GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Hafnia paralvei ATCC 29927

Align PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose (characterized)
to candidate WP_061059309.1 M988_RS19200 PTS N-acetylgalactosamine transporter subunit IID

Query= TCDB::P69805
         (286 letters)



>NCBI__GCF_001655005.1:WP_061059309.1
          Length = 286

 Score =  161 bits (408), Expect = 1e-44
 Identities = 104/298 (34%), Positives = 167/298 (56%), Gaps = 29/298 (9%)

Query: 2   SEMVDTTQTTT-----------EKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMV 50
           SE+V+T  T+            +  LT+ DI  +  RS L Q  +N+ERMQA GF  +  
Sbjct: 3   SEIVNTENTSVPATTAGQDNPPKTVLTRGDITRLGFRSALLQSGFNYERMQATGFASAQS 62

Query: 51  PAIRRLYPENNEARKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGI 110
           P ++++Y  + +A   ++R +LEF NT    A  ++G+ ++LEE+  +        I G+
Sbjct: 63  PLLKKIYANDKDALSASMRDNLEFINTNTNAAGFLMGLLISLEERHESR-----DLIKGL 117

Query: 111 KVGLMGPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFN---LVRLATRYY 167
           KV L GPLAG+GD IFW T+ P+ A + A  A  GS+LGPL+FF+++    L+R+   + 
Sbjct: 118 KVALFGPLAGIGDAIFWFTLLPIVAGVCASFASQGSILGPLIFFVVYAALFLLRVVWTHL 177

Query: 168 GVAYGYSKGIDIVKDMGGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTG 227
           G + G  K ID ++   G     ++  A+ILG+ V+G L+  + H+    V ++I    G
Sbjct: 178 GYSLGV-KAIDKLRSSSGA----ISRAATILGVTVIGGLIASYVHLT---VTAKIAVTAG 229

Query: 228 KEHVTTVQTILDQLMPGLVPLLLTFACMWLLR-KKVNPLWIIVGFFVIGIAGYACGLL 284
            E V+  +   D++ P L+PL  T    +LLR KKV+P+ +I+  FV+ IA    G+L
Sbjct: 230 HE-VSIQEAFFDKVFPNLLPLGYTLLMYYLLRAKKVSPVTLILVTFVLSIALSWLGVL 286


Lambda     K      H
   0.326    0.143    0.436 

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: 216
Number of extensions: 13
Number of successful extensions: 5
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: 286
Length of database: 286
Length adjustment: 26
Effective length of query: 260
Effective length of database: 260
Effective search space:    67600
Effective search space used:    67600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 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