GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Psychromonas ossibalaenae JAMM 0738

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_019614095.1 G327_RS0107245 PTS glucose transporter subunit IIBC

Query= BRENDA::P45604
         (651 letters)



>NCBI__GCF_000381745.1:WP_019614095.1
          Length = 483

 Score =  356 bits (913), Expect = e-102
 Identities = 197/476 (41%), Positives = 297/476 (62%), Gaps = 26/476 (5%)

Query: 1   MNILGFFQRLGRALQLPIAVLPVAALLLRFGQ------PDLLNVPFIAQAGGAIFDNLAL 54
           MNI G  Q++G++L LP++VLP+A +LL  G       PD+++   + QAGGA+F N+AL
Sbjct: 1   MNIFGSLQKVGKSLMLPVSVLPIAGILLGVGAAKFSVLPDVVS-QLMEQAGGAVFGNMAL 59

Query: 55  IFAIGVASSWSKDNAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNR 114
           +FAIGVA  ++K N G A LA AVGY++M + + T+ P  N GVL GII G +A A++NR
Sbjct: 60  LFAIGVALGFTK-NDGVAGLAAAVGYYIMMQTVETLAPGANTGVLGGIIAGGIAAAMFNR 118

Query: 115 WAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAG-ALG 173
           +  I LPD+L FF GKR VPI TG   +I+ A+   +WPP+  AI S  +W       + 
Sbjct: 119 FYNITLPDYLGFFAGKRAVPIMTGLSAIIMGAVLAVIWPPIGSAIASFSDWAAHQNPTVA 178

Query: 174 SGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGF 233
            GI+G + R LIP GLH + N   +F+ G  T+A G   +G +  + + D T     +GF
Sbjct: 179 FGIYGVVERSLIPFGLHHIWNVPFFFEAGSCTSATGEQLNGILTCYLSADDTTRAAGNGF 238

Query: 234 ------FPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFL 287
                 +   MFGLP AA+A+  AA    R  V G++ S A+T+FLTG+TEP+EF FLF+
Sbjct: 239 GQLAGGYMFKMFGLPAAAIAIAHAAKPENRAKVMGIMASAALTSFLTGITEPIEFAFLFV 298

Query: 288 APLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVF 347
           AP+LY +HA+L G +  +   LG+  G SFS G ID+++   L A ++ +   +V+G+++
Sbjct: 299 APVLYAVHALLAGSAFVVTNMLGMVHGTSFSHGLIDFLV---LSANAEKMIYFVVIGLIY 355

Query: 348 FFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLK 407
             VY+ +F  VI+  +LKTPGRE+       EEA    + G +++    +AA GG  N++
Sbjct: 356 AAVYYTVFRVVIKALDLKTPGREE-------EEAEEAVQLGSSEIPVLLVAAFGGKANIE 408

Query: 408 AIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMK 463
            +DACITRLR++V + A V+ A  K+LGA+GVV ++   +Q I G K++++  +M+
Sbjct: 409 NLDACITRLRISVHNIALVDKAELKKLGAAGVV-ISGNGVQAIFGTKSDNLKTDME 463


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: 734
Number of extensions: 42
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: 483
Length adjustment: 36
Effective length of query: 615
Effective length of database: 447
Effective search space:   274905
Effective search space used:   274905
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. 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:

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:

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:

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:

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