GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= BRENDA::Q97UA1
         (478 letters)



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

 Score =  354 bits (909), Expect = e-102
 Identities = 193/471 (40%), Positives = 276/471 (58%), Gaps = 7/471 (1%)

Query: 10  KWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILL 69
           +W+ G+ +   +INP+D   V+ +        V  AI  A A F  WS +    R   L 
Sbjct: 14  QWVAGA-DYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWSTSGIQARHDALD 72

Query: 70  KAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPN 129
           K G  +    +E   L+  EEGKTL +++ EVTR+ N+ KF+     ++SG  +PS  P 
Sbjct: 73  KVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSVRPG 132

Query: 130 TRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLS 189
             +   +E LGVV LITPWNFP++IP WK+APALA GN  VIKPA   P     L E++S
Sbjct: 133 VNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAEIIS 192

Query: 190 KAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLE 249
           +AG P G  NLV+G G  VGD +V+   +  +SFTGS  VG++I   V   +R  ++QLE
Sbjct: 193 RAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQI--AVNCVSRQAKVQLE 250

Query: 250 LGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKK 309
           +GGKN   +   ADL  A ELAV+  F  TGQ CTA+SRLI+   ++ +F   + ER++ 
Sbjct: 251 MGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTAGIHDKFVAAMAERMQS 310

Query: 310 WRVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEPTIF 366
            +VG   +   D+GPVV E Q  +DL+YI+ G++ GA+L+ GG ++    +GYFL PT+F
Sbjct: 311 IKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGGLVTCDTEGYFLAPTLF 370

Query: 367 EGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRV 426
               + MR+ +EEIFGPV +V    D + A+ + N  ++G +AGI  + +K  N F    
Sbjct: 371 ADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRHS 430

Query: 427 EAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477
           +AG++ VN PT G++   PFGG K S   + +E G  A EFY   KT Y G
Sbjct: 431 QAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYTVVKTSYIG 480


Lambda     K      H
   0.316    0.135    0.389 

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: 576
Number of extensions: 19
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: 478
Length of database: 481
Length adjustment: 34
Effective length of query: 444
Effective length of database: 447
Effective search space:   198468
Effective search space used:   198468
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: 51 (24.3 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