GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Shewanella sp. ANA-3

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>FitnessBrowser__ANA3:7025959
          Length = 496

 Score =  218 bits (556), Expect = 3e-61
 Identities = 152/469 (32%), Positives = 236/469 (50%), Gaps = 39/469 (8%)

Query: 23  YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82
           Y+NGE+T A S  + E   P  G   G+++     +   A+  A++ F++  WS++ P  
Sbjct: 7   YVNGEHT-AASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDT--WSQVTPLN 63

Query: 83  RKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAID--KIYD 140
           R   + +F  L++QH +ELA L TL+ GK + D+               GE I   ++ +
Sbjct: 64  RARVLFKFKALVEQHMDELAQLITLEHGKVLDDA--------------RGELIRGLEVVE 109

Query: 141 EVAATPH-------DQLG-----LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSV 188
                PH       +Q+G         + +GVV  I P+NFP+M+  W    A++ GN+ 
Sbjct: 110 FACGIPHLLKGEHTEQVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTF 169

Query: 189 ILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKI 248
           I+KPSEK P   +RIAEL  +AG+P GV NV+ G    V   L+ H D+  + F GST I
Sbjct: 170 IMKPSEKDPSAVMRIAELLTQAGLPAGVFNVVNGDKEAVDTLLS-HEDIQAVSFVGSTPI 228

Query: 249 AKQLLIYSGES-NMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSR 307
           A+   IYS  S + KRV    G K+  ++  DA +L  A  A  GA   + GE C A S 
Sbjct: 229 AE--YIYSTASKHGKRVQALGGAKNHMLLMPDA-DLDQAVSALMGAAYGSAGERCMAISV 285

Query: 308 LLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARL 367
           +L    + DK +  ++  ++  K GN L P   +G L+  Q +  V  ++++G  +GA L
Sbjct: 286 VLAVGDVGDKLVDKLLPQIQQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATL 345

Query: 368 VAGGKR--TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDT 425
           V  G++        G ++   +FD V+  M+I +EEIFGPVLS++       A+A+ N  
Sbjct: 346 VVDGRQLTVADHQQGYFLGACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQH 405

Query: 426 PYGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMT-APFGGFKQS 473
            +G   A++T     A      ++ G V VN      M    FGG+K+S
Sbjct: 406 EFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRS 454


Lambda     K      H
   0.316    0.132    0.390 

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: 546
Number of extensions: 30
Number of successful extensions: 5
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: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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