GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas fluorescens GW456-L13

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_5044 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5044
          Length = 481

 Score =  274 bits (700), Expect = 6e-78
 Identities = 169/477 (35%), Positives = 250/477 (52%), Gaps = 10/477 (2%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKED---IDYAAQTAAEAF 57
           +A+ ++  NYINGEWV      Y   +NP+  E+   +    K D   +  A   A  AF
Sbjct: 1   VADTKRFDNYINGEWVAG--GDYSTNINPS--ELTDAIGDYAKADLAQVHAAIDAARAAF 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 SERTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEH-PEIKAISFVGSKPVGEYV 236
           ++  P     L E+  +AG P GVFN+V G+  VV   L H P++  ISF GS  VG  +
Sbjct: 177 ADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVHSPKVDGISFTGSVGVGRQI 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+ +   ++ + YI+ G  EGARLV  G   
Sbjct: 297 HDQFVEAMAERMKSIKVGHALKAGTDIGPVVSQAQLEQDMKYIDIGQSEGARLVSGGGLV 356

Query: 357 VSD-DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415
             D +GYF+ PT+F +    M I ++EIF PV +++RV + + A+ +AN +EF   A + 
Sbjct: 357 TCDTEGYFLAPTLFADSEASMRISQEEIFGPVANIVRVADYEAALAMANDTEFGLSAGIA 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: 553
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 (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