GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Paraburkholderia bryophila 376MFSha3.1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate H281DRAFT_04190 H281DRAFT_04190 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Burk376:H281DRAFT_04190
          Length = 397

 Score =  330 bits (847), Expect = 6e-95
 Identities = 180/389 (46%), Positives = 257/389 (66%), Gaps = 12/389 (3%)

Query: 6   IRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP- 63
           I +  L GKRV +R D NVP  D G + +DTRIRA++P +K AL+ GA V++ SHLGRP 
Sbjct: 11  IAEGKLSGKRVFIRADLNVPQDDQGNITEDTRIRASVPAVKAALDAGAAVMVTSHLGRPT 70

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           +G+  PE SLAPVAKR +ELLG++V  V   V + V  A      GEV+LLEN R + GE
Sbjct: 71  EGDFKPEDSLAPVAKRFAELLGRDVPLVANWVENGVNVA-----PGEVVLLENCRVNKGE 125

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVT 182
            K+  ELA+  A L DI+VNDAFGTAHRA A+  GIA++ P + AG L+  E++ L K  
Sbjct: 126 KKDSDELAQKMAKLCDIYVNDAFGTAHRAEATTHGIAKYAPIACAGPLLAAELEALGKAL 185

Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242
             P++P V ++ G+KVS K+ ++ +L EK D++++GG +  TF+ A G ++G S  E D 
Sbjct: 186 GAPKRPLVAIVAGSKVSTKLTILKSLAEKVDQLIVGGGIANTFMLAAGLKIGKSLAEADL 245

Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302
           ++ AK +++ AK +G  + +P D V A++  P  + ++  + D + +  + LDIGPET +
Sbjct: 246 VNEAKAIIDAAKARGASVPIPTDVVTAKEFSPTAKAEIKAVAD-VEDDDLILDIGPETAQ 304

Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362
               +L  A T+VWNGP+GVFE D F  GTK +A AIA      A ++ GGGD+ AA+ K
Sbjct: 305 ALAAQLEKAGTIVWNGPVGVFEFDQFGNGTKTLADAIA---RSSAFSIAGGGDTLAAIAK 361

Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGI 391
           +G+ DK S++STGGGA LEFLEGK+LP +
Sbjct: 362 YGIHDKVSYISTGGGAFLEFLEGKKLPAV 390


Lambda     K      H
   0.317    0.137    0.386 

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: 594
Number of extensions: 29
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: 654
Length of database: 397
Length adjustment: 34
Effective length of query: 620
Effective length of database: 363
Effective search space:   225060
Effective search space used:   225060
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: 41 (21.6 bits)
S2: 52 (24.6 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