GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Herbaspirillum seropedicae SmR1

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate HSERO_RS03345 HSERO_RS03345 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__HerbieS:HSERO_RS03345
          Length = 396

 Score =  321 bits (822), Expect = 4e-92
 Identities = 179/389 (46%), Positives = 248/389 (63%), Gaps = 13/389 (3%)

Query: 6   IRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP- 63
           I +  L+GKRV +R D NVP  D G + +DTRIRA++P I+ A + GA V++ SHLGRP 
Sbjct: 10  ISNKQLQGKRVFIRADLNVPQDDAGNITEDTRIRASVPAIREAQQAGAAVMVTSHLGRPT 69

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           +GE  PE SLAPVAKRLSELLG EVK V   V D V     +++ G+V+LLEN R + GE
Sbjct: 70  EGEFKPEDSLAPVAKRLSELLGSEVKLVANWV-DGV-----DVQPGQVVLLENCRLNKGE 123

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVT 182
            KN  ELA+  A L DI+VNDAFGTAHRA A+  G+A+F P + AG L+  E+  L K  
Sbjct: 124 KKNSDELAQKIAKLCDIYVNDAFGTAHRAEATTYGVAKFAPVACAGPLLAAELDALGKAL 183

Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242
             P +P V ++ G+KVS K+ ++  L EK D +++GG +  TF+ A G ++G S  E D 
Sbjct: 184 NQPARPLVAIVAGSKVSTKLTILKTLAEKVDNLIVGGGIANTFMLAAGLKIGKSLAEPDL 243

Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302
           +D AK +++   ++G  + +P D V+ ++  P     V    D + +  M  DIGP+T  
Sbjct: 244 VDDAKAIIDLMAKRGASVPIPTDVVVGKEFSPTAAATVKAAAD-VADDDMIFDIGPQTAA 302

Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362
              ++L  A T+VWNGP+GVFE D F  GT+ +A AIAA       ++ GGGD+ AA+ K
Sbjct: 303 ALAEQLGRAGTIVWNGPVGVFEFDQFGGGTETLARAIAA---SSGFSIAGGGDTLAAIAK 359

Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGI 391
           + + DK  ++STGGGA LEFLEGK LP +
Sbjct: 360 YNIADKVGYISTGGGAFLEFLEGKTLPAV 388


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: 644
Number of extensions: 30
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: 396
Length adjustment: 34
Effective length of query: 620
Effective length of database: 362
Effective search space:   224440
Effective search space used:   224440
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