Alignments for a candidate for nagF in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Desulfovibrio vulgaris Miyazaki F

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 8502167 DvMF_2877 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>FitnessBrowser__Miya:8502167
          Length = 591

 Score =  308 bits (788), Expect = 8e-88
 Identities = 194/576 (33%), Positives = 301/576 (52%), Gaps = 18/576 (3%)

Query: 288 LAPNTLAGVCAAPGVAVGKLV------RWDDADIDPPEKANGTSAAESRLLDKAIATVDA 341
           +A   L G+  + GV++GK        R    +I PP    G + +E   L++A + V  
Sbjct: 1   MAREILQGIAVSAGVSIGKAFFTNRRRRSVSFEIIPP----GAADSEVARLEQAASDVRD 56

Query: 342 DLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQI 400
           DL    RD         A I + H ++ +DP L+ AA   I      A +A  +A+ A  
Sbjct: 57  DL-ARARDNVPAELRDHAAIINSHMMICQDPKLIRAASQRIRDHHICAEWALDQAVEAIA 115

Query: 401 AILTNIEDALLAERAADLRDIEKRV-LRALGYTSATARTLPEEAVLAAEEFTPSDLSTLD 459
           A  + IED  + ER  D+R + +R+  R +G  +   RT  E  VL A + TP+D   L 
Sbjct: 116 AAFSAIEDPYIRERVQDVRAVAERIQTRLVGRHAEPLRTPDERIVLMAHDLTPADAMGLP 175

Query: 460 RSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPT 519
             ++ +   A GG TSH  ILAR   IPA+V V     ++ +G  V+V+A  G +   P 
Sbjct: 176 TVKIMSFATAEGGKTSHTGILARSLQIPAVVGVSSLEESVADGDLVIVDALRGLIVVDPD 235

Query: 520 ELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSV 579
           E ++      + +  + +++ RR S   A T DG  I+V ANI  +++    ++ G D V
Sbjct: 236 ETELADYTDLKYQFENYQKSIRRQSTLPAETLDGYRIDVQANIELVEEVPQVLDGGGDGV 295

Query: 580 GLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPN 639
           GL RTE  F++R  +PT +E    Y  +   LS R  + RTLDVGADK +   +   EPN
Sbjct: 296 GLYRTEYAFLNRRTSPTEEELYDEYSQLAGLLSPRRVVFRTLDVGADKMLSEQSQLEEPN 355

Query: 640 PALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARE 699
           PALGLR IR      D+   QLR +L     G+  +L PM++ + EL + +  ++E   E
Sbjct: 356 PALGLRAIRFCLRHQDVFRRQLRAILRASAHGSASLLFPMISGLHELRQAKHILNEVRAE 415

Query: 700 LGRT-----EPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAA 754
           L          + VG+M+E+PSA ++++ LAQ  DF SIGTNDL QY+L +DR    ++ 
Sbjct: 416 LDAAGLPYDPDMPVGIMVELPSAVMISEALAQEVDFFSIGTNDLIQYSLGIDRGNKHVSY 475

Query: 755 QADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPG 814
               LHPA++R I   V  A + G  V VCG +A DP  +P+L+G+ +  +S+ P ++PG
Sbjct: 476 LYQPLHPAIVRSIKYVVDSAHRMGISVCVCGEVASDPYCLPILLGMQIDAISIAPQAIPG 535

Query: 815 IKARVRNLDYQLCRQRAQDALALESAQAVRAASRET 850
           IK  +R  + + C++  +D L+  +   +    +ET
Sbjct: 536 IKHILRRTNMEECKELLRDVLSASTVSTINRMVKET 571


Lambda     K      H
   0.317    0.133    0.371 

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: 986
Number of extensions: 38
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 854
Length of database: 591
Length adjustment: 39
Effective length of query: 815
Effective length of database: 552
Effective search space:   449880
Effective search space used:   449880
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 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:

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