GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Klebsiella michiganensis M5al

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__Koxy:BWI76_RS13425
          Length = 475

 Score =  345 bits (886), Expect = 2e-99
 Identities = 196/472 (41%), Positives = 283/472 (59%), Gaps = 7/472 (1%)

Query: 23  LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82
           L IN + V  + +      +P+T EEI  + EA +  ++ AVEAA  AF  SWS + P+ 
Sbjct: 5   LLINGKLVAGEGEAV-PVFNPATGEEIVSIAEATAAQVEAAVEAADQAF-ISWSQTTPRS 62

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGD-VALTAAYFRSCAGWTDKIKGSV 141
           R + L  LA++IDEHA TLA +E+L+ GK L C   D +   A  FR  AG    + G  
Sbjct: 63  RAECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPGMA 122

Query: 142 I-ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200
             E  + H +  RR+P+GV   I PWN+PL+MA+WKL P L  G   V+K +E TPL+AL
Sbjct: 123 AGEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLTAL 182

Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260
            L  L KE   P GV+NV+ G G T G P+++H K++ V+ TGS ATG HI+   A S++
Sbjct: 183 KLGELAKEI-FPAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTA-SSI 240

Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320
           K+  +ELGGK+P IVFDDAD+ + ++ + T  FYN G+ C A  RIY Q GIYD++V + 
Sbjct: 241 KRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVEKL 300

Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKK-EGATVITGGERFGNKGYFI 379
             A  SLK+G P  E T +G  +SQ  LD++   +D  +      VI GG +    GY+ 
Sbjct: 301 GAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAPGNGYYY 360

Query: 380 KPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAIS 439
           +PT+    +++  IV+ E+FGPVV+IT F   E+ ++ ANDS+YGLA+ V T ++  A  
Sbjct: 361 QPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHR 420

Query: 440 VSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491
           +S ++  G  WVNT+      +P GG   SG G++M    L++YT ++ V I
Sbjct: 421 LSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMI 472


Lambda     K      H
   0.316    0.133    0.389 

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: 572
Number of extensions: 26
Number of successful extensions: 6
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: 495
Length of database: 475
Length adjustment: 34
Effective length of query: 461
Effective length of database: 441
Effective search space:   203301
Effective search space used:   203301
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 (21.6 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