GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dechlorosoma suillum PS

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Dsui_1557 Dsui_1557 3-phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__PS:Dsui_1557
          Length = 394

 Score =  321 bits (823), Expect = 3e-92
 Identities = 175/394 (44%), Positives = 256/394 (64%), Gaps = 12/394 (3%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSH 59
           M  + + D+D+KGKRV +R D NVP  + G + DDTRIRA++P I+ ALE+GA V++ SH
Sbjct: 1   MNVLKLADLDVKGKRVFIRADLNVPQDETGRITDDTRIRASVPAIQMALEKGAAVMVTSH 60

Query: 60  LGRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTR 118
           LGRP +GE  PE SLAP+A RL+ELLG++V  +     D       E+K G+V+LLEN R
Sbjct: 61  LGRPTEGEMKPEDSLAPIAHRLAELLGRKVPVI-----DNWVDGGFEVKPGDVVLLENCR 115

Query: 119 FHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKF 177
            + GE KN+ ELA+  A L D++VNDAFGTAHRA A+  GIA++ P + AG L+  E+  
Sbjct: 116 VNKGEKKNNDELAQKLAKLCDVYVNDAFGTAHRAEATTHGIAKYAPVACAGPLLGAELDA 175

Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSR 237
           L +   NP++P V ++ G+KVS K+ ++ +L  K D++++GG +  TF+ A    +G S 
Sbjct: 176 LGRALENPKRPLVAIVAGSKVSTKLTILKSLAGKVDQLIVGGGIANTFMVADDLPIGESL 235

Query: 238 VEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIG 297
            E D ++ A+ +++   E+G  + +P D V+A ++        V  +D  P+  M LDIG
Sbjct: 236 AELDLVEEARNIMDMMDERGASVPIPEDVVVANELSVHARANRVDANDVQPDD-MILDIG 294

Query: 298 PETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSA 357
           P+T       ++ A T+VWNGP+GVFE D F  GTK +A AIA      A ++ GGGD+ 
Sbjct: 295 PKTSAKLASIIAHAGTIVWNGPVGVFEFDQFGGGTKMLAAAIA---HSPAFSIAGGGDTL 351

Query: 358 AAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGI 391
           AA+ K+G+E +  ++STGGGA LEFLEGK+LP +
Sbjct: 352 AAIAKYGIEKQIDYISTGGGAFLEFLEGKKLPAV 385


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: 663
Number of extensions: 42
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: 394
Length adjustment: 34
Effective length of query: 620
Effective length of database: 360
Effective search space:   223200
Effective search space used:   223200
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