GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pandoraea thiooxydans ATSB16

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_047213081.1 PATSB16_RS05695 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_001931675.1:WP_047213081.1
          Length = 284

 Score =  245 bits (625), Expect = 8e-70
 Identities = 121/250 (48%), Positives = 179/250 (71%), Gaps = 1/250 (0%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           +LE+ G+ + FGGL AV+ ++ +V+  Q+V +IGPNGAGKTTVFN +TG Y+PT G IR 
Sbjct: 15  LLELEGVGISFGGLRAVDDLSFRVQRGQIVGLIGPNGAGKTTVFNLITGVYKPTNGHIRW 74

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
            G+E+ GL   KIA +G+ RTFQ +RLF +MT +EN++  +H  +   +  GL  TPA R
Sbjct: 75  RGQEVTGLQPDKIAAQGIRRTFQTIRLFADMTVLENVVAGEHLQIKQRWWQGLLNTPAQR 134

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           R E+  ++ A   L+++NL + A+ +A +L YG QRR+E+AR ++ RP +++LDEPAAGL
Sbjct: 135 REEQALVDRAMEVLQQLNLVDVAHENATSLPYGVQRRVELARTLVARPELIILDEPAAGL 194

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           N  E+  L   I  +R +  VTV+L+EHDM +VM+++D+IVVIN G  +A+G P +IR+N
Sbjct: 195 NEFESAGLNDTIRAIR-DAGVTVILVEHDMSVVMNVTDNIVVINFGKKIAEGKPAEIRNN 253

Query: 245 PDVIKAYLGE 254
           P VI+AYLG+
Sbjct: 254 PLVIEAYLGQ 263


Lambda     K      H
   0.320    0.137    0.391 

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: 212
Number of extensions: 10
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: 255
Length of database: 284
Length adjustment: 25
Effective length of query: 230
Effective length of database: 259
Effective search space:    59570
Effective search space used:    59570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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