GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Cupriavidus basilensis 4G11

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Cup4G11:RR42_RS16980
          Length = 401

 Score =  405 bits (1042), Expect = e-118
 Identities = 203/365 (55%), Positives = 260/365 (71%), Gaps = 3/365 (0%)

Query: 11  AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70
           A  AA A  A + + VVKIGH AP++G  AH GKDNENGAR+A+EE+N  G+ I GKKIK
Sbjct: 35  APAAATAPAAGSGDVVVKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGKKIK 94

Query: 71  FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130
            ELV EDDA DPK GTA AQKL DAKV  VVGHLNSG +IPASK+Y+D GI  ++ ++TN
Sbjct: 95  LELVGEDDAGDPKTGTAVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPSSTN 154

Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190
           P+ TK G+KTTFR++A D   G  LA YA  +L  K+VAI+DD TAYG+G+AD F+KTA 
Sbjct: 155 PDYTKQGFKTTFRVVATDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEKTAK 214

Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250
           A G+ VV  + T DKATDF AILT IK K PD I YGGMD  GGP  +Q ++LG+ + K 
Sbjct: 215 ASGVNVVAREATNDKATDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISS-KI 273

Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310
            GGDG+CT ++A+LA  A  + N+IC+E G +L+KM  G  +  +Y A++    Q+Y+P+
Sbjct: 274 VGGDGVCTDKVAELAGDA--VSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPF 331

Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370
           TYDA  +IVDAMKRANS +P     E+ K+++KG+   IAF+  G+MK   ITLY YKD 
Sbjct: 332 TYDAVMVIVDAMKRANSTEPAAILAEMPKTNYKGLIGNIAFDEKGDMKEGTITLYEYKDK 391

Query: 371 KKTPL 375
           KKT L
Sbjct: 392 KKTVL 396


Lambda     K      H
   0.315    0.131    0.375 

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: 447
Number of extensions: 12
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: 375
Length of database: 401
Length adjustment: 30
Effective length of query: 345
Effective length of database: 371
Effective search space:   127995
Effective search space used:   127995
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: 50 (23.9 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