GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Sinorhizobium meliloti 1021

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate SMc02437 SMc02437 phosphoenolpyruvate phosphotransferase PTSP (enzyme I-Ntr) protein

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



>FitnessBrowser__Smeli:SMc02437
          Length = 755

 Score =  282 bits (722), Expect = 5e-80
 Identities = 191/553 (34%), Positives = 294/553 (53%), Gaps = 20/553 (3%)

Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLI---DES 464
           + G +   GI +G V++ +P+++      E    ELQRL  AL  +   I  ++   D S
Sbjct: 183 IEGNSYGEGIGLGYVVLHEPRIVVTNLLNEDTEHELQRLAEALGSLRISIDDMLSRRDVS 242

Query: 465 QVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEA-LHDKLLA 523
                R +  T++    D     +++  ++ GL+AEAA +E ++S  + +   L D  L 
Sbjct: 243 MEGEHRAVLETYRMFAHDRGWVRKLEEAIRNGLTAEAA-VERVQSETKARMIRLTDPYLR 301

Query: 524 ERAADLRDVGRRVLACLTGVEAE-QAPDEPY--ILVMDEVAPSDVATLNAQRVAGILTAG 580
           ER  D  D+  R+L  L+G  A+  A D P   I+V   +  +++     + V G++   
Sbjct: 302 ERMHDFDDLANRLLRQLSGYGAKLSAADFPNDAIVVARAMGAAELLDYPRENVRGLVLEE 361

Query: 581 GGATSHSAIIARALGIPAIVGAGPGVLGLARNT-LLLLDGERGELLVAPSGAQLEQARSE 639
           G  TSH  I+ARA+GIP +VG   G + LA N   +++DG+  ++ + P  A L++A  E
Sbjct: 362 GAVTSHVVIVARAMGIP-VVGQAAGAVALAENRDAIIVDGDDAKVHLRPM-ADLQRAYEE 419

Query: 640 RAAREERKHLANERRMDAA-VTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVF 698
           +     R+        D   +T+DG  + +  N G   + P     GAEGIGL RTEL F
Sbjct: 420 KVRFRARRQAQFRALRDVEPLTKDGKRITLQMNAGLLVDLPHLNEAGAEGIGLFRTELQF 479

Query: 699 MNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIR 758
           M  S  P    QEA YR V++   G+P+  RTLD+GGDK +PY+    EENP LG R IR
Sbjct: 480 MIASTMPKAEEQEAFYRNVMKQTAGKPVTFRTLDIGGDKVVPYFRAAEEENPALGWRAIR 539

Query: 759 LSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMV-------DRLRVELP 811
           LSL RP +L TQ RA+L +  G  L++M PMV  + E ++A+ ++        +L  +LP
Sbjct: 540 LSLDRPGLLRTQFRAMLRATAGAELKMMLPMVTEVAELKSARELLQKEIERQSKLGEQLP 599

Query: 812 VADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPA 871
              LQ G M+E+P+       L  EVDF S+G+NDL Q+ +A+DRG+  +S + D L   
Sbjct: 600 -RKLQFGAMLEVPALLWQLDELMAEVDFVSVGSNDLFQFAMAVDRGNARVSERFDILGRP 658

Query: 872 VLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVREL 931
            LR++   V A   +   V +CGE+A+  L+   L+GLG   +S+S  ++  VKA +  L
Sbjct: 659 FLRILREIVRAGERNNTPVTLCGEMASKPLSAMALLGLGFRSVSMSPTAVGPVKAMLLAL 718

Query: 932 DFAACQRLAQQAL 944
           D      L + AL
Sbjct: 719 DAGRLNELLEAAL 731


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: 1340
Number of extensions: 73
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: 960
Length of database: 755
Length adjustment: 42
Effective length of query: 918
Effective length of database: 713
Effective search space:   654534
Effective search space used:   654534
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: 56 (26.2 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