Alignments for a candidate for nagF in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Maridesulfovibrio zosterae DSM 11974

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_027722883.1 H589_RS0115585 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_000425265.1:WP_027722883.1
          Length = 823

 Score =  464 bits (1195), Expect = e-135
 Identities = 279/699 (39%), Positives = 392/699 (56%), Gaps = 11/699 (1%)

Query: 151 PLLVLRARDGAAAEASRQLSSTNVTE-EARQQVTLVHAGGLHARPAARAREAARGFDARV 209
           P  ++R   G +   SR   + +V++ +    VT++   GLHARPA    + A+ +D+ +
Sbjct: 132 PAEIVRVLSGESRSVSRPAPTLDVSDFDVSIDVTIMGEHGLHARPATFFVDIAKKYDSEI 191

Query: 210 EVRYEGRKAAIESVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVEEKP 269
           +V ++GR    +S+  LL LG   G T+ +   G  A+ A+A +  E   E  GE  E+ 
Sbjct: 192 QVEFDGRSGNGKSLASLLKLGISGGKTMRIHAKGDDASLALATL-KEAVDEGLGEESEEA 250

Query: 270 ARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAES 329
           A    P  +   RP        T+ G  A+PG+A G + ++  + I     A      ES
Sbjct: 251 A---IPRIEHGWRPQD---VKQTIPGCTASPGLATGPVHQYTHSRIVVEAIAKDPKH-ES 303

Query: 330 RLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAG 389
             L  AIA    +L     +   +     A IF  H   L+DP +L     LI  GKSAG
Sbjct: 304 SELAHAIAAARLNLRHLYNEVRAKSGEPRAAIFRAHEAFLDDPEILVETEALIRNGKSAG 363

Query: 390 FAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRAL-GYTSATARTLPEEAVLAAE 448
           +AWR+ I  ++ IL   +D LLA RA DLRD+ +RVLR L G       T     +L AE
Sbjct: 364 YAWRQVIDDRVHILEQHDDELLAARAMDLRDVGRRVLRHLAGVVQDQPFTPSRPVILLAE 423

Query: 449 EFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVN 508
           + TPSD + LD S +     + GG TSH+AI+AR  GIPA+VA G ++  I + T  +++
Sbjct: 424 DLTPSDTAQLDPSLILGFCTSGGGPTSHSAIIARSLGIPAIVAAGPSILEIVDDTIAIID 483

Query: 509 ATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDA 568
             +G L   P+  D+E A   +  L ++R    R   + A+T+DG  IEV ANI  + +A
Sbjct: 484 GDSGNLYLEPSPSDIETADAAKLELEELRNEEYRARYEPALTTDGERIEVVANIGRVSEA 543

Query: 569 KTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKE 628
           + AV  G + VGL+RTE LF+ R   P  +E  QSY+ +V+AL+G   IIRTLD+G DK 
Sbjct: 544 ENAVNAGGEGVGLMRTEFLFLERDTPPDEEEQFQSYKTMVEALNGLPIIIRTLDIGGDKA 603

Query: 629 VDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIR 688
           V YL LPPE NP LG RGIRL   RP+    QLR +      G +RI+ PM+  + EL  
Sbjct: 604 VAYLDLPPEDNPFLGERGIRLCLNRPEFFLVQLRAIFRASKYGPIRIMFPMIATLDEL-E 662

Query: 689 IRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRC 748
             KR+ E AR     E +E+G+M+EVPS   +A + AQ  DF SIGTNDLTQY +A+DR 
Sbjct: 663 AAKRLAEKARIEVGAEALEIGIMVEVPSVVSMAREFAQVVDFFSIGTNDLTQYVMAIDRV 722

Query: 749 QADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVD 808
              LAA+AD LHPAVLR+I   V+ +D+ G W GVCG LAG+PL   +L GLGV ELS+ 
Sbjct: 723 HPTLAAKADSLHPAVLRMIDQVVKASDEAGIWTGVCGGLAGEPLGATILAGLGVKELSMV 782

Query: 809 PVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAAS 847
             S+  +KAR+R++  +  R+ AQ AL+    + VRA S
Sbjct: 783 VPSIAAVKARIRSISMKQARELAQKALSCRDNKQVRALS 821


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: 1390
Number of extensions: 61
Number of successful extensions: 4
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: 823
Length adjustment: 42
Effective length of query: 812
Effective length of database: 781
Effective search space:   634172
Effective search space used:   634172
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