GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07300 in Burkholderia phytofirmans PsJN

Align Inositol transport system sugar-binding protein (characterized)
to candidate BPHYT_RS12000 BPHYT_RS12000 sugar ABC transporter substrate-binding protein

Query= reanno::Phaeo:GFF715
         (316 letters)



>FitnessBrowser__BFirm:BPHYT_RS12000
          Length = 351

 Score =  312 bits (800), Expect = 7e-90
 Identities = 158/336 (47%), Positives = 215/336 (63%), Gaps = 28/336 (8%)

Query: 9   MLATTVAAAPMMLATTASAEGEKYILVSHAPDSDSWWNTIKNGIALAGEQMNVEVEYRNP 68
           ++A     A       A A    ++LVSHAPDSD++WNTI+N I  A E  NVE +YRNP
Sbjct: 16  LVAALALTAGFAAQPAARAVDAHFVLVSHAPDSDTFWNTIRNAIEQADEDFNVETDYRNP 75

Query: 69  PTGDLADMARIIEQAAASGPNGIITTLSDYDVLSGPIKAAVDSGVDVIIMNSGTPDQARE 128
           P GDLADM+R+IEQAAA   +G+ITT++D+DVL   I+      + ++ +NSGT +Q+ +
Sbjct: 76  PNGDLADMSRLIEQAAARNYDGVITTIADFDVLKSSIEKVTAKKIALVTINSGTNEQSAQ 135

Query: 129 VGALMYVGQPEYDAGHAAGMRAKADGVGSFLCVNHYISSPSSTERCQGFADGLGVDLGDQ 188
           + A+M++GQPEY AG AAG +AKA GV +FLCVNH+ ++P S +RC+GFAD +G D    
Sbjct: 136 LAAIMHIGQPEYLAGKAAGEKAKAAGVKTFLCVNHFATNPVSFDRCRGFADAIGADYKTS 195

Query: 189 MIDSGQDPAEIKNRVLAYLNTNPETDAILTLGPTSADPTLLALDENGMAGDIYFGTFDLG 248
            IDSGQDP EI+++V AYL  +P+TDA+LTLGP  A  TL A+D+ G+AG I+F TFD  
Sbjct: 196 TIDSGQDPTEIQSKVSAYLRNHPKTDAVLTLGPPPASATLKAIDQMGIAGKIFFCTFDFS 255

Query: 249 EEIVKGLKSGVINWGIDQQPFLQAYLPVVVL-------------------------TNYH 283
           +EI K ++ G I + IDQQP+LQ Y+ V VL                             
Sbjct: 256 DEIAKAIRDGTIAFAIDQQPYLQGYMAVAVLAIAKKERTTDPVKIRQVLKENVKFKARLE 315

Query: 284 RYGVLPG---NNINSGPGFVTKDGLEKVEEFAGEYR 316
            YG+ P     NI SGP F+TK  L+KV ++AG+YR
Sbjct: 316 MYGLEPSYGPKNIRSGPSFITKANLDKVVKYAGQYR 351


Lambda     K      H
   0.315    0.134    0.393 

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: 361
Number of extensions: 6
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: 316
Length of database: 351
Length adjustment: 28
Effective length of query: 288
Effective length of database: 323
Effective search space:    93024
Effective search space used:    93024
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: 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