GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Acidovorax sp. GW101-3H11

Align Inositol transport system permease protein (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC

Query= reanno::WCS417:GFF2333
         (340 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3036
          Length = 319

 Score =  185 bits (469), Expect = 2e-51
 Identities = 107/311 (34%), Positives = 172/311 (55%), Gaps = 20/311 (6%)

Query: 33  IGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLAL 92
           I L+     +  + + FL ++Q   L++ QV ++ ++AIG T VI+T GIDLS G V+AL
Sbjct: 18  IALILACAFFATQSERFL-SAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMAL 76

Query: 93  SAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIAT 152
             ++   +A     S  V            +A G+ V +L G ING ++    +PPFI T
Sbjct: 77  GGIVMTKMAADYGLSAPV-----------AIACGMAVTMLFGLINGLLVTKIKLPPFIVT 125

Query: 153 LGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG--------AMPVIIFLVVAVIFHIALR 204
           LG +  A    + Y+  Q ++ +    TA+G+             ++ L + ++   ALR
Sbjct: 126 LGTLNIAFAATQLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVTWFALR 185

Query: 205 YTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGM 264
            T  G++ YA+G + +A R +GI   + L+ VY +AGL  G+A +++ AR   G    G 
Sbjct: 186 ETAPGRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQ 245

Query: 265 SYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIV 324
           +  LDAI+A V+GGTSL GG G I GT++GALI+GV  +G T +GV +  Q ++ G++++
Sbjct: 246 TENLDAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVI 305

Query: 325 VAVVIDQYRNK 335
           +AV  DQ   K
Sbjct: 306 LAVATDQLSRK 316


Lambda     K      H
   0.325    0.140    0.394 

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: 220
Number of extensions: 12
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: 340
Length of database: 319
Length adjustment: 28
Effective length of query: 312
Effective length of database: 291
Effective search space:    90792
Effective search space used:    90792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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