Alignments for a candidate for fruI in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Chromobacterium vaccinii MWU205

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate WP_046156459.1 VL52_RS07480 phosphoenolpyruvate--protein phosphotransferase

Query= SwissProt::P45597
         (838 letters)



>NCBI__GCF_000971335.1:WP_046156459.1
          Length = 830

 Score =  353 bits (907), Expect = e-101
 Identities = 247/674 (36%), Positives = 335/674 (49%), Gaps = 26/674 (3%)

Query: 171 PSGLHARPATRWAETARGFSARAQVR--AGDQAADAKSLVGLLQLGLRAGDSITVSAKGS 228
           P+G+HARPA+R AE   GF A  + R     Q ADAKS++ L+   +   D + +   G 
Sbjct: 12  PNGIHARPASRIAEFCAGFGAAIRWRNQRNGQWADAKSVLSLIAGDILFNDVVDIEIDGE 71

Query: 229 DAPALLKRL-RAVMDSLTAQEKADAERAAQRRAAP----VIGWTPPQAQPAIVGIGASPG 283
            A  +   L R +  +L   ++  A   A  RA P     +  +P   QPA        G
Sbjct: 72  GAARVADELGRFLRQTLPCCDEPVAAAPAASRALPRSLAELSPSPCFGQPA------GQG 125

Query: 284 VAIG--IVHRLRAAQTEVADQPIGLGDGGVLLHDALTRTRQQLAAIQDDTQRRLGASDAA 341
           VAIG   VHR      E A+ P+       L   AL   R+ LA          G   A 
Sbjct: 126 VAIGELCVHR-GFRMPEPAELPLSTDRDADLA--ALAVARRTLAEQLRQQAEHQGGEAAG 182

Query: 342 IFKAQAELLNDTDLITRTCQLMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRD 401
           + +A   +L+D D   R    + +G G A +    V    + L+   +  L  R  D+RD
Sbjct: 183 VSRAHLAILSDPDFRARLDAAVADGAGPARAVAVVVAHYRAQLSKSASEYLREREMDIRD 242

Query: 402 VGRRVLAQLDPAAAGAGLTDLPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPTSHT 461
           VGRR+L  L P    AG   LPE   +L A DL+PS+   LD D V GL  A+GG TSHT
Sbjct: 243 VGRRLLEALAPEIQRAGEA-LPEA-ALLWAEDLAPSELLALDRDKVKGLLLARGGLTSHT 300

Query: 462 AILSRTLGLPALVAAGGQLLDIEDGV--TAIIDGSSGRLYINPSELDLDAARTHIAEQQA 519
            IL+R   LP L   G Q   I DG+  TA++D   G L+ +P  + LD  R   A   A
Sbjct: 301 IILARAFSLPVLT--GVQRAAIADGIGRTAVLDAGLGALFQSPDTVVLDYYREEEALLAA 358

Query: 520 IREREAAQRALPAETTDGHHIDIGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGSTP 579
            R+R A      A + DGH +++  N+    +      QGA+GVGL RTE LF++    P
Sbjct: 359 QRQRLAKASGGIAASADGHRLELAVNIASAAEAQQGFAQGADGVGLFRTEMLFMDADEPP 418

Query: 580 TEDEQYQTYLAMARALDGRPLIVRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRPD 639
            EDEQ+Q Y  + R   GRP+I+R  DIGGDK    L  P E NPFLG R  R+   +  
Sbjct: 419 GEDEQFQCYAEVVRLAAGRPVIIRTFDIGGDKPARCLPAPQESNPFLGYRAIRMYPDQEA 478

Query: 640 LLEPQLRALYRAAKDGARLSIMFPMITSVPELISLREICARIRAELDAPE-LPIGIMIEV 698
               QLRA+ RA+  G  + +M PM+ ++ E    R +    RA L   E +P+GIM+EV
Sbjct: 479 AFRAQLRAILRASALGP-VKVMIPMVATLGEARWARRLLEEERAALGRAEPVPLGIMLEV 537

Query: 699 PAAAAQADVLARHADFFSIGTNDLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDGA 758
           P+   Q D   R  DFFS+G+NDLTQY+ A DR N  +    DSLHPA L  +       
Sbjct: 538 PSVLFQLDAFCREVDFFSVGSNDLTQYLFAADRDNERVGNLYDSLHPAFLAALNQAAATI 597

Query: 759 RKHDRWVGVCGGLAGDPFGASLLAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQA 818
            +H RW+G+CG  A  P    L  G+G+ ELSM+   +   + RLR       ++L  +A
Sbjct: 598 HRHGRWIGLCGEAAAAPHALPLFLGMGLDELSMSAPSLQECRRRLRELDADRCRELLGRA 657

Query: 819 LQCETAEQVRALEA 832
           L C    +VRAL A
Sbjct: 658 LACADGAEVRALVA 671



 Score = 39.7 bits (91), Expect = 7e-07
 Identities = 32/108 (29%), Positives = 51/108 (47%), Gaps = 9/108 (8%)

Query: 43  GYDASMRRREGLANTFLGHGLAIPHGVGEDRHLVRRDGIAVLQLPEGVEW--NPGQTTRL 100
           G +  +  RE   +T LGHG AIPH   +  H V    + + +L + V+W  + GQ   +
Sbjct: 718 GMEEDLWLREQAYSTGLGHGFAIPH--AKSGH-VLHPTLCLARLAQPVDWGASDGQPVDM 774

Query: 101 VVGIAAQS----DTHITLLRRLTRLIQDPAQLEALFTTDDPAVIVAAL 144
           V+ +A  +      H+    RL RL+      +AL    DP  ++A L
Sbjct: 775 VLLLAFNAADAGAAHLKFFSRLARLVMHEDFRQALRAERDPERLLALL 822


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: 1552
Number of extensions: 73
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 838
Length of database: 830
Length adjustment: 42
Effective length of query: 796
Effective length of database: 788
Effective search space:   627248
Effective search space used:   627248
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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 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