Alignments for a candidate for nagF in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Paraburkholderia bryophila 376MFSha3.1

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate H281DRAFT_01852 H281DRAFT_01852 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>FitnessBrowser__Burk376:H281DRAFT_01852
          Length = 851

 Score =  611 bits (1576), Expect = e-179
 Identities = 358/841 (42%), Positives = 494/841 (58%), Gaps = 27/841 (3%)

Query: 8   LTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTL 67
           + L APLSG ++ L  VPDPVFA   +GDGI+IDP ++ L +P  G V  +  + HAVT+
Sbjct: 10  IELVAPLSGVMVPLETVPDPVFAQKMVGDGISIDPTSHELLSPLPGKVTQLHSSSHAVTI 69

Query: 68  RADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLV 127
              +G E+LLH+GLDTV L+GEGF+ LVKEG  V+ GQ L+RFD   V     SL++ +V
Sbjct: 70  TGASGLEVLLHIGLDTVLLRGEGFTPLVKEGDTVATGQPLIRFDPVYVGAKAASLLTQMV 129

Query: 128 LTNSEDF-QVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHA 186
           + N +   + +P        G+  L +      +    A ++GA V   + + +  G+HA
Sbjct: 130 IANGDRVTRYVPAEGLVTAAGDVALTVELADDTAKDQTARTTGAIVSDEVTLPNPAGMHA 189

Query: 187 RPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQA 246
           RPAA+    A  + S+ +L     SA+  S++ +MGL     D V++   G DA  A   
Sbjct: 190 RPAAVFVGAAKKYESEIRLLHGSNSANAKSIVSIMGLATKFGDRVRIQATGPDAGEAASV 249

Query: 247 LLNALSTAVND---DSHAAAPTPIA------------QRTRTAEAGVLNGVCAAPGLVGG 291
           L   L+    +   D+ A  PT +A            +R + A+   L GV A+PGL  G
Sbjct: 250 LARLLAEGSGEKPADAPAFPPTSLAPASGSSGEPAVVKRAQPADVNELTGVSASPGLAVG 309

Query: 292 PLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTE--EEQIFAA 349
            + Q     +       + + +   L+ A  + R  I      A K K T+  + QI  A
Sbjct: 310 KIVQFRQQVIDVKEAGESPQRERVRLEAAHHEARQNIE-----ALKAKLTDPSKAQILDA 364

Query: 350 HLALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQR 409
           HL LLEDP L   AI SI +G +A  AW  + E Q   L++L NPLL ERA D+RD+ +R
Sbjct: 365 HLELLEDPDLNGMAIGSISEGKSAGFAWRAAFEQQAATLEKLDNPLLRERAGDVRDVGRR 424

Query: 410 VLRALLG-QDWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGK 468
           VL  L G Q    DVPAG+I+ A EL+PSD   L +  V G C   GGATSHVAILAR  
Sbjct: 425 VLALLAGMQQAQIDVPAGSILIAEELSPSDTASLDRTKVLGFCTTTGGATSHVAILARSL 484

Query: 469 GLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQA 528
           G+P +  +    LQ   G  VVLD   G L   P +  +E+  +      ++RE ++  A
Sbjct: 485 GIPAICGIDEDALQLADGTLVVLDGSHGSLRRNPSAGEVEKARERISRQAEKREEEKLAA 544

Query: 529 HTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAY 588
              A T DG R+EV AN+ ++ EA DA+  GA+GVGLLR+EFLF DR TAP E EQ   Y
Sbjct: 545 SKLAMTADGHRVEVVANIRNAKEARDAVAAGAEGVGLLRSEFLFDDRDTAPSEDEQASEY 604

Query: 589 QAVLDAMG-DKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRA 647
            AV +A+G ++ ++IRT+D GGDK L Y+PLP E NP LGLRG+R++  RP++   QLRA
Sbjct: 605 CAVAEALGRERPLVIRTLDAGGDKPLSYMPLPKEDNPFLGLRGVRVSLDRPDIFRTQLRA 664

Query: 648 LLQVSPLQRCRILLPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQ 707
           +L+ +P+    ++ PMV  ++E+L  ++ L     + A    +++GVMIEVPAAAL+AE 
Sbjct: 665 ILRAAPIGNLHVMFPMVAAIEEVLAAKKILLEEAGDRA--NSIKVGVMIEVPAAALIAEP 722

Query: 708 LAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGV 767
           LA   DF SIGTNDL+QYTLAMDR H  LA + DALHPA+LRLI  T  GA KH +WVGV
Sbjct: 723 LAREVDFFSIGTNDLTQYTLAMDRGHPKLARQADALHPAVLRLIGMTVEGAHKHGKWVGV 782

Query: 768 CGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAV 827
           CG +ASD +A PVL+GLG+ ELSVS P VG IK ++ +L  A  R+ +A ++ L +A  V
Sbjct: 783 CGGIASDAIAVPVLVGLGVDELSVSVPAVGSIKAQLARLTMAQARQLAAEVVRLGTAAEV 842

Query: 828 R 828
           R
Sbjct: 843 R 843


Lambda     K      H
   0.318    0.133    0.379 

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: 1539
Number of extensions: 74
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: 851
Length adjustment: 42
Effective length of query: 796
Effective length of database: 809
Effective search space:   643964
Effective search space used:   643964
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 17 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)
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 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