRCPILDEAAALRAVDAADHAWADGMGAWPTMGVAERIRHVEDFARRMAARRTE 139

Query: 77  LASLITLEMGKLLREAKGE-------VALAASILNYYGEQGPSFLEPKTIPVPQGEAAVL 129
           +  ++  E+ K  ++A GE       +      L         F+  K I      A + 
Sbjct: 140 VVRIMMWEICKSWQDASGEFDRTMEYLRDTIDALKDLDRASSRFVIEKGI-----YAQIR 194

Query: 130 HAPLGVLLGIEPWNYPLYQVVRFAAPNLVVGNTVLLKHSELCPQSALALEQLFHDAGVPQ 189
            APLG +L + P+NYPL +      P L++GN V++K   L       L + F DA  P 
Sbjct: 195 RAPLGPVLCMGPYNYPLNETFCTLMPALIMGNPVIVKTPRLGRLLYSPLMEAFRDA-FPA 253

Query: 190 GAYTNLFLRIADIEQVIAHPAVQGVSLTGSERAGASVAELAGR--HLKKCVLELGGSDPF 247
           G    L      ++ ++A   +  ++  GS  A A    LA    H  +CVL L   +  
Sbjct: 254 GVVNILHGDRRIVKPIMASGRINVLAFIGSSTA-ADALRLAHPYPHRLRCVLGLDAKNAG 312

Query: 248 IVLDAEDLDTTVKAAATGRLSNTGQACIAAKRLMVVDDLYDEFVSRLGQTFSAFVPGDPA 307
           IVLD  D+D TV  A  G  S  GQ C A K L V     DEF++R+ +       G P 
Sbjct: 313 IVLDCADMDLTVAEALQGSFSFNGQRCTALKMLFVHQKRLDEFLARMDEGIRKLRIGMPW 372

Query: 308 DPSTRLGPLSSEQAARDLQAQVQDAIDKGATVVAGGQRPEHPGAFVQPTVLTDVTPDMRA 367
           D   R+ PL     +  L   VQDA  +G  V   G    H      PTV+   TP MR 
Sbjct: 373 DEGVRITPLPVPGKSAYLDDLVQDAAAQGGKVANSG-GGTHAETLYHPTVVCPATPQMRV 431

Query: 368 YHEELFGPVAVVYRVRDEDEAVALANASTYGLGGAVFSSDLDRAQRVAERL--DTGMVWI 425
           YHEE FGPV  V    D +  V     S YG   ++F +D D   R+ + +      V I
Sbjct: 432 YHEEQFGPVIPVIPFTDIETPVRYVVGSQYGQQLSIFGNDPDDVARLIDPMVNQVCRVNI 491

Query: 426 NHPTSSAAD-LPFGGVKRSGFGRELSSMGMLEFTNQKLVRA 465
           N       D  PF G K S  G    S  +  F+ + LV A
Sbjct: 492 NSQCQRGPDTFPFTGRKDSAEGTLSVSDALRCFSIRTLVAA 532


Lambda     K      H
   0.317    0.133    0.384 

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: 623
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: 477
Length of database: 560
Length adjustment: 35
Effective length of query: 442
Effective length of database: 525
Effective search space:   232050
Effective search space used:   232050
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.

Links

Downloads

Related tools

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