GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Klebsiella michiganensis M5al

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BWI76_RS21985 BWI76_RS21985 aldehyde dehydrogenase

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



>FitnessBrowser__Koxy:BWI76_RS21985
          Length = 506

 Score =  333 bits (854), Expect = 8e-96
 Identities = 186/487 (38%), Positives = 274/487 (56%), Gaps = 17/487 (3%)

Query: 4   YRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTV 61
           Y N+I+G++VE      F + +PVDG+ + Q   +D + +D A+ A H A   AWG+T+ 
Sbjct: 19  YGNFIDGKFVEPIGGEFFMNTSPVDGSNIGQFPRSDAKDIDFALDAAHRAA-DAWGKTSA 77

Query: 62  AERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPL 121
             RA +L ++AD I+   +    AE  D GKP+      D+P    +FR FA  L+    
Sbjct: 78  QHRANLLLQVADRIEANLEYLAVAESWDNGKPIRETLNADLPLAVDHFRYFAGCLRAQEG 137

Query: 122 DTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEET 181
            T + D       + Y   +PLGVVG I PWN PLL+  WK+APALA GN VV KP+E+T
Sbjct: 138 STAEID----ETTVAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEQT 193

Query: 182 PGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRA 241
           P + TLL E++  +  P GV N+V GFG + AGE + T+  I  I FTG +  G  IM  
Sbjct: 194 PLSITLLLEIIGDL-FPAGVLNVVQGFGKE-AGEALATSKRIAKIAFTGSTPVGRHIMAC 251

Query: 242 AATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYVE 295
           AA ++ P + ELGGK+  I FAD         EK ++G++   F + G+VC C  R  ++
Sbjct: 252 AAENIIPCTVELGGKSPNIYFADVMEGEEEYIEKAVEGLVLG-FFNQGEVCTCPSRALIQ 310

Query: 296 RPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGG 355
             IY  F+   +++V  ++ G P D  T +G   S +  DK+LSY K+AR+EG ++L GG
Sbjct: 311 ESIYEPFMARVMDKVAQIRRGDPFDTDTMIGAQASRQQFDKILSYIKIARDEGGKILTGG 370

Query: 356 GVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYG 415
                    D GF+++PT+I G     R  +EE+FGP+  V+ F  EAEA+++AN T++G
Sbjct: 371 ERASISAELDNGFYIQPTLIQGR-NDMRSFQEEIFGPVIGVTTFKDEAEALSIANQTQFG 429

Query: 416 LSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475
           L A  WT + N  +R+   ++ G  W N + +      FGG   SG+GRE    +LN Y 
Sbjct: 430 LGAGVWTRDTNLAYRMGRGIKAGRVWTNCYHIYPAHAAFGGYKQSGVGRETHKMALNAYQ 489

Query: 476 ELTNVCV 482
           +  N+ V
Sbjct: 490 QTKNLLV 496


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: 638
Number of extensions: 29
Number of successful extensions: 7
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