Alignments for a candidate for nagEcba in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagEcba in Clostridium tyrobutyricum FAM22553

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_039653499.1 PN53_RS12165 glucose PTS transporter subunit IIA

Query= BRENDA::P45604
         (651 letters)



>NCBI__GCF_000816635.1:WP_039653499.1
          Length = 667

 Score =  487 bits (1253), Expect = e-142
 Identities = 273/657 (41%), Positives = 393/657 (59%), Gaps = 52/657 (7%)

Query: 3   ILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGVAS 62
           I    Q++G++L LP++VLP A +LLR GQPDLLN+P+I  AG AIF NL +IFA+GVA 
Sbjct: 5   IFSVLQKIGKSLMLPVSVLPAAGILLRLGQPDLLNMPYIEAAGNAIFTNLPMIFAVGVAI 64

Query: 63  SWSKDNAGSAALAGAVGYFVMT--------------------------KAM--------V 88
            +S   A  AALA  VG  ++                           KA         +
Sbjct: 65  GFSGGEA-VAALAAVVGELILENIEKLASSNAATALAQTTAASHHMTLKAFMETQVYQNI 123

Query: 89  TINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIF 148
                INMGV  GII G+VA  +YNR+  IKLP  L FFGGKRFVPI T    LI+ AI 
Sbjct: 124 VTKTTINMGVFGGIIIGIVAALLYNRFHSIKLPQVLGFFGGKRFVPIVTSAAALIIGAIG 183

Query: 149 GYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAA 208
             +W PVQ  I +    + S  ALG   +    RLLIP GLH +   +  +Q G F +  
Sbjct: 184 VSIWVPVQGWIDTMAN-LASNSALGPAFYAAGKRLLIPVGLHHIYYPVFLYQFGHFISN- 241

Query: 209 GTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVA 268
           G  + GD  R++ GD TAG+FM+  FPI+MFGLPGAALAM  AA K++R  + GM++S A
Sbjct: 242 GITYIGDSPRYFHGDPTAGIFMASEFPILMFGLPGAALAMIAAAKKSKRKQMAGMMISSA 301

Query: 269 ITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMY 328
             AF+TG+TEP+EF F+F+AP+L++ H ++   S  + + L I  G++FSA  IDY+L +
Sbjct: 302 FVAFVTGITEPIEFSFIFVAPILFVFHVLVAFCSGLVTSFLHIRLGYTFSASFIDYILGF 361

Query: 329 SLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEG 388
                +++ W++  +GV FF +YF++F  +IR  NLKTPGRED+  + +       + + 
Sbjct: 362 RY---AEHPWLIWPVGVAFFLLYFVVFYFLIRAMNLKTPGREDEDGEEIVHINVKGSAK- 417

Query: 389 LTQLATSYIAAVGGTDNLKAIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQ 448
               A   + A+GG DN+K +DACITRLRLT+ D A V++   + LGA+G++K    ++Q
Sbjct: 418 ----AAKVLEAIGGKDNIKVLDACITRLRLTLNDPA-VDEKTLRALGAAGIMKAG-NSVQ 471

Query: 449 VIVGAKAESIGDEMKKVVTRGPVAAAAAAPAGNVATAAPAAKPQAVANAKTVESLVSPIT 508
           V+ G +AE I D++K ++  G V   +    G   +    +K  AV+    V  L+SP  
Sbjct: 472 VVFGTEAERIKDDIKAIIANGGVVEESETQQGEDTSGGSESK--AVSG---VNLLLSPAD 526

Query: 509 GDVVALEQVPDEAFASKAVGDGIAVKPTDNIVVAPAAGTVVKIFNTNHAFCLETNNGAEI 568
           G++V LE+VPD  F+ K +GDG AV P+ + + APA G +  +F T HAF + T  G E+
Sbjct: 527 GEIVTLEEVPDPTFSEKLLGDGFAVIPSGDNIYAPADGEITVLFPTKHAFAITTAQGLEL 586

Query: 569 VVHMGIDTVALEGKGFKRLVEEGTDVKAGEPILEMDLDFLNANARSMISPVVCSNSD 625
           ++H+GIDTVAL G+GF   V++G  VK G+ IL +D  F+ +  ++MI+PV+ +N D
Sbjct: 587 LIHIGIDTVALNGEGFTAHVKQGDKVKKGDLILNLDSKFIKSKGKNMITPVIVTNMD 643


Lambda     K      H
   0.323    0.138    0.406 

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: 967
Number of extensions: 45
Number of successful extensions: 7
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: 651
Length of database: 667
Length adjustment: 38
Effective length of query: 613
Effective length of database: 629
Effective search space:   385577
Effective search space used:   385577
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 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