GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Burkholderia phytofirmans PsJN

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate BPHYT_RS35665 BPHYT_RS35665 ABC transporter permease

Query= reanno::Smeli:SM_b21653
         (298 letters)



>FitnessBrowser__BFirm:BPHYT_RS35665
          Length = 296

 Score =  149 bits (376), Expect = 8e-41
 Identities = 97/286 (33%), Positives = 152/286 (53%), Gaps = 9/286 (3%)

Query: 17  WLFVAPALGLITLFMVYPIAWSLWMSFQ--SGRGMTLKFAGFANIVRLWNDPVFIKALTN 74
           WL +AP+L L    + YPI   +W S    S  G    F G  N   +++DP F+ A   
Sbjct: 13  WLLIAPSLVLALFIISYPIFNIVWQSLHEVSRFGAIRDFTGLQNFYTIFSDPAFLAAARR 72

Query: 75  TMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD 134
           T+ + +  V   +L+++ +A +LN     GRGV RT + LP   SL   +V+++  F  D
Sbjct: 73  TLVWTICVVGGTVLISVPVALVLNQD-FYGRGVARTIVMLPWSVSLTMTAVVWRWAFNDD 131

Query: 135 -GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIYE 193
            G+VN TLQ +GL + PI WL  P  A  + I         + +   L  L ++   IYE
Sbjct: 132 YGMVNVTLQRLGLISGPIHWLATPELAFPVEIAVGILVSVPFTVTILLGGLSSVPGDIYE 191

Query: 194 VARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLTL 253
            AR+DG  AW +   LT+PLL+P I  T +++ I     F  ++ +T+  GGP N+T  L
Sbjct: 192 AARMDGASAWQQFRKLTMPLLRPFINMTILLNVIYVFNSFPIIWVMTQ--GGPDNSTHIL 249

Query: 254 SLYIYNLTFRFMPNLGYAATVSYVIVVLVAL--LAFVQFFAARERD 297
             Y+Y L FR +   G AA VS +++V++ +  +A+++   A+E D
Sbjct: 250 VTYLYELGFR-LGRPGEAAAVSLIMLVMLFIFSIAYLRLQPAKEGD 294


Lambda     K      H
   0.330    0.142    0.447 

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: 274
Number of extensions: 19
Number of successful extensions: 7
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: 298
Length of database: 296
Length adjustment: 26
Effective length of query: 272
Effective length of database: 270
Effective search space:    73440
Effective search space used:    73440
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 (21.9 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 (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