GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16925 in Paraburkholderia bryophila 376MFSha3.1

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_02176 H281DRAFT_02176 monosaccharide ABC transporter membrane protein, CUT2 family

Query= uniprot:A0A161GM94
         (322 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02176 H281DRAFT_02176
           monosaccharide ABC transporter membrane protein, CUT2
           family
          Length = 321

 Score =  203 bits (516), Expect = 5e-57
 Identities = 120/307 (39%), Positives = 186/307 (60%), Gaps = 13/307 (4%)

Query: 26  MLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85
           +LLA + + VL  +  ++F S  N+       S   + +  M + + +G  DLSVG+V A
Sbjct: 7   ILLALVALVVLGLVRYEHFASAYNITSFWRYNSMFALISVGMAFVIITGGIDLSVGTVAA 66

Query: 86  CAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLA 145
            + VVAA+     +  ++ + A    GL VG++NG++I +L++   I TLAT     G+A
Sbjct: 67  MSSVVAALA--SAHGGWVAVVAGCAAGLAVGVLNGVIITRLKILPFIVTLATSLGAHGVA 124

Query: 146 YIFANGKAVGVSQESFFV-FGNGQMFGVPVPILITIVCFLFFGWL-LNYTTYGRNTMAIG 203
            +     AV ++ +S F  FG G +FG+P+P ++  +  +  GWL L  T +GR+++AIG
Sbjct: 125 LLLGKNDAVSIASDSNFANFGQGDLFGLPIPGIVAALVAV-AGWLALRSTRFGRHSLAIG 183

Query: 204 GNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVL 263
           G++EAA L G+NVDRT ++ +AV G++  +AGVILA++  +GQP  G G+EL  ISA VL
Sbjct: 184 GSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGVGWELFAISAVVL 243

Query: 264 GGVSLSGGIGMIRHVIAGVLILAIIENAMNLKN------IDTFYQYVIRGSILLLAVVID 317
           GG  L+GG G I   IAGVL+L ++ N +N +N      +  ++Q VIRG  LLL +V+ 
Sbjct: 244 GGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVIRGVFLLLVIVLQ 303

Query: 318 R--LKQR 322
              LKQR
Sbjct: 304 ARVLKQR 310


Lambda     K      H
   0.330    0.144    0.420 

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: 282
Number of extensions: 15
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: 322
Length of database: 321
Length adjustment: 28
Effective length of query: 294
Effective length of database: 293
Effective search space:    86142
Effective search space used:    86142
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 (21.8 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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