GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N2C3

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO356_07955 AO356_07955 omega amino acid--pyruvate aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07955
          Length = 449

 Score =  268 bits (686), Expect = 2e-76
 Identities = 163/445 (36%), Positives = 243/445 (54%), Gaps = 23/445 (5%)

Query: 16  LSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELV 75
           L  D H  P+T  +   ++  R+I  AEG ++ D +G K+ D+++GLW    G+ R+E+ 
Sbjct: 15  LKLDAHWMPYTANRNF-QRDPRLIVAAEGSWLVDDKGRKVYDSLSGLWTCGAGHTRKEIQ 73

Query: 76  QAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVR 135
           +A  +Q+  L  Y+  FQ  HP   +LA+ I  + P  +NHVFFT SGSE  DT ++MVR
Sbjct: 74  EAVAKQLGTLD-YSPGFQYGHPLSFQLAEKITSLTPGNLNHVFFTDSGSECADTAVKMVR 132

Query: 136 HYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGM---KALHEQGDFPIPGIVH-IAQPYW 191
            YW  KGQ  K  +IGR  GYHG  +AG SLGG+   + L  Q    +  + H +     
Sbjct: 133 AYWRLKGQATKTKMIGRARGYHGVNIAGTSLGGVSGNRKLFGQAMMDVDHLPHTLLASNA 192

Query: 192 YGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREI 251
           Y  G    P E G+  A++L K I      N+AA   EP+ G+ GV+VPP+ Y  ++REI
Sbjct: 193 YSRG---MPKEGGIALADELLKLIELHDASNIAAVFVEPMAGSAGVLVPPEGYLKRLREI 249

Query: 252 LAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVE 311
             ++ IL + DEVI GFGRTG  FG+  +G  PDLM IAK +T+G IPMG V+   EI +
Sbjct: 250 CDQHSILLVFDEVITGFGRTGSMFGADSFGVTPDLMCIAKQVTNGAIPMGAVIASSEIYQ 309

Query: 312 V-LNQ-----GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQE 365
             +NQ       EF HG+TYS HPVA A  L  + +L++E +++ V AE AP+ +     
Sbjct: 310 TFMNQPTPEYAVEFPHGYTYSAHPVACAAGLAALDLLQKENLVQSV-AEIAPHFENALHG 368

Query: 366 LADHPLVGEARGVGMVAALELV-KNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMI 424
           L     V + R  G+  A+++  ++     R  + G+ +      ++ G  +R  GDT+ 
Sbjct: 369 LKGAKNVIDIRNYGLAGAIQIAGRDGDAIVRPFEAGMAL------WKAGFYVRFGGDTLQ 422

Query: 425 ISPPLVIDPSQIDELITLARKCLDQ 449
             P     P  +D L     + L++
Sbjct: 423 FGPTFNSKPQDLDRLFDAVGEVLNK 447


Lambda     K      H
   0.320    0.138    0.425 

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: 537
Number of extensions: 29
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: 456
Length of database: 449
Length adjustment: 33
Effective length of query: 423
Effective length of database: 416
Effective search space:   175968
Effective search space used:   175968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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