GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Acidovorax sp. GW101-3H11

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3036
          Length = 319

 Score =  198 bits (503), Expect = 2e-55
 Identities = 116/305 (38%), Positives = 177/305 (58%), Gaps = 5/305 (1%)

Query: 40  FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99
           F +L+L   FF+  S  F+   N   ILQ   V  V+AI  T VI+T+GIDLS G +M  
Sbjct: 17  FIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMAL 76

Query: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLS 159
             ++   +  ++G+  P+ IA  +    L G I+G+++ K+K+PPFI TLG + +    +
Sbjct: 77  GGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAAT 136

Query: 160 LVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGR 219
            + SG + I  +   G +A+     +G    +  +  AVL+L L  +     L +T  GR
Sbjct: 137 QLYSGAQTIT-DIPAGMTALGNTFQLGQ---TAIVWGAVLMLALYLV-TWFALRETAPGR 191

Query: 220 YTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDA 279
           + +A+G++ EA RL+G+  D   + VY  +G   GIA L+  +R  +  P  GQ   LDA
Sbjct: 192 HVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDA 251

Query: 280 IAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLD 339
           I+AVV+GGTSL GG G ILGT++GA I+ V  NGL +M V+  +Q +VTG+++ILAV  D
Sbjct: 252 ISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATD 311

Query: 340 ILRRR 344
            L R+
Sbjct: 312 QLSRK 316


Lambda     K      H
   0.326    0.139    0.398 

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: 225
Number of extensions: 11
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: 347
Length of database: 319
Length adjustment: 28
Effective length of query: 319
Effective length of database: 291
Effective search space:    92829
Effective search space used:    92829
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 (21.7 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