GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E2

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 481

 Score =  278 bits (712), Expect = 2e-79
 Identities = 168/475 (35%), Positives = 252/475 (53%), Gaps = 6/475 (1%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPAT-KEVLCQVPISTKEDIDYAAQTAAEAFKT 59
           +A+ ++  NYING+WV      Y   +NP+   +V+ +   +    ++ A + A  AF  
Sbjct: 1   VADSKRFDNYINGQWVAGA--DYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPA 58

Query: 60  WSKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAP 119
           WS   +  R   L      +   +EEL  L+  E GK   EA+GEV R     +F AG  
Sbjct: 59  WSTSGIQARHDALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGEC 118

Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179
             + GD + S+   V     R  +GVVG I P+NFP+ +P W    A+A GN  ++KP+E
Sbjct: 119 LRLSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAE 178

Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYK 238
             P     L E+  +AG P G FN+V G+  VV  IL   P++  ISF GS  VG  +  
Sbjct: 179 LVPGCAWALAEIISRAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQIAV 238

Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298
                  +VQ   G KN  I+L+DA+L+  V   V +AF S G+RC A + + V  GI D
Sbjct: 239 NCVSRQAKVQLEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTAGIHD 298

Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS 358
           +F+A + E++  IK+G+ L  G  +GPV+ E    + L YI+ G  EGARLV  G     
Sbjct: 299 KFVAAMAERMQSIKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGGLVTC 358

Query: 359 D-DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417
           D +GYF+ PT+F +    M I ++EIF PV +V+RV + + A+ +AN +EF   A + T+
Sbjct: 359 DTEGYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATT 418

Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472
           +     +F+ +  AGM+ +NL         PF G K S +G+    G+ + +FYT
Sbjct: 419 SLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYT 472


Lambda     K      H
   0.318    0.136    0.396 

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: 556
Number of extensions: 33
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: 487
Length of database: 481
Length adjustment: 34
Effective length of query: 453
Effective length of database: 447
Effective search space:   202491
Effective search space used:   202491
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 (21.7 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 preprint 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