GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E2

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf6N2E2_1143 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1143
          Length = 557

 Score =  252 bits (644), Expect = 2e-71
 Identities = 182/516 (35%), Positives = 260/516 (50%), Gaps = 29/516 (5%)

Query: 56  KTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLA 115
           + AL W     G +A  +Y +L   + R  + LR  G+ KGD V  +         V LA
Sbjct: 46  RIALFWEG-RDGSDATWTYRDLQDNAARFANFLRAQGVGKGDKVAGLLPRTAELLIVVLA 104

Query: 116 VIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKF------ 169
             + G V  P  T      +++R        +++D++    + E  G   +         
Sbjct: 105 TWRIGAVYQPLFTAFGPKAIEHRVGSSGARIVVTDAVNRPKLNEIAGCPTIVTVGGEKGQ 164

Query: 170 -LIDGKRETWNSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSIT- 227
            ++ G    W  + + SS  EP    GED  +  FTSGTTG  K     A+S P+ +I  
Sbjct: 165 GIVRGDYSFWAEVANHSSQCEPLMLTGEDPFLLMFTSGTTGPAK-----ALSVPLKAIVA 219

Query: 228 ----TASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGE 283
               T   V +R  D   N++  GWA   +     PL +G  +    Y+G          
Sbjct: 220 FQSYTRDAVDLRPEDAFWNVADPGWAYGIYFGVTGPLAMGHPITF--YDGPFTLESTCRV 277

Query: 284 VENLGVTSFCAPPTAWRQFITLDLDQFRFE---RLRSVVSAGEPLNPEVIKIWKDKFNLT 340
           +   G+T+    PTA+R  I    +QF      +LR V SAGEPLNPEVI+ + D  N+ 
Sbjct: 278 INKYGITNLTGSPTAYRLLIAGG-EQFARSIKGKLRIVSSAGEPLNPEVIRWFADNLNVV 336

Query: 341 IRDFYGQTETTAMVGNFPFLK--VKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVK 398
           I D YGQTE   ++ N   L+  V  G+ G   P + I +LD+  +E+    + G + V 
Sbjct: 337 IHDHYGQTELGMVLCNHHGLEHPVHLGAAGFASPGHRIVVLDENQRELGVG-QPGILAVD 395

Query: 399 LNPRPIGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGP 458
            +  P+  F GY  E    ++F   YY +GD    + +G   FVGR DDVI TS YRVGP
Sbjct: 396 RSQSPMCWFAGY--EGAPTKAFVGDYYLSGDTVELNLDGSISFVGRSDDVITTSGYRVGP 453

Query: 459 FEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSP 518
           F+VESAL+EHPAV EAAV+G PD  R +LVKA++VL   Y  S ELAEE+R  ++  L+ 
Sbjct: 454 FDVESALIEHPAVVEAAVIGKPDPERTELVKAFVVLSTQYRASPELAEELRLHVRKRLAA 513

Query: 519 YKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKK 554
           +  PR IEFV +LPKT SGK++R  LR +E  K ++
Sbjct: 514 HAYPREIEFVSDLPKTPSGKLQRFILRNQEIAKAQE 549


Lambda     K      H
   0.318    0.137    0.402 

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: 679
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: 564
Length of database: 557
Length adjustment: 36
Effective length of query: 528
Effective length of database: 521
Effective search space:   275088
Effective search space used:   275088
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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