GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Pf1N1B4_1109 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 481

 Score =  275 bits (704), Expect = 2e-78
 Identities = 169/477 (35%), Positives = 253/477 (53%), Gaps = 10/477 (2%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKED---IDYAAQTAAEAF 57
           +A+ ++  NYINGEWV      Y   +NP+  E+   +    K D   +  A   A  AF
Sbjct: 1   VADAKRYDNYINGEWVSGA--DYSANINPS--ELTDTIGDYAKADLAQVHAAIDAARAAF 56

Query: 58  KTWSKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAG 117
             WS   +  R   L      +   +EEL  L+  E GK   EA+GEV R     +F AG
Sbjct: 57  PAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAG 116

Query: 118 APSLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKP 177
               + GD L S+   V     R  +GVVG I P+NFP+ +P W    A+A GN  +LKP
Sbjct: 117 ECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKP 176

Query: 178 SERTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVV-NGILEHPEIKAISFVGSKPVGEYV 236
           ++  P     L E+  +AG P GVFN+V G+  VV + +++ P++  ISF GS  VG  +
Sbjct: 177 ADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQI 236

Query: 237 YKKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGI 296
                    +VQ   G KN  I+L+DA+L+  V   V +AF S G+RC A +   V  GI
Sbjct: 237 AVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGI 296

Query: 297 ADEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN 356
            D+F+  + E++  IK+G+ L  G  +GPV+ +   ++ L YI+ G  EGARLV  G   
Sbjct: 297 HDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLV 356

Query: 357 VSD-DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415
             D +GYF+ PT+F + T  M I ++EIF PV +++RV + + A+ +AN +EF   A + 
Sbjct: 357 ACDTEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIA 416

Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472
           T++     +F+ +  AGM+ +NL         PF G K S +G+    G+ + +FYT
Sbjct: 417 TTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-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: 566
Number of extensions: 32
Number of successful extensions: 4
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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