Alignments for a candidate for nagF in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Halomonas desiderata SP1

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_086509381.1 BZY95_RS07800 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_002151265.1:WP_086509381.1
          Length = 963

 Score =  451 bits (1160), Expect = e-131
 Identities = 309/718 (43%), Positives = 401/718 (55%), Gaps = 45/718 (6%)

Query: 160 GAAAEASRQLSSTNVTEEARQQVT-------LVHAGGLHARPAARAREAARGFDARVEVR 212
           GAAAE     ++T +   A +          +++A GLHARPA +  +AAR     ++VR
Sbjct: 256 GAAAELPSADAATVLARLAGESAAAHTRLARVLNAHGLHARPAKQLVQAAREQGLPIQVR 315

Query: 213 Y-EGRKAAIE--SVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVEEKP 269
             EG  AA+   S+  ++ LGA  G  +     G  A  A+ A+   +       V    
Sbjct: 316 LAEGGGAAVSASSLTKVINLGARRGQQLLFSAEGEGAQQALDAVCRAVADGLGEHVLPFD 375

Query: 270 ARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAES 329
             +    PQA A P           GV A+PG+A+           D PE+A    A + 
Sbjct: 376 ESRERSMPQADAAPVEPLPDDVPHPGVAASPGLAIAPAFVLQTPRFDYPERA-ADPAEQQ 434

Query: 330 RLLDKAIATVDADLDTTVRDASQRGAVGE-AGIFSVHRVLLEDPTLLDAARDLISLGKSA 388
           R L +A+A   A L+  VR A  RG  GE A I S+H  +L DP L +AAR+ I  G+SA
Sbjct: 435 RRLRQALAEGAAQLEALVRQA--RG--GEVAQILSMHEEMLTDPELFEAAREGIQEGRSA 490

Query: 389 GFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEA----V 444
             AW EAI         + D LLAERAADLRD+ +RVL  L         LPE      +
Sbjct: 491 ESAWWEAIETAAHAQEMLADRLLAERAADLRDVGRRVLGVLCEVQ-----LPEPPETPYI 545

Query: 445 LAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQ 504
           L  ++  PSD++ LD  RV  L+ ARGGAT+H+AILAR  GIPA+V  G+ +  +  G +
Sbjct: 546 LVTDDIGPSDVARLDTQRVRGLLTARGGATAHSAILARALGIPAVVGAGERVLTLAGGQE 605

Query: 505 VVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQA----AVTSDGRAIEVAA 560
           ++++   GR+  AP+    ER      RLA+ RE     + QA    A T DG  +EVAA
Sbjct: 606 LILDGERGRVIPAPS---AERRASAEQRLAE-RERREAEAWQARFAPAQTRDGHRVEVAA 661

Query: 561 NIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRT 620
           N+     A  AVE GA+ +GLLRTE LF+  A  P      + Y+  +DAL GR  + RT
Sbjct: 662 NLGNTAHAADAVERGAEGIGLLRTEFLFMAHAREPDLATQIEEYREALDALEGRPLVART 721

Query: 621 LDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLL-AVQPLGA------- 672
           LDVG DK + Y  +P E NP LGLRGIRL+  RP++L+ QLR LL A  P  +       
Sbjct: 722 LDVGGDKPLPYWPVPKEDNPFLGLRGIRLSLTRPEVLETQLRALLMAAAPAASEAADKPR 781

Query: 673 -VRILLPMVTDVGELIRIRKRIDEFARELGRTE---PIEVGVMIEVPSAALLADQLAQHA 728
            +RI+LPMV DVGE    R   +    E+   E    +++GVMIEVPSAALLA  LA   
Sbjct: 782 PLRIMLPMVKDVGEFRATRAIFERLLDEIPAAERATDVQLGVMIEVPSAALLASALAAEV 841

Query: 729 DFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALA 788
           DF S+GTNDLTQYTLA+DR   +L+AQADGLHPAVLRLI  TV  A  HGKWVGVCG LA
Sbjct: 842 DFFSVGTNDLTQYTLAIDRDHPELSAQADGLHPAVLRLIEMTVAAAHAHGKWVGVCGELA 901

Query: 789 GDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846
            D LA+P+LVGLGV ELSV    VP +KAR+R  D    R +AQ ALA  +++AVR A
Sbjct: 902 SDTLAVPVLVGLGVDELSVSARQVPLVKARLREFDLAEARAQAQLALAQATSEAVRDA 959


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: 1872
Number of extensions: 86
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: 854
Length of database: 963
Length adjustment: 43
Effective length of query: 811
Effective length of database: 920
Effective search space:   746120
Effective search space used:   746120
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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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