GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Desulfoscipio geothermicus DSM 3669

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_092483768.1 BM299_RS10535 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::psRCH2:GFF3291
         (960 letters)



>NCBI__GCF_900115975.1:WP_092483768.1
          Length = 588

 Score =  422 bits (1084), Expect = e-122
 Identities = 235/563 (41%), Positives = 346/563 (61%), Gaps = 17/563 (3%)

Query: 408 VNGIAASPGIAIGPVLVRKP-QVIDYPKRG----ESPVIELQRLDAALDKVHADIGTLID 462
           + G   S GI  G VL+ +P +  + P R     E    EL+RL  A +K + ++  LI+
Sbjct: 6   IRGTGVSEGIRSGKVLLYQPLRNQNLPGRAVISEEEVNHELERLQLAREKAYRELHALIE 65

Query: 463 ESQVASIRD---IFTTHQAMLKDPALREEVQVRL-QKGLSAEAAWMEEIESAAQQQEALH 518
            +++   +D   I    QA L DPA   E++  + Q+  +AE A  E +E  A   E ++
Sbjct: 66  RARIELGKDKAAILMAQQAFLNDPAFYPEMEKEIRQQKYTAEKAVTEVVERFAGLFEGMN 125

Query: 519 DKLLAERAADLRDVGRRVLACLTGVEAEQAPD--EPYILVMDEVAPSDVATLNAQRVAGI 576
           D+ L ER+AD+RDVG R+++CL G +  Q  +  E  ILV D++APSD   LN + + G 
Sbjct: 126 DQYLRERSADVRDVGNRLVSCLQGKKGLQLAEIKEEVILVADDLAPSDTVQLNKKYILGF 185

Query: 577 LTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQA 636
           +T  GG TSH+AI++R+LGIPAIVG G  +  +     L++DG  G  +V P+   +++ 
Sbjct: 186 VTRVGGKTSHTAILSRSLGIPAIVGIGEAIKQIHDGDWLIIDGSTGACIVNPNPRLMKEY 245

Query: 637 RSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTEL 696
             +R   E+      E     A T DG  VE++ANIG+  E   A+  GAEGIGL RTE 
Sbjct: 246 EEKRKIEEQALRQLEEFTFKPAATTDGFRVEMSANIGSPAEAKPALEQGAEGIGLYRTEF 305

Query: 697 VFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRG 756
           +FMN +Q P++  Q   Y++V+  +E RP+++RTLD+GGDK LPY  +P E NPFLG R 
Sbjct: 306 LFMNEAQMPSEEKQFEAYKQVVATMENRPVIIRTLDIGGDKELPYLSLPKEMNPFLGYRA 365

Query: 757 IRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPV---- 812
           IRLSL + +++ TQLRA+L ++    ++IMFPM+ +++EWR AKA++  +R  L      
Sbjct: 366 IRLSLDQRELMVTQLRAILRASAYGKVKIMFPMIASLEEWRQAKAILAEVRDRLTKEGVD 425

Query: 813 --ADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHP 870
               ++VG+M+E+PS A++A   A+EVDFFSIGTNDL QYTLA+DR +  +    D LHP
Sbjct: 426 FDPSVEVGMMVEVPSTAILADQFAKEVDFFSIGTNDLVQYTLAVDRMNEKVGYLYDHLHP 485

Query: 871 AVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRE 930
           AV+ L+   +EA+H  GKW G+CG +A D LA PLL+GLG+DE S+ A SI  VK  + +
Sbjct: 486 AVIHLVKKVIEASHREGKWTGMCGGMAGDPLAAPLLIGLGLDEWSMVAGSIKKVKQVISQ 545

Query: 931 LDFAACQRLAQQALMLPGAHEVR 953
           ++   CQ+L  + L L    +VR
Sbjct: 546 VNHEECQKLLGEVLELSTTDDVR 568


Lambda     K      H
   0.317    0.134    0.384 

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: 1006
Number of extensions: 30
Number of successful extensions: 3
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: 960
Length of database: 588
Length adjustment: 40
Effective length of query: 920
Effective length of database: 548
Effective search space:   504160
Effective search space used:   504160
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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