GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-13349
         (490 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  350 bits (899), Expect = e-101
 Identities = 191/491 (38%), Positives = 283/491 (57%), Gaps = 17/491 (3%)

Query: 3   QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60
           +Y N+I G+WV       FD+ +PVDG V  QV  +D   ++ A+ A HAA + AWG+T+
Sbjct: 18  RYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAA-KDAWGKTS 76

Query: 61  VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120
           V ER+ +L +IAD +++  +    AE  + GK V      D+P    +FR FA  ++   
Sbjct: 77  VTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQE 136

Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180
                 D       ++Y   +PLGVVG I PWN PLL+  WKIAPALA GN +V KP+E+
Sbjct: 137 GSAADID----NNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 192

Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240
           TP +  ++ E++  + +P GV N+V+GFG + AG+ +  +  I  + FTG ++ G  I++
Sbjct: 193 TPVSILVMVELIQDL-LPAGVLNIVNGFGTE-AGQALAVSKRIAKLAFTGSTQIGHHILK 250

Query: 241 AAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYV 294
            AA  + P + ELGGK+  I FAD         +K ++GM+ A F + G+VC C  RV +
Sbjct: 251 CAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVLI 309

Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354
              IY++F+D  + R K +K G P D  T +G   S E  DK+LSY ++ R EGA+VL+G
Sbjct: 310 AESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIG 369

Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414
           G   +    + +GF++EPTI+ G     R  +EE+FGP+  V+ F  EAEA+A+ANDT+Y
Sbjct: 370 GTSCQLSGDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEY 428

Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474
           GL A  WT ++NR  R+   ++ G  W+N +        FGG   SGIGRE     L+ Y
Sbjct: 429 GLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHY 488

Query: 475 SELTNVCVRID 485
               N+ V  D
Sbjct: 489 QNTKNLLVSYD 499


Lambda     K      H
   0.321    0.137    0.420 

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: 626
Number of extensions: 24
Number of successful extensions: 8
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: 490
Length of database: 506
Length adjustment: 34
Effective length of query: 456
Effective length of database: 472
Effective search space:   215232
Effective search space used:   215232
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 (21.8 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