Alignments for a candidate for fruI in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Moritella dasanensis ArB 0140

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate WP_017220595.1 A923_RS0105175 phosphoenolpyruvate--protein phosphotransferase

Query= SwissProt::P45597
         (838 letters)



>NCBI__GCF_000276805.1:WP_017220595.1
          Length = 815

 Score =  382 bits (982), Expect = e-110
 Identities = 249/679 (36%), Positives = 368/679 (54%), Gaps = 24/679 (3%)

Query: 135 DDPAVIVAALTGDRAPDTSAAPATDLAERFEWTIAYPSGLHARPATRWAETARGFSARAQ 194
           D+P  ++A +T   A D +A   +       W +  P G+HARP+     T     A  +
Sbjct: 136 DEPEPVIAVVTS--AVDKAALSTS-------WRVQNPHGIHARPSALIVATMAAIDATIE 186

Query: 195 VRAGDQAADAKSLVGLLQLGLRAGDSITVSAKGSDAPALLKRLRAVMDSLTAQEKADAER 254
           +   D+ A+AKSL  + +L ++ GD I + A G++A   +     + D    +  A+   
Sbjct: 187 LGRRDERANAKSLNSIAKLNVQCGDEICLYASGAEAELAIAEFIRLADGHFGESIANDIA 246

Query: 255 AAQRRAAPVIGWTPPQAQPAIVGIGASPGVAIGIVHRLRAAQTEVADQPI-GLGDGGVLL 313
           +    +      +  + + A+ G+    G+  G V    A    + ++    +    + L
Sbjct: 247 SVNAISNEYSVSSQEKVEGALTGLAVCGGIVTGPVIHFDAVMPAIPERSFESVEMENIRL 306

Query: 314 HDALTRTRQQLAAIQDDTQRRLGASDAAIFKAQAELLNDTDLITRTCQLMVEGHGVA-WS 372
             A+ +  +QL     DT+  LG   A IFKA   +L D +L+    +L VE   +A  +
Sbjct: 307 DSAIQKVTEQLVQQASDTELTLGKEHAEIFKAHMIMLADPELLADV-RLRVEQDMIAEQA 365

Query: 373 WHQAVEQIASGLAALGNPVLAGRAADLRDVGRRVLAQLDPAAAGAGLTDLPEQPCILLAG 432
           W +A   IA    AL +  +  R AD++D+ R+V+ QL   + G G  +L  QP +LLA 
Sbjct: 366 WLEATALIAEQYRALKSTYMQEREADVKDIARQVMLQLCGKSQG-GRIELA-QPSVLLAK 423

Query: 433 DLSPSDTANLDTDCVLGLATAQGGPTSHTAILSRTLGLPALVAAGGQLLDIEDGVTAIID 492
           DL PSDTA LD   VL +  + GG TSH+ IL+R +G+PA++     L  +E G    +D
Sbjct: 424 DLLPSDTAQLDPQKVLAICLSGGGKTSHSVILARAMGIPAIIRLENCLELVEPGQVVTVD 483

Query: 493 GSSGRLYINPS---ELDLDAARTHIAEQQAIREREAAQRALPAETTDGHHIDIGANVNLP 549
           G SG L++ P+   + +L+  R    +  +  +  AAQ   PA TTDG+  ++ AN+   
Sbjct: 484 GFSGLLWLTPTADKQQELEERRKTWLDHTS-NQLLAAQE--PAMTTDGYRFNVMANIGGL 540

Query: 550 EQVAMALTQGAEGVGLMRTEFLFLERGSTPTEDEQYQTYLAMARALDGRPLIVRALDIGG 609
           E V+ AL  GAEGVGL+RTEF+F      P+E +QY  Y  +A AL  RPL +R+LD+GG
Sbjct: 541 EDVSAALDAGAEGVGLLRTEFMFQSHAELPSEQDQYIVYRDIAAALGNRPLTIRSLDVGG 600

Query: 610 DKQVAHLELPHEENPFLGVRGARLLLRRPDLLEPQLRALYRAAKDGARLSIMFPMITSVP 669
           DK +    +  E+NPFLG+RG RL L    L + QLRA+ R A + + + +M PMI    
Sbjct: 601 DKPLLSYPMTAEDNPFLGLRGVRLCLADHILFKDQLRAVLRVAAEHSNVQLMIPMIAQPS 660

Query: 670 ELISLREICARIRAELDAPE----LPIGIMIEVPAAAAQADVLARHADFFSIGTNDLTQY 725
           ELI+++ + +  R EL  PE    L IGIMIEVPAA   AD LA+ ADFFSIGTNDLTQY
Sbjct: 661 ELIAVKTLVSTCREELGLPERDYPLAIGIMIEVPAAVFNADELAQEADFFSIGTNDLTQY 720

Query: 726 VLAIDRQNPELAAEADSLHPAVLRMIRSTIDGARKHDRWVGVCGGLAGDPFGASLLAGLG 785
           V+A DR NP +A   D    AV+  I  T +  +K +  VG+CG +AGD     LL  LG
Sbjct: 721 VMAADRGNPAVADLVDYKQQAVINAIAMTCEAGQKANIPVGMCGEMAGDSDMTELLIRLG 780

Query: 786 VQELSMTPNDIPAVKARLR 804
           V +LS + + IP VKA++R
Sbjct: 781 VTKLSASASMIPGVKAKVR 799


Lambda     K      H
   0.318    0.134    0.385 

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: 1400
Number of extensions: 64
Number of successful extensions: 6
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: 838
Length of database: 815
Length adjustment: 42
Effective length of query: 796
Effective length of database: 773
Effective search space:   615308
Effective search space used:   615308
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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