GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0085 in Microvirga lotononidis WSM3557

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_040638997.1 MICLODRAFT_RS18595 TAXI family TRAP transporter solute-binding subunit

Query= reanno::psRCH2:GFF85
         (317 letters)



>NCBI__GCF_000262405.1:WP_040638997.1
          Length = 314

 Score =  373 bits (958), Expect = e-108
 Identities = 187/308 (60%), Positives = 238/308 (77%), Gaps = 2/308 (0%)

Query: 11  AAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYN-KIDGAKTSVQATKASVE 69
           AAA A   ++    A  FIN+LTGGTSGVYYP+GVALS+ ++ K+ G++ SVQATKASVE
Sbjct: 8   AAALALAGASIPAQAQDFINVLTGGTSGVYYPLGVALSKVFSEKVQGSRPSVQATKASVE 67

Query: 70  NLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESGI 129
           NL LLQ G+GE+ F+LGDS+   W G E+AGFK+ L +LR +   Y NYIQIVA+ ESGI
Sbjct: 68  NLTLLQQGKGEIGFTLGDSLAMGWAGDEEAGFKSKLDKLRGVTAIYPNYIQIVATQESGI 127

Query: 130 KTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDA 189
           K+L DLKGKR+SVGAPKSGTELNARAI   AGL YKD+G+VE+LP+ ESVEL+KNRQLDA
Sbjct: 128 KSLADLKGKRLSVGAPKSGTELNARAILHGAGLTYKDLGKVEYLPFGESVELMKNRQLDA 187

Query: 190 TLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADVPTVA 249
           TLQS+GLG+++IRDL++++P+  VEIPA +VEK+    Y+   IPA TY GQ A V T A
Sbjct: 188 TLQSAGLGVSSIRDLSTSVPIVVVEIPAAIVEKV-GTPYVKATIPANTYGGQTAPVETAA 246

Query: 250 ITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAERF 309
           + N LVTH  V DE  YQMTK ++++L  L  AH+AAKDIKLE+A   +P+P+HPGA+R+
Sbjct: 247 VVNYLVTHSGVKDETVYQMTKAIYESLPDLSAAHAAAKDIKLESALSGMPVPMHPGAQRY 306

Query: 310 YKEAGVLK 317
           + E GV K
Sbjct: 307 FDEKGVKK 314


Lambda     K      H
   0.314    0.131    0.359 

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: 19
Number of successful extensions: 3
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: 317
Length of database: 314
Length adjustment: 27
Effective length of query: 290
Effective length of database: 287
Effective search space:    83230
Effective search space used:    83230
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: 42 (22.0 bits)
S2: 48 (23.1 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