GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kauB 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)



>lcl|FitnessBrowser__ANA3:7025959 Shewana3_3107
           methylmalonate-semialdehyde dehydrogenase [acylating]
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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