GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Megamonas funiformis YIT 11815

Align PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized)
to candidate WP_008538996.1 HMPREF9454_RS07865 PTS mannose transporter subunit IID

Query= SwissProt::P69805
         (283 letters)



>NCBI__GCF_000245775.1:WP_008538996.1
          Length = 271

 Score =  395 bits (1016), Expect = e-115
 Identities = 188/271 (69%), Positives = 224/271 (82%), Gaps = 2/271 (0%)

Query: 11  KKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHLE 70
           KKL+ +D+   F+RSN  QGSWN ERMQALGFCF MVP I++LY    E RKQAI+RHLE
Sbjct: 2   KKLSSNDLFWTFIRSNFLQGSWNMERMQALGFCFGMVPIIKKLY--EGEERKQAIKRHLE 59

Query: 71  FFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRPV 130
           F+NTQPFV API+GV  A+EEQ+ANG +I DG INGIKVG+MGPLAGVGDPIFWGT+RP+
Sbjct: 60  FYNTQPFVTAPIIGVVAAMEEQKANGKDIQDGVINGIKVGMMGPLAGVGDPIFWGTLRPI 119

Query: 131 FAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGFLQKLTE 190
            AALGA +AM GSLLGP+LFF+LFN+VRL  R+YG+ YGY+KG DI++D+ G  LQK+TE
Sbjct: 120 CAALGASLAMGGSLLGPILFFVLFNVVRLLIRWYGIKYGYTKGTDIIQDVAGNTLQKITE 179

Query: 191 GASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTFA 250
           GASILGLFVMGALVNKWT VNIP+V+S +T Q G    TTVQ+ILDQLMPGL+PLLLTF 
Sbjct: 180 GASILGLFVMGALVNKWTTVNIPVVISEVTMQDGSVVTTTVQSILDQLMPGLIPLLLTFL 239

Query: 251 CMWLLRKKVNPLWIIVGFFVIGIAGYACGLL 281
           CM L++KKVN +WII G F +GI GY  G+L
Sbjct: 240 CMKLMKKKVNAIWIIFGLFAVGIIGYGLGIL 270


Lambda     K      H
   0.326    0.143    0.439 

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: 332
Number of extensions: 13
Number of successful extensions: 2
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: 283
Length of database: 271
Length adjustment: 25
Effective length of query: 258
Effective length of database: 246
Effective search space:    63468
Effective search space used:    63468
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