Alignments for a candidate for nagF in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Geotalea uraniireducens Rf4

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_011939747.1 GURA_RS14785 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_000016745.1:WP_011939747.1
          Length = 782

 Score =  314 bits (804), Expect = 1e-89
 Identities = 192/563 (34%), Positives = 293/563 (52%), Gaps = 10/563 (1%)

Query: 290 PNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRD 349
           P +L G   +PG + GK+   +    D  E        E R   + IA   A + T   +
Sbjct: 210 PFSLTGTAVSPGFSWGKIYILNRNTKDCIELERIRPRPEERKRFQ-IALEKAKIQTLYME 268

Query: 350 ASQRGAVG--EAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIE 407
                 +   +A IF  H +++ED   +    DLI     A  A +E +   +   + +E
Sbjct: 269 KRVAEILSKEDAAIFHSHLMIMEDRGFVAKIVDLIDSDYGASRAVKEVVGYYVQAFSKME 328

Query: 408 DALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALV 467
           D  L ER+AD+ DI +R++ AL   S T     E+ ++ A++  PSD++T+D  ++  +V
Sbjct: 329 DPYLRERSADMEDIGRRIIDALNGNSRTQAKFREKRIIVADDILPSDMATMDHEKILGIV 388

Query: 468 MARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAP-TELDVERA 526
             +G   SHAAI+A+  GIPA++ V   +  I    +V+V+ T+G +   P   + VE  
Sbjct: 389 TEKGNVNSHAAIMAKSLGIPAVLGVDGLMKHIALRNEVIVDGTSGHIYINPDNSIKVEYE 448

Query: 527 RLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTEL 586
           RL+R      RE +      A  T DG  + + ANI  L+D K A+ NGA+ VGL RTE 
Sbjct: 449 RLQRDFSLKQRELDGLRDLPAE-TKDGVRVSLRANIGLLNDVKVALANGAEGVGLYRTEF 507

Query: 587 LFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRG 646
            ++ R + P   E    Y+ I++   G T  IRTLD+G DK + Y   P E NP +G R 
Sbjct: 508 PYMARKSFPNRVEQYTLYRKILEGFHGHTVAIRTLDIGGDKGLSYFAYPKEDNPFMGWRS 567

Query: 647 IRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEP- 705
           IR++     +  +QL G+L     G   I+ PM++ V E+  I++ + E   EL + E  
Sbjct: 568 IRVSLEEEGIFREQLAGILMASTYGKATIMFPMISSVDEIRTIKRILKEVQNELVQDEKP 627

Query: 706 ----IEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHP 761
               I +G+M+E+P+A  +AD L +  DF SIGTNDL QYT+A DR    +    D  HP
Sbjct: 628 FDTDIRLGIMVEIPAAVQIADILIKEVDFFSIGTNDLIQYTMAADRNNPKVKKYYDPYHP 687

Query: 762 AVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRN 821
           AVL  I      A K  K V +CG +A DP+   LL+G+G+T+ S+    +P IK  +R 
Sbjct: 688 AVLHSIKQVADAAKKAHKQVSLCGEMAADPVTAVLLLGMGITDFSLSAPYIPLIKQAIRC 747

Query: 822 LDYQLCRQRAQDALALESAQAVR 844
           +D    R+ A+ AL +ES+ A+R
Sbjct: 748 VDMAEARRIAEHALQMESSSAIR 770


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: 1116
Number of extensions: 47
Number of successful extensions: 3
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: 782
Length adjustment: 41
Effective length of query: 813
Effective length of database: 741
Effective search space:   602433
Effective search space used:   602433
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 Apr 09 2024. 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 2024 update 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