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_086509481.1 BZY95_RS08245 phosphoenolpyruvate-protein phosphotransferase PtsP

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>NCBI__GCF_002151265.1:WP_086509481.1
          Length = 753

 Score =  312 bits (800), Expect = 4e-89
 Identities = 215/620 (34%), Positives = 325/620 (52%), Gaps = 19/620 (3%)

Query: 220 MMGLAITEQAQVHVSCRGSDAEAALQALLTTLSTALVEE-AHASAPPP-EPPRANAEEGV 277
           M+G+ + +QA+     R  D E   +A L T+   L    AHA A      P     + +
Sbjct: 121 MLGVLVVQQAEK----RRYDEED--EAFLITMGAQLAGVLAHALATGSLSKPTLPGGQAM 174

Query: 278 LHGVCAAPGLVTGPLV---RLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHA 334
             GV A+PG+  G +V    L+ +    D+    +E +  RL +A+ +VR EI    E  
Sbjct: 175 FTGVPASPGMAIGEVVVVAPLADLDSVPDLIPTDVEHEIARLKEAIERVREEIRAAGERL 234

Query: 335 RARQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTL 394
             R    E A+F  +  +L +  L    +  I +G  AP A +  +    Q L+++    
Sbjct: 235 ANRISAQELALFEVYQQMLSEAALSQEVEKRIREGQWAPGALADVVRRHVQYLERVDDDY 294

Query: 395 LAERANDLRDLRQRVLRVLLGEAWQF--DVAAGAIVAAQELTPSDLLQLSAQGVAGVCMV 452
           L ERA D+RDL +RVL  L  E  Q   +     I+   E++ + L ++  + +AG+  V
Sbjct: 295 LRERAADVRDLGRRVLAHLQEETPQTPANFPESTILVGDEISVAMLGEVPRERLAGLVSV 354

Query: 453 EGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQA 512
            G +TSHVAI+AR  G+P +  + D  L +  G  VVLD   GRL + P+ E  A+    
Sbjct: 355 RGSSTSHVAIVARAMGIPTVSGMVDLPLPRLSGAEVVLDGHRGRLFVRPSDELKARYSSL 414

Query: 513 QTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFV 572
                AL    +     P+ T DG  + +  N   + +   SL     GVGL RTE  F+
Sbjct: 415 IAEEAALTEVLEHEQDLPSETPDGHVMPLMVNTGLAIDTAASLKKRISGVGLYRTEVPFM 474

Query: 573 DRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRL 632
                P E+EQ + Y+  LE+    PV++RT+D+GGDK L Y P+  EANP LG RGIR+
Sbjct: 475 IAERFPGEQEQARLYRDQLESFAPLPVVMRTLDIGGDKDLPYFPI-EEANPFLGWRGIRV 533

Query: 633 AQVRPDLLDQQLRALLQ-TRPLDRCRILLPMVTEVDELLHIRKRLDALGSELG----LSE 687
               P++L  QLRA+L+  + LD  +ILLPMVT VDE+    + LD    ELG    +S 
Sbjct: 534 TLDHPEVLMVQLRAMLRAAQGLDNLQILLPMVTNVDEVDDALRLLDRAIRELGEEGVVSP 593

Query: 688 RPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALL 747
           RP++GVM+EVPA     + LAE  DF S+G+NDL+QY LA+DR++  +A+  D+ HPA+L
Sbjct: 594 RPRVGVMLEVPATLYQLDALAERVDFFSVGSNDLTQYLLAVDRNNPRVASLYDSCHPAVL 653

Query: 748 RLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDA 807
             +A+    + +  + + VCG LA DP    +L+G+G   LS++ P +  ++  +R +  
Sbjct: 654 CAMARLAEESRRLKKPISVCGELAGDPAGALLLMGMGFDSLSMNAPSLPRVRAAIRRVSI 713

Query: 808 AQCARLSNELLNLGSALAVR 827
                L  E L L + +AVR
Sbjct: 714 DAAKALVQETLALNTPVAVR 733


Lambda     K      H
   0.319    0.134    0.386 

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: 63
Number of successful extensions: 5
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: 837
Length of database: 753
Length adjustment: 41
Effective length of query: 796
Effective length of database: 712
Effective search space:   566752
Effective search space used:   566752
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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