Alignments for a candidate for fruI in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Marivita geojedonensis DPG-138

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_085636031.1 MGEO_RS07095 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1146
         (953 letters)



>NCBI__GCF_002115805.1:WP_085636031.1
          Length = 746

 Score =  264 bits (675), Expect = 1e-74
 Identities = 197/633 (31%), Positives = 307/633 (48%), Gaps = 30/633 (4%)

Query: 333 KLLSLGARRGQVLEFIAEPTIAADALPALLAAIEEGLGEEVEPLPAV-SQHREVIADVAE 391
           KL  L  +  +  EF A+   A + +  +LA + E LG  V    A+ ++H + +     
Sbjct: 128 KLGVLVVQSKEAREFSADEIYALEVVAMVLAEMTE-LGAFVGEGAALRARHTQPV----- 181

Query: 392 VLLAPASGSLIQAIAAAPGIAIGPAHIQVQQVIDYPLRGESAAIERERLKQALADVRRDI 451
                    LI+ + A  G A G   +   +V+   L  +  A ER RL +A+ ++R  +
Sbjct: 182 ---------LIRGVTAQEGTAEGHVWLHEPRVVVTNLVADDPAKERARLTEAVENLRISV 232

Query: 452 EGLIERSKAKAIR-EIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQES 510
           + L+  +   + + ++   ++   +       ++  + +G SAEAA          +   
Sbjct: 233 DQLLAVASGDSEQVQVLEAYRMFANSKGWMRRMEENIDRGLSAEAAVEKEQSDVRARMLQ 292

Query: 511 LQDALLAERAADLRDIGRRVLAQLSGVETP---AEPEQPYILVMDEVGPSDVARLDPTRV 567
             DA L ER  DL D+  R+L  L+G       A PE P ILV   +GP ++      ++
Sbjct: 293 ATDAYLRERLHDLDDLSNRLLRILTGQGNKTGAALPEDP-ILVARNIGPGELLEYG-RQL 350

Query: 568 AGILTARGGATAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATL 627
            GI+   G   +H+AIVARAL IP ++ A    +    G  +++DG +G +H+  D   +
Sbjct: 351 RGIILEEGSVGSHAAIVARALAIPLVINAKRIQIEALNGDHVMVDGDQGVVHLRPDDTVV 410

Query: 628 QRATEERDTRELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLR 687
               ++   +    +  A  R +PA+T  G  + +  N G  A + S    GAEG+GL R
Sbjct: 411 NAFRDKMAMQAKAQERYASIRDKPAVTLCGKTIRLDMNAGLMADLPSLESSGAEGVGLFR 470

Query: 688 TELIFMAHSQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLG 747
           TEL F+  SQ P        Y RVLD   G+ +V RTLD+G DK LPY    +E NP LG
Sbjct: 471 TELQFLVRSQMPKRTELAALYARVLDAAQGKRVVFRTLDIGSDKVLPYMAAEEEPNPALG 530

Query: 748 VRGIRLTLQRPQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTE-------RL 800
            R IR+ L +P VM  QL+ALLRAA+ RPL IMFP +   DE+R AR   +       +L
Sbjct: 531 WRAIRVGLDKPGVMRMQLQALLRAANGRPLSIMFPFIAQYDEYRLARAEVDKAVAREKKL 590

Query: 801 RLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQAD 860
              +P   L++G M+E PS A  +    +EV+F S+G NDL Q+  A DR +  +  + D
Sbjct: 591 GHTLP-EKLEIGAMLETPSLAFASKRFYEEVEFLSIGGNDLKQFFFAADRENERVRRRYD 649

Query: 861 GLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKA 920
            L+ + L  I+  V    A    +  CGE A  P+    L  +G+  LS+   S+  VK 
Sbjct: 650 TLNVSFLTFIEDIVARCAATNTRLSFCGEDAGRPVEALCLAAIGLHSLSMRPASVGPVKH 709

Query: 921 RIRELSLTQTQTLAQQALAVGSANEVRALVEAL 953
            +R  +L   + +   A   G  +   A++E L
Sbjct: 710 LLRRCNLDDVRKVIHDARDAGEQSVRPAVMEYL 742


Lambda     K      H
   0.318    0.135    0.381 

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: 1231
Number of extensions: 54
Number of successful extensions: 2
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: 953
Length of database: 746
Length adjustment: 42
Effective length of query: 911
Effective length of database: 704
Effective search space:   641344
Effective search space used:   641344
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources